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Protein

Ribosome maturation protein SBDS

Gene

SBDS

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Required for the assembly of mature ribosomes and ribosome biogenesis. Together with EFL1, triggers the GTP-dependent release of EIF6 from 60S pre-ribosomes in the cytoplasm, thereby activating ribosomes for translation competence by allowing 80S ribosome assembly and facilitating EIF6 recycling to the nucleus, where it is required for 60S rRNA processing and nuclear export. Required for normal levels of protein synthesis. May play a role in cellular stress resistance. May play a role in cellular response to DNA damage. May play a role in cell proliferation.4 Publications

GO - Molecular functioni

  • microtubule binding Source: UniProtKB
  • poly(A) RNA binding Source: UniProtKB
  • ribosome binding Source: UniProtKB
  • rRNA binding Source: UniProtKB

GO - Biological processi

  • bone marrow development Source: UniProtKB
  • bone mineralization Source: UniProtKB
  • cell proliferation Source: UniProtKB
  • inner cell mass cell proliferation Source: Ensembl
  • leukocyte chemotaxis Source: UniProtKB
  • mature ribosome assembly Source: UniProtKB
  • mitotic spindle organization Source: UniProtKB
  • rRNA processing Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

Ribosome biogenesis

Enzyme and pathway databases

BioCyciZFISH:ENSG00000126524-MONOMER.
SIGNORiQ9Y3A5.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribosome maturation protein SBDS
Alternative name(s):
Shwachman-Bodian-Diamond syndrome protein
Gene namesi
Name:SBDS
ORF Names:CGI-97
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 7

Organism-specific databases

HGNCiHGNC:19440. SBDS.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • nucleolus Source: UniProtKB
  • nucleoplasm Source: UniProtKB-SubCell
  • nucleus Source: UniProtKB
  • spindle pole Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Cytoskeleton, Nucleus

Pathology & Biotechi

Involvement in diseasei

Shwachman-Diamond syndrome (SDS)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAutosomal recessive disorder characterized by pancreatic exocrine insufficiency, hematologic dysfunction, and skeletal abnormalities.
See also OMIM:260400
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0153908N → K in SDS. 1 PublicationCorresponds to variant rs28942099dbSNPEnsembl.1
Natural variantiVAR_07167333K → T in SDS. 1 Publication1
Natural variantiVAR_01539144E → G in SDS. 1 Publication1
Natural variantiVAR_01539267K → E in SDS. 1 Publication1
Natural variantiVAR_01539387I → S in SDS. 1 Publication1
Natural variantiVAR_015394126R → T in SDS; strongly reduced release of EIF6 from pre-60S ribosome subunits. 2 PublicationsCorresponds to variant rs113993995dbSNPEnsembl.1
Natural variantiVAR_015395169R → C in SDS. 1 PublicationCorresponds to variant rs113993996dbSNPEnsembl.1
Natural variantiVAR_015396212I → T in SDS. 1 PublicationCorresponds to variant rs79344818dbSNPEnsembl.1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi151K → N: Strongly reduced release of EIF6 from pre-60S ribosome subunits. 1 Publication1

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNETi51119.
MalaCardsiSBDS.
MIMi260400. phenotype.
OpenTargetsiENSG00000126524.
Orphaneti88. Idiopathic aplastic anemia.
811. Shwachman-Diamond syndrome.
PharmGKBiPA134978742.

Polymorphism and mutation databases

BioMutaiSBDS.
DMDMi28380824.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources1 Publication
ChainiPRO_00001237622 – 250Ribosome maturation protein SBDSAdd BLAST249

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1 Publication1

Keywords - PTMi

Acetylation

Proteomic databases

EPDiQ9Y3A5.
MaxQBiQ9Y3A5.
PaxDbiQ9Y3A5.
PeptideAtlasiQ9Y3A5.
PRIDEiQ9Y3A5.

PTM databases

iPTMnetiQ9Y3A5.
PhosphoSitePlusiQ9Y3A5.

Expressioni

Tissue specificityi

Widely expressed.

Gene expression databases

BgeeiENSG00000126524.
CleanExiHS_SBDS.
ExpressionAtlasiQ9Y3A5. baseline and differential.
GenevisibleiQ9Y3A5. HS.

Organism-specific databases

HPAiHPA028891.

Interactioni

Subunit structurei

Associates with the 60S ribosomal subunit. Interacts with NPM1, RPA1 and PRKDC. May interact with NIP7 (PubMed:17643419). Found in a complex consisting of the 60S ribosomal subunit, SBDS and EFL1 (PubMed:26479198).4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
ACDQ96AP02EBI-1046471,EBI-717666

GO - Molecular functioni

  • microtubule binding Source: UniProtKB

Protein-protein interaction databases

BioGridi119307. 59 interactors.
IntActiQ9Y3A5. 6 interactors.
MINTiMINT-3085538.
STRINGi9606.ENSP00000246868.

Structurei

Secondary structure

1250
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni6 – 8Combined sources3
Beta strandi14 – 21Combined sources8
Beta strandi26 – 35Combined sources10
Helixi36 – 40Combined sources5
Helixi47 – 50Combined sources4
Beta strandi51 – 55Combined sources5
Beta strandi56 – 59Combined sources4
Turni60 – 63Combined sources4
Beta strandi64 – 66Combined sources3
Helixi68 – 74Combined sources7
Helixi80 – 89Combined sources10
Beta strandi90 – 93Combined sources4
Beta strandi97 – 103Combined sources7
Helixi107 – 116Combined sources10
Turni122 – 125Combined sources4
Helixi130 – 140Combined sources11
Helixi150 – 164Combined sources15
Beta strandi168 – 170Combined sources3
Beta strandi174 – 177Combined sources4
Helixi180 – 186Combined sources7
Turni187 – 189Combined sources3
Helixi190 – 193Combined sources4
Beta strandi196 – 200Combined sources5
Beta strandi203 – 205Combined sources3
Beta strandi208 – 210Combined sources3
Helixi214 – 216Combined sources3
Helixi217 – 227Combined sources11
Turni228 – 231Combined sources4
Beta strandi232 – 236Combined sources5
Beta strandi240 – 242Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2KDONMR-A1-250[»]
2L9NNMR-A1-250[»]
5AN9electron microscopy3.30J1-250[»]
5ANBelectron microscopy4.10J1-250[»]
5ANCelectron microscopy4.20J1-250[»]
ProteinModelPortaliQ9Y3A5.
SMRiQ9Y3A5.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9Y3A5.

Family & Domainsi

Sequence similaritiesi

Belongs to the SDO1/SBDS family.Curated

Phylogenomic databases

eggNOGiKOG2917. Eukaryota.
COG1500. LUCA.
GeneTreeiENSGT00390000008135.
HOGENOMiHOG000216685.
HOVERGENiHBG039762.
InParanoidiQ9Y3A5.
KOiK14574.
OMAiTIDSETR.
PhylomeDBiQ9Y3A5.
TreeFamiTF300881.

Family and domain databases

Gene3Di3.30.1250.10. 1 hit.
InterProiIPR018978. Ribosome_mat_SBDS_C.
IPR018023. Ribosome_mat_SBDS_CS.
IPR019783. Ribosome_mat_SBDS_N.
IPR002140. Sdo1/SBDS.
[Graphical view]
PfamiPF01172. SBDS. 1 hit.
PF09377. SBDS_C. 1 hit.
[Graphical view]
SUPFAMiSSF89895. SSF89895. 1 hit.
TIGRFAMsiTIGR00291. RNA_SBDS. 1 hit.
PROSITEiPS01267. UPF0023. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9Y3A5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSIFTPTNQI RLTNVAVVRM KRAGKRFEIA CYKNKVVGWR SGVEKDLDEV
60 70 80 90 100
LQTHSVFVNV SKGQVAKKED LISAFGTDDQ TEICKQILTK GEVQVSDKER
110 120 130 140 150
HTQLEQMFRD IATIVADKCV NPETKRPYTV ILIERAMKDI HYSVKTNKST
160 170 180 190 200
KQQALEVIKQ LKEKMKIERA HMRLRFILPV NEGKKLKEKL KPLIKVIESE
210 220 230 240 250
DYGQQLEIVC LIDPGCFREI DELIKKETKG KGSLEVLNLK DVEEGDEKFE
Length:250
Mass (Da):28,764
Last modified:January 23, 2007 - v4
Checksum:iD35C43003C05F5A7
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti41 – 43SGV → RAW in AAD34092 (PubMed:10810093).Curated3
Sequence conflicti89T → A in AAD34092 (PubMed:10810093).Curated1
Sequence conflicti105E → G in AAD34092 (PubMed:10810093).Curated1
Sequence conflicti114I → F in AAD34092 (PubMed:10810093).Curated1
Sequence conflicti126R → G in AAD34092 (PubMed:10810093).Curated1
Sequence conflicti143S → L in AAD34092 (PubMed:10810093).Curated1
Sequence conflicti146T → P in AAD34092 (PubMed:10810093).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0153908N → K in SDS. 1 PublicationCorresponds to variant rs28942099dbSNPEnsembl.1
Natural variantiVAR_07167333K → T in SDS. 1 Publication1
Natural variantiVAR_01539144E → G in SDS. 1 Publication1
Natural variantiVAR_01539267K → E in SDS. 1 Publication1
Natural variantiVAR_01539387I → S in SDS. 1 Publication1
Natural variantiVAR_015394126R → T in SDS; strongly reduced release of EIF6 from pre-60S ribosome subunits. 2 PublicationsCorresponds to variant rs113993995dbSNPEnsembl.1
Natural variantiVAR_015395169R → C in SDS. 1 PublicationCorresponds to variant rs113993996dbSNPEnsembl.1
Natural variantiVAR_015396212I → T in SDS. 1 PublicationCorresponds to variant rs79344818dbSNPEnsembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY169963 mRNA. Translation: AAN77490.1.
AF151855 mRNA. Translation: AAD34092.1.
AK001779 mRNA. Translation: BAA91905.1.
AK289609 mRNA. Translation: BAF82298.1.
CH471140 Genomic DNA. Translation: EAX07906.1.
BC065700 mRNA. Translation: AAH65700.1.
CCDSiCCDS5537.1.
RefSeqiNP_057122.2. NM_016038.2.
UniGeneiHs.110445.

Genome annotation databases

EnsembliENST00000246868; ENSP00000246868; ENSG00000126524.
GeneIDi51119.
KEGGihsa:51119.
UCSCiuc003tvm.2. human.

Cross-referencesi

Web resourcesi

SBDSbase

SBDS mutation db

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY169963 mRNA. Translation: AAN77490.1.
AF151855 mRNA. Translation: AAD34092.1.
AK001779 mRNA. Translation: BAA91905.1.
AK289609 mRNA. Translation: BAF82298.1.
CH471140 Genomic DNA. Translation: EAX07906.1.
BC065700 mRNA. Translation: AAH65700.1.
CCDSiCCDS5537.1.
RefSeqiNP_057122.2. NM_016038.2.
UniGeneiHs.110445.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2KDONMR-A1-250[»]
2L9NNMR-A1-250[»]
5AN9electron microscopy3.30J1-250[»]
5ANBelectron microscopy4.10J1-250[»]
5ANCelectron microscopy4.20J1-250[»]
ProteinModelPortaliQ9Y3A5.
SMRiQ9Y3A5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119307. 59 interactors.
IntActiQ9Y3A5. 6 interactors.
MINTiMINT-3085538.
STRINGi9606.ENSP00000246868.

PTM databases

iPTMnetiQ9Y3A5.
PhosphoSitePlusiQ9Y3A5.

Polymorphism and mutation databases

BioMutaiSBDS.
DMDMi28380824.

Proteomic databases

EPDiQ9Y3A5.
MaxQBiQ9Y3A5.
PaxDbiQ9Y3A5.
PeptideAtlasiQ9Y3A5.
PRIDEiQ9Y3A5.

Protocols and materials databases

DNASUi51119.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000246868; ENSP00000246868; ENSG00000126524.
GeneIDi51119.
KEGGihsa:51119.
UCSCiuc003tvm.2. human.

Organism-specific databases

CTDi51119.
DisGeNETi51119.
GeneCardsiSBDS.
GeneReviewsiSBDS.
HGNCiHGNC:19440. SBDS.
HPAiHPA028891.
MalaCardsiSBDS.
MIMi260400. phenotype.
607444. gene.
neXtProtiNX_Q9Y3A5.
OpenTargetsiENSG00000126524.
Orphaneti88. Idiopathic aplastic anemia.
811. Shwachman-Diamond syndrome.
PharmGKBiPA134978742.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2917. Eukaryota.
COG1500. LUCA.
GeneTreeiENSGT00390000008135.
HOGENOMiHOG000216685.
HOVERGENiHBG039762.
InParanoidiQ9Y3A5.
KOiK14574.
OMAiTIDSETR.
PhylomeDBiQ9Y3A5.
TreeFamiTF300881.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000126524-MONOMER.
SIGNORiQ9Y3A5.

Miscellaneous databases

ChiTaRSiSBDS. human.
EvolutionaryTraceiQ9Y3A5.
GeneWikiiSBDS.
GenomeRNAii51119.
PROiQ9Y3A5.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000126524.
CleanExiHS_SBDS.
ExpressionAtlasiQ9Y3A5. baseline and differential.
GenevisibleiQ9Y3A5. HS.

Family and domain databases

Gene3Di3.30.1250.10. 1 hit.
InterProiIPR018978. Ribosome_mat_SBDS_C.
IPR018023. Ribosome_mat_SBDS_CS.
IPR019783. Ribosome_mat_SBDS_N.
IPR002140. Sdo1/SBDS.
[Graphical view]
PfamiPF01172. SBDS. 1 hit.
PF09377. SBDS_C. 1 hit.
[Graphical view]
SUPFAMiSSF89895. SSF89895. 1 hit.
TIGRFAMsiTIGR00291. RNA_SBDS. 1 hit.
PROSITEiPS01267. UPF0023. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSBDS_HUMAN
AccessioniPrimary (citable) accession number: Q9Y3A5
Secondary accession number(s): A8K0P4, Q96FX0, Q9NV53
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 155 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 7
    Human chromosome 7: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

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.