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Protein

H/ACA ribonucleoprotein complex non-core subunit NAF1

Gene

NAF1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

RNA-binding protein required for the maturation of box H/ACA snoRNPs complex and ribosome biogenesis. During assembly of the H/ACA snoRNPs complex, it associates with the complex and disappears during maturation of the complex and is replaced by GAR1 to yield mature H/ACA snoRNPs complex. Acts as a competitive binder for CBF5 probably required to prevent non-cognate RNAs from being loaded during transport of the particle by inducing a non-productive conformation of CBF5.5 Publications

GO - Molecular functioni

  • RNA binding Source: SGD

GO - Biological processi

  • box H/ACA snoRNP assembly Source: SGD
  • pseudouridine synthesis Source: InterPro
  • rRNA processing Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

Ribosome biogenesis, rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-33145-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
H/ACA ribonucleoprotein complex non-core subunit NAF1
Alternative name(s):
Nuclear assembly factor 1
Gene namesi
Name:NAF1
Ordered Locus Names:YNL124W
ORF Names:N1888
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIV

Organism-specific databases

EuPathDBiFungiDB:YNL124W.
SGDiS000005068. NAF1.

Subcellular locationi

GO - Cellular componenti

  • intracellular ribonucleoprotein complex Source: UniProtKB-KW
  • nucleoplasm Source: SGD
  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002034281 – 492H/ACA ribonucleoprotein complex non-core subunit NAF1Add BLAST492

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei255PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP53919.
PRIDEiP53919.

PTM databases

iPTMnetiP53919.

Interactioni

Subunit structurei

During assembly of the complex, component of the small nucleolar ribonucleoprotein particles containing H/ACA-type snoRNAs (H/ACA snoRNPs) which contains CBF5, NAF1, NHP2 and NOP10 proteins. Interacts with SHQ1. Interacts directly with CBF5. Interacts with hyperphosphorylated C-terminal domain (CTD) of RNA polymerase II large subunit (RPB1).4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CBF5P333226EBI-28887,EBI-4105
NHP2P324953EBI-28887,EBI-12014

Protein-protein interaction databases

BioGridi35703. 96 interactors.
DIPiDIP-4345N.
IntActiP53919. 255 interactors.
MINTiMINT-501196.

Structurei

Secondary structure

1492
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi137 – 147Combined sources11
Beta strandi150 – 155Combined sources6
Beta strandi169 – 172Combined sources4
Beta strandi177 – 180Combined sources4
Beta strandi183 – 186Combined sources4
Beta strandi188 – 190Combined sources3
Beta strandi192 – 196Combined sources5
Helixi199 – 201Combined sources3
Helixi202 – 209Combined sources8
Turni210 – 213Combined sources4
Beta strandi214 – 219Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2V3MX-ray2.74A/B/C/D/E/F109-232[»]
ProteinModelPortaliP53919.
SMRiP53919.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP53919.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni172 – 230RNA-bindingAdd BLAST59

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi55 – 81Ser-richAdd BLAST27
Compositional biasi361 – 456Pro-richAdd BLAST96
Compositional biasi419 – 488Gln-richAdd BLAST70

Domaini

The central region (136-221) reveals a striking structural homology with the core domain of GAR1.1 Publication

Sequence similaritiesi

Belongs to the NAF1 family.Curated

Phylogenomic databases

GeneTreeiENSGT00390000004697.
InParanoidiP53919.
KOiK14763.
OMAiINTEDCD.
OrthoDBiEOG092C3IL1.

Family and domain databases

InterProiIPR007504. H/ACA_rnp_Gar1/Naf1.
IPR009000. Transl_B-barrel.
[Graphical view]
PfamiPF04410. Gar1. 1 hit.
[Graphical view]
SUPFAMiSSF50447. SSF50447. 1 hit.

Sequencei

Sequence statusi: Complete.

P53919-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSDDLFSKAL ENPDQDLNVE LPKDDVDLGL LGDGGNERKT DEPVADAERS
60 70 80 90 100
TGLGSGSSES ESDSGSDSDS DSGSSGSEDD SADQDVEGED EGGDAIENED
110 120 130 140 150
EDEDPSPSGP ILSKNEILEE TVPELPEDYE ISEKTIITPI GVLKSAFENN
160 170 180 190 200
IIIHATMSGE KRVLKEGSIF CLEDRTLIGM LTEVFGPLQN PFYRIKLPDS
210 220 230 240 250
KKNLFDELKV RLGEKAFIVT PDAHWIDTFE LKRNKGTDAS NGYDEELPEE
260 270 280 290 300
EQEFSDDEKE ALFKKMKKQQ RQRKKRDNRK LANDSDNVKV KRARQPKANS
310 320 330 340 350
LPKLVPPLGM SSNAPMQHGY KSRNARENIK RESSATSNRN GSSPVPITQH
360 370 380 390 400
HQQQFSANNY PFPQQPNGMP YPPYSPFPQP TNFQYPPPPF GQATPAQFSN
410 420 430 440 450
TVPYGSLPPA YNNMSPPTQQ SFMPMTQSQP PLPYGVPPMN QMQNPMYIQP
460 470 480 490
PPQAPPQGNG NFQQVMELHQ ILLQQQQQQH QYQHQHQQDP RT
Length:492
Mass (Da):54,949
Last modified:October 1, 1996 - v1
Checksum:i5A496278070F6255
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti378P → A in strain: YJM269, YJM270, YJM326 and YJM1129. 1 Publication1
Natural varianti423M → I in strain: YJM627. 1 Publication1
Natural varianti424P → S in strain: YJM269, YJM270, YJM326 and YJM1129. 1 Publication1
Natural varianti426T → A in strain: SK1, V1-09, YJM269, YJM270, YJM280, YJM320, YJM326, YJM339, YJM627, YJM789 and YJM1129. 1 Publication1
Natural varianti480H → N in strain: V1-09 and YJM627. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z69382 Genomic DNA. Translation: CAA93381.1.
Z71400 Genomic DNA. Translation: CAA96005.1.
EF125216 Genomic DNA. Translation: ABN58535.1.
EF125217 Genomic DNA. Translation: ABN58543.1.
EF125218 Genomic DNA. Translation: ABN58552.1.
EF125219 Genomic DNA. Translation: ABN58561.1.
EF125220 Genomic DNA. Translation: ABN58570.1.
EF125221 Genomic DNA. Translation: ABN58579.1.
EF125222 Genomic DNA. Translation: ABN58588.1.
EF125223 Genomic DNA. Translation: ABN58597.1.
EF125224 Genomic DNA. Translation: ABN58606.1.
EF125225 Genomic DNA. Translation: ABN58615.1.
EF125226 Genomic DNA. Translation: ABN58624.1.
EF125228 Genomic DNA. Translation: ABN58642.1.
BK006947 Genomic DNA. Translation: DAA10425.1.
PIRiS63065.
RefSeqiNP_014275.3. NM_001182962.3.

Genome annotation databases

EnsemblFungiiYNL124W; YNL124W; YNL124W.
GeneIDi855599.
KEGGisce:YNL124W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z69382 Genomic DNA. Translation: CAA93381.1.
Z71400 Genomic DNA. Translation: CAA96005.1.
EF125216 Genomic DNA. Translation: ABN58535.1.
EF125217 Genomic DNA. Translation: ABN58543.1.
EF125218 Genomic DNA. Translation: ABN58552.1.
EF125219 Genomic DNA. Translation: ABN58561.1.
EF125220 Genomic DNA. Translation: ABN58570.1.
EF125221 Genomic DNA. Translation: ABN58579.1.
EF125222 Genomic DNA. Translation: ABN58588.1.
EF125223 Genomic DNA. Translation: ABN58597.1.
EF125224 Genomic DNA. Translation: ABN58606.1.
EF125225 Genomic DNA. Translation: ABN58615.1.
EF125226 Genomic DNA. Translation: ABN58624.1.
EF125228 Genomic DNA. Translation: ABN58642.1.
BK006947 Genomic DNA. Translation: DAA10425.1.
PIRiS63065.
RefSeqiNP_014275.3. NM_001182962.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2V3MX-ray2.74A/B/C/D/E/F109-232[»]
ProteinModelPortaliP53919.
SMRiP53919.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35703. 96 interactors.
DIPiDIP-4345N.
IntActiP53919. 255 interactors.
MINTiMINT-501196.

PTM databases

iPTMnetiP53919.

Proteomic databases

MaxQBiP53919.
PRIDEiP53919.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYNL124W; YNL124W; YNL124W.
GeneIDi855599.
KEGGisce:YNL124W.

Organism-specific databases

EuPathDBiFungiDB:YNL124W.
SGDiS000005068. NAF1.

Phylogenomic databases

GeneTreeiENSGT00390000004697.
InParanoidiP53919.
KOiK14763.
OMAiINTEDCD.
OrthoDBiEOG092C3IL1.

Enzyme and pathway databases

BioCyciYEAST:G3O-33145-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP53919.
PROiP53919.

Family and domain databases

InterProiIPR007504. H/ACA_rnp_Gar1/Naf1.
IPR009000. Transl_B-barrel.
[Graphical view]
PfamiPF04410. Gar1. 1 hit.
[Graphical view]
SUPFAMiSSF50447. SSF50447. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiNAF1_YEAST
AccessioniPrimary (citable) accession number: P53919
Secondary accession number(s): B0KZR2
, B0KZS1, B0KZT9, B0KZZ3, B0L002, D6W159
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: November 2, 2016
This is version 130 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 1810 molecules/cell in log phase SD medium.1 Publication

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. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.