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Protein

Diphthine synthase

Gene

dphB

Organism
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Status
Reviewed-Annotation score:

Annotation score:4 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

S-adenosyl-L-methionine-dependent methyltransferase that catalyzes the trimethylation of the amino group of the modified target histidine residue in translation elongation factor 2 (EF-2), to form an intermediate called diphthine. The three successive methylation reactions represent the second step of diphthamide biosynthesis.UniRule annotation1 Publication

Miscellaneous

The diphthine intermediate is not stable in vitro and readily eliminates the trimethylamino group. It is not known whether the elimination reaction also occurs physiologically.

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: peptidyl-diphthamide biosynthesis

This protein is involved in the pathway peptidyl-diphthamide biosynthesis, which is part of Protein modification.UniRule annotation1 Publication
View all proteins of this organism that are known to be involved in the pathway peptidyl-diphthamide biosynthesis and in Protein modification.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei10S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation2 Publications1
Binding sitei87S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenUniRule annotation2 Publications1
Binding sitei90S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation2 Publications1
Binding sitei166S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenUniRule annotation2 Publications1
Binding sitei209S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenUniRule annotation2 Publications1
Binding sitei234S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation2 Publications1

<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

  • diphthine synthase activity Source: UniProtKB

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 functionMethyltransferase, Transferase
LigandS-adenosyl-L-methionine

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
MetaCyc:MONOMER-18825
PHOR70601:G1G39-711-MONOMER

BRENDA Comprehensive Enzyme Information System

More...
BRENDAi
2.1.1.98 5244

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...
UniPathwayi
UPA00559

<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:
Diphthine synthase1 PublicationUniRule annotation (EC:2.1.1.98UniRule annotation1 Publication)
Alternative name(s):
Diphthamide biosynthesis methyltransferaseUniRule annotation
<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:dphBUniRule annotation
Synonyms:dph51 Publication
Ordered Locus Names:PH0725
<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>OrganismiPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
<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 identifieri70601 [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 lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
<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
  • UP000000752 <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

<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 ‘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_00001561261 – 265Diphthine synthaseAdd BLAST265

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
O58456

<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

Homodimer.UniRule annotation2 Publications

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
70601.PH0725

<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

1265
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
O58456

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

More...
SMRi
O58456

Database of comparative protein structure models

More...
ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
O58456

<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

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni115 – 116S-adenosyl-L-methionine bindingUniRule annotation2 Publications2

<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 diphthine synthase family.UniRule annotationCurated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
arCOG04161 Archaea
COG1798 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000205302

KEGG Orthology (KO)

More...
KOi
K20215

Identification of Orthologs from Complete Genome Data

More...
OMAi
LQNYRFG

Database of Orthologous Groups

More...
OrthoDBi
POG093Z0BZB

Family and domain databases

Conserved Domains Database

More...
CDDi
cd11647 Diphthine_synthase, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.30.950.10, 1 hit
3.40.1010.10, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_01084 Diphthine_synth, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR000878 4pyrrol_Mease
IPR035996 4pyrrol_Methylase_sf
IPR014777 4pyrrole_Mease_sub1
IPR014776 4pyrrole_Mease_sub2
IPR004551 Dphthn_synthase

The PANTHER Classification System

More...
PANTHERi
PTHR10882:SF0 PTHR10882:SF0, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00590 TP_methylase, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF036432 Diphthine_synth, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF53790 SSF53790, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00522 dph5, 1 hit

<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.

O58456-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MVLYFIGLGL YDERDITVKG LEIAKKCDYV FAEFYTSLMA GTTLGRIQKL
60 70 80 90 100
IGKEIRVLSR EDVELNFENI VLPLAKENDV AFLTPGDPLV ATTHAELRIR
110 120 130 140 150
AKRAGVESYV IHAPSIYSAV GITGLHIYKF GKSATVAYPE GNWFPTSYYD
160 170 180 190 200
VIKENAERGL HTLLFLDIKA EKRMYMTANE AMELLLKVED MKKGGVFTDD
210 220 230 240 250
TLVVVLARAG SLNPTIRAGY VKDLIREDFG DPPHILIVPG KLHIVEAEYL
260
VEIAGAPREI LRVNV
Length:265
Mass (Da):29,576
Last modified:August 1, 1998 - v1
<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:iE0F313144BEECC91
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
BA000001 Genomic DNA Translation: BAA29816.1

Protein sequence database of the Protein Information Resource

More...
PIRi
F71119

NCBI Reference Sequences

More...
RefSeqi
WP_010884823.1, NC_000961.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
BAA29816; BAA29816; BAA29816

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
1443058

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
pho:PH0725

<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
BA000001 Genomic DNA Translation: BAA29816.1
PIRiF71119
RefSeqiWP_010884823.1, NC_000961.1

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
1VCEX-ray2.10A/B1-265[»]
1WNGX-ray2.10A/B1-265[»]
2DEKX-ray1.65A/B1-265[»]
2DSGX-ray2.00A/B1-265[»]
2DSHX-ray2.00A/B1-265[»]
2DSIX-ray2.20A/B1-265[»]
2DV3X-ray1.90A/B1-265[»]
2DV4X-ray2.20A/B1-265[»]
2DV5X-ray2.20A/B1-265[»]
2DV7X-ray2.30A/B1-265[»]
2DXVX-ray1.90A/B1-265[»]
2DXWX-ray1.80A/B1-265[»]
2DXXX-ray1.75A/B1-265[»]
2E07X-ray1.90A/B1-265[»]
2E08X-ray2.00A/B1-265[»]
2E15X-ray1.80A/B1-265[»]
2E16X-ray2.00A/B1-265[»]
2E17X-ray1.90A/B1-265[»]
2E4NX-ray1.80A/B1-265[»]
2E4RX-ray2.20A/B1-265[»]
2E7RX-ray1.80A/B1-265[»]
2E8HX-ray2.10A/B1-265[»]
2E8QX-ray2.50A/B1-265[»]
2E8RX-ray2.00A/B1-265[»]
2E8SX-ray2.50A/B1-265[»]
2ED3X-ray2.50A/B1-265[»]
2ED5X-ray2.10A/B1-265[»]
2EEQX-ray2.50A/B1-265[»]
2EGBX-ray1.90A/B1-265[»]
2EGLX-ray1.80A/B1-265[»]
2EGSX-ray1.90A/B1-265[»]
2EH2X-ray2.00A/B1-265[»]
2EH4X-ray2.10A/B1-265[»]
2EH5X-ray2.30A/B1-265[»]
2EHCX-ray1.80A/B1-265[»]
2EHLX-ray1.60A/B1-265[»]
2EJJX-ray2.10A/B1-265[»]
2EJKX-ray2.40A/B1-265[»]
2EJZX-ray1.85A/B1-265[»]
2EK2X-ray2.20A/B1-265[»]
2EK3X-ray2.80A/B1-265[»]
2EK4X-ray2.20A/B1-265[»]
2EK7X-ray2.00A/B1-265[»]
2EKAX-ray2.30A/B1-265[»]
2EL0X-ray2.40A/B1-265[»]
2EL1X-ray2.20A/B1-265[»]
2EL2X-ray2.30A/B1-265[»]
2EL3X-ray2.40A/B1-265[»]
2ELDX-ray2.30A/B1-265[»]
2ELEX-ray2.40A/B1-265[»]
2EMRX-ray2.40A/B1-265[»]
2EMUX-ray2.20A/B1-265[»]
2EN5X-ray1.90A/B1-265[»]
2ENIX-ray2.50A/B1-265[»]
2HR8X-ray2.80A/B1-265[»]
2HUQX-ray2.20A/B1-265[»]
2HUTX-ray2.40A/B1-265[»]
2HUVX-ray2.10A/B1-265[»]
2HUXX-ray2.40A/B1-265[»]
2OWFX-ray2.20A1-265[»]
2OWGX-ray2.10A/B1-265[»]
2OWKX-ray2.00A/B1-265[»]
2OWUX-ray2.20A/B1-265[»]
2OWVX-ray2.80A/B1-265[»]
2P2XX-ray2.90A/B1-265[»]
2P5CX-ray2.40A/B1-265[»]
2P5FX-ray2.50A/B1-265[»]
2P6DX-ray2.40A/B1-265[»]
2P6IX-ray2.20A/B1-265[»]
2P6KX-ray2.10A/B1-265[»]
2P6LX-ray2.00A/B1-265[»]
2P9DX-ray2.10A/B1-265[»]
2PB4X-ray2.10A/B1-265[»]
2PB5X-ray2.10A/B1-265[»]
2PB6X-ray2.20A/B1-265[»]
2PCAX-ray2.00A/B1-265[»]
2PCGX-ray2.20A/B1-265[»]
2PCHX-ray2.00A/B1-265[»]
2PCIX-ray2.00A/B1-265[»]
2PCKX-ray2.60A/B1-265[»]
2PCMX-ray2.40A/B1-265[»]
2Z6RX-ray1.50A/B1-265[»]
ProteinModelPortaliO58456
SMRiO58456
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi70601.PH0725

Proteomic databases

PRIDEiO58456

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA29816; BAA29816; BAA29816
GeneIDi1443058
KEGGipho:PH0725

Phylogenomic databases

eggNOGiarCOG04161 Archaea
COG1798 LUCA
HOGENOMiHOG000205302
KOiK20215
OMAiLQNYRFG
OrthoDBiPOG093Z0BZB

Enzyme and pathway databases

UniPathwayi
UPA00559

BioCyciMetaCyc:MONOMER-18825
PHOR70601:G1G39-711-MONOMER
BRENDAi2.1.1.98 5244

Miscellaneous databases

EvolutionaryTraceiO58456

Family and domain databases

CDDicd11647 Diphthine_synthase, 1 hit
Gene3Di3.30.950.10, 1 hit
3.40.1010.10, 1 hit
HAMAPiMF_01084 Diphthine_synth, 1 hit
InterProiView protein in InterPro
IPR000878 4pyrrol_Mease
IPR035996 4pyrrol_Methylase_sf
IPR014777 4pyrrole_Mease_sub1
IPR014776 4pyrrole_Mease_sub2
IPR004551 Dphthn_synthase
PANTHERiPTHR10882:SF0 PTHR10882:SF0, 1 hit
PfamiView protein in Pfam
PF00590 TP_methylase, 1 hit
PIRSFiPIRSF036432 Diphthine_synth, 1 hit
SUPFAMiSSF53790 SSF53790, 1 hit
TIGRFAMsiTIGR00522 dph5, 1 hit

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 nameiDPHB_PYRHO
<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: O58456
<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: October 10, 2003
Last sequence update: August 1, 1998
Last modified: December 5, 2018
This is version 107 of the entry and version 1 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 programProkaryotic 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. PATHWAY comments
    Index of metabolic and biosynthesis pathways
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