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Protein

DNA topoisomerase 2-associated protein PAT1

Gene

PAT1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Activator of decapping that functions as a general and active mechanism of translational repression and required for P-body formation. First decay factor recruited to mRNA, at a time when the mRNA is still associated with translation factors. Subsequently, PAT1 recruits the hepta-heterodimer LSM1-LSM7 complex to P-bodies. In association with the LSM1-LSM7 complex, stabilizes the 3' terminus of mRNAs. This association is also required for mosaic virus genomic RNA translation. Modulates the rates of mRNA-decapping that occur following deadenylation. Might be required for promoting the formation or the stabilization of the preinitiation translation complexes. Required for 40S ribosomal subunit joining to capped and/or polyadenylated mRNA. With other P-body components, enhances the formation of retrotransposition-competent Ty1 virus-like particles. Necessary for accurate chromosome transmission during cell division.19 Publications

Miscellaneous

Present with 656 molecules/cell in log phase SD medium.1 Publication

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

  • chromatin binding Source: SGD
  • mRNA binding Source: SGD
  • RNA binding Source: SGD

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionRepressor, RNA-binding
Biological processCell cycle, Cell division, mRNA processing, Translation regulation

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
YEAST:G3O-29376-MONOMER

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
DNA topoisomerase 2-associated protein PAT1
Alternative name(s):
Decapping activator and translational repressor PAT1
Topoisomerase II-associated protein PAT1
mRNA turnover protein 1
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:PAT1
Synonyms:MRT1
Ordered Locus Names:YCR077C
ORF Names:YCR77C
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri559292 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002311 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome III

Organism-specific databases

Saccharomyces Genome Database

More...
SGDi
S000000673 PAT1

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemovedCombined sources
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000582352 – 796DNA topoisomerase 2-associated protein PAT1Add BLAST795

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei2N-acetylserineCombined sources1
Modified residuei456PhosphoserineCombined sources1
Modified residuei457PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQB - The MaxQuant DataBase

More...
MaxQBi
P25644

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P25644

PRoteomics IDEntifications database

More...
PRIDEi
P25644

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
P25644

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Associates with the 40S ribosomal subunit. Associates with the heptameric LSM1-LSM7 complex. Interacts directly with LSM2 and LSM3 within the LSM1-LSM7 complex. Interacts with DHH1, LSM1, LSM5, RPB4, RPB7 and with topoisomerase TOP2. Interacts with CDC33, PAB1, TIF4631 and TIF4632 in an RNA-dependent manner. Binds mRNAs.9 Publications

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction_section%27">Interaction</a> section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="http://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated on a monthly basis. Each binary interaction is displayed on a separate line.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
31052, 1182 interactors

ComplexPortal: manually curated resource of macromolecular complexes

More...
ComplexPortali
CPX-112 Lsm1-7-Pat1 complex

Database of interacting proteins

More...
DIPi
DIP-883N

Protein interaction database and analysis system

More...
IntActi
P25644, 56 interactors

Molecular INTeraction database

More...
MINTi
P25644

STRING: functional protein association networks

More...
STRINGi
4932.YCR077C

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1796
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

More...
ProteinModelPortali
P25644

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
P25644

Database of comparative protein structure models

More...
ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes the position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi114 – 235Pro-richAdd BLAST122
Compositional biasi133 – 192Gln-richAdd BLAST60

<p>This subsection of the ‘Family and domains’ section provides general information on the biological role of a domain. The term ‘domain’ is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

The region at residues 254 to 422 is required for stimulation of decapping. The region at residues 422 to 763 is required for PAT1 and LSM1 to accumulate in P-bodies and responsible for translation repression and P-body assembly.1 Publication

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the PAT1 family.Curated

Phylogenomic databases

Ensembl GeneTree

More...
GeneTreei
ENSGT00520000055649

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000246501

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P25644

KEGG Orthology (KO)

More...
KOi
K12617

Identification of Orthologs from Complete Genome Data

More...
OMAi
PHPFIAF

Database of Orthologous Groups

More...
OrthoDBi
EOG092C0SJ9

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR039900 Pat1-like
IPR019167 PAT1_dom

The PANTHER Classification System

More...
PANTHERi
PTHR21551 PTHR21551, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF09770 PAT1, 2 hits

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

P25644-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSFFGLENSG NARDGPLDFE ESYKGYGEHE LEENDYLNDE TFGDNVQVGT
60 70 80 90 100
DFDFGNPHSS GSSGNAIGGN GVGATARSYV AATAEGISGP RTDGTAAAGP
110 120 130 140 150
LDLKPMESLW STAPPPAMAP SPQSTMAPAP APQQMAPLQP ILSMQDLERQ
160 170 180 190 200
QRQMQQQFMN FHAMGHPQGL PQGPPQQQFP MQPASGQPGP SQFAPPPPPP
210 220 230 240 250
GVNVNMNQMP MGPVQVPVQA SPSPIGMSNT PSPGPVVGAT KMPLQSGRRS
260 270 280 290 300
KRDLSPEEQR RLQIRHAKVE KILKYSGLMT PRDKDFITRY QLSQIVTEDP
310 320 330 340 350
YNEDFYFQVY KIIQRGGITS ESNKGLIARA YLEHSGHRLG GRYKRTDIAL
360 370 380 390 400
QRMQSQVEKA VTVAKERPSK LKDQQAAAGN SSQDNKQANT VLGKISSTLN
410 420 430 440 450
SKNPRRQLQI PRQQPSDPDA LKDVTDSLTN VDLASSGSSS TGSSAAAVAS
460 470 480 490 500
KQRRRSSYAF NNGNGATNLN KSGGKKFILE LIETVYEEIL DLEANLRNGQ
510 520 530 540 550
QTDSTAMWEA LHIDDSSYDV NPFISMLSFD KGIKIMPRIF NFLDKQQKLK
560 570 580 590 600
ILQKIFNELS HLQIIILSSY KTTPKPTLTQ LKKVDLFQMI ILKIIVSFLS
610 620 630 640 650
NNSNFIEIMG LLLQLIRNNN VSFLTTSKIG LNLITILISR AALIKQDSSR
660 670 680 690 700
SNILSSPEIS TWNEIYDKLF TSLESKIQLI FPPREYNDHI MRLQNDKFMD
710 720 730 740 750
EAYIWQFLAS LALSGKLNHQ RIIIDEVRDE IFATINEAET LQKKEKELSV
760 770 780 790
LPQRSQELDT ELKSIIYNKE KLYQDLNLFL NVMGLVYRDG EISELK
Length:796
Mass (Da):88,511
Last modified:July 27, 2011 - v4
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i2DBE1210C173E468
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti688D → V in CAC42990 (PubMed:1574125).Curated1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
X59720 Genomic DNA Translation: CAC42990.1
BK006937 Genomic DNA Translation: DAA07549.2

Protein sequence database of the Protein Information Resource

More...
PIRi
S53590

NCBI Reference Sequences

More...
RefSeqi
NP_010002.3, NM_001178786.2

Genome annotation databases

Ensembl fungal genome annotation project

More...
EnsemblFungii
YCR077C_mRNA; YCR077C_mRNA; YCR077C

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
850440

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
sce:YCR077C

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X59720 Genomic DNA Translation: CAC42990.1
BK006937 Genomic DNA Translation: DAA07549.2
PIRiS53590
RefSeqiNP_010002.3, NM_001178786.2

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4BRWX-ray2.80B5-79[»]
4C8QX-ray3.70H456-783[»]
4N0AX-ray3.15H/I/J422-796[»]
4OGPX-ray2.15A/B473-796[»]
4OJJX-ray2.32A/B/C473-796[»]
5LM5X-ray2.60A/B435-796[»]
5LMFX-ray2.15A/B435-796[»]
5LMGX-ray1.89A/B435-796[»]
ProteinModelPortaliP25644
SMRiP25644
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31052, 1182 interactors
ComplexPortaliCPX-112 Lsm1-7-Pat1 complex
DIPiDIP-883N
IntActiP25644, 56 interactors
MINTiP25644
STRINGi4932.YCR077C

PTM databases

iPTMnetiP25644

Proteomic databases

MaxQBiP25644
PaxDbiP25644
PRIDEiP25644

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYCR077C_mRNA; YCR077C_mRNA; YCR077C
GeneIDi850440
KEGGisce:YCR077C

Organism-specific databases

SGDiS000000673 PAT1

Phylogenomic databases

GeneTreeiENSGT00520000055649
HOGENOMiHOG000246501
InParanoidiP25644
KOiK12617
OMAiPHPFIAF
OrthoDBiEOG092C0SJ9

Enzyme and pathway databases

BioCyciYEAST:G3O-29376-MONOMER

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P25644

Family and domain databases

InterProiView protein in InterPro
IPR039900 Pat1-like
IPR019167 PAT1_dom
PANTHERiPTHR21551 PTHR21551, 1 hit
PfamiView protein in Pfam
PF09770 PAT1, 2 hits

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiPAT1_YEAST
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P25644
Secondary accession number(s): D6VR80, Q8NKJ3
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: July 27, 2011
Last modified: December 5, 2018
This is version 161 of the entry and version 4 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  2. Yeast chromosome III
    Yeast (Saccharomyces cerevisiae) chromosome III: entries and gene names
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families
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