Q9Y3A5 (SBDS_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ribosome maturation protein SBDS

Alternative name(s):
Shwachman-Bodian-Diamond syndrome protein

Gene names

Name:	SBDS
ORF Names:	CGI-97

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	250 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Required for the assembly of mature ribosomes and ribosome biogenesis. Together with EFTUD1, 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. Ref.9 Ref.10 Ref.11 Ref.14
Subunit structure	Associates with the 60S ribosomal subunit. Interacts with NPM1, RPA1 and PRKDC. May interact with NIP7. Ref.8 Ref.9 Ref.10
Subcellular location	Cytoplasm. Nucleus › nucleolus. Nucleus › nucleoplasm. Cytoplasm › cytoskeleton › spindle. Note: Primarily detected in the cytoplasm, and at low levels in nucleus and nucleolus (Ref.10 and Ref.8). Detected in the nucleolus during G1 and G2 phase of the cell cycle, and diffusely distributed in the nucleus during S phase. Detected at the mitotic spindle. Colocalizes with the microtubule organizing center during interphase (Ref.11). Ref.7 Ref.8 Ref.10 Ref.11
Tissue specificity	Widely expressed.
Involvement in disease	Shwachman-Diamond syndrome (SDS) [MIM:260400]: Autosomal recessive disorder characterized by pancreatic exocrine insufficiency, hematologic dysfunction, and skeletal abnormalities. Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.1 Ref.14
Sequence similarities	Belongs to the SDO1/SBDS family.

Ontologies

Keywords
Biological process	Ribosome biogenesis
Cellular component	Cytoplasm Cytoskeleton Nucleus
Disease	Disease mutation
PTM	Acetylation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	bone marrow development Inferred from mutant phenotype PubMed 15342903. Source: UniProtKB bone mineralization Inferred from mutant phenotype PubMed 17920346. Source: UniProtKB cell proliferation Inferred from mutant phenotype Ref.11. Source: UniProtKB inner cell mass cell proliferation Inferred from electronic annotation. Source: Compara leukocyte chemotaxis Inferred from direct assay PubMed 14743349. Source: UniProtKB mature ribosome assembly Inferred from direct assay Ref.14. Source: UniProtKB mitotic spindle stabilization Inferred from direct assay PubMed 18324336. Source: UniProtKB rRNA processing Inferred from mutant phenotype Ref.9. Source: UniProtKB ribosomal large subunit biogenesis Inferred from Biological aspect of Ancestor. Source: RefGenome
Cellular_component	cytoplasm Inferred from direct assay Ref.7PubMed 18324336. Source: UniProtKB nucleolus Inferred from direct assay Ref.7Ref.8. Source: UniProtKB nucleoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell spindle pole Inferred from direct assay PubMed 18324336Ref.11. Source: UniProtKB
Molecular_function	microtubule binding Inferred from direct assay PubMed 18324336. Source: UniProtKB rRNA binding Inferred from direct assay Ref.8. Source: UniProtKB ribosome binding Inferred from direct assay Ref.14. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.6

Chain

2 – 250

249

Ribosome maturation protein SBDS

PRO_0000123762

Amino acid modifications

Modified residue

2

1

N-acetylserine Ref.6

Natural variations

Natural variant

8

1

N → K in SDS. Ref.1
Corresponds to variant rs28942099 [ dbSNP | Ensembl ].

VAR_015390

Natural variant

44

1

E → G in SDS. Ref.1

VAR_015391

Natural variant

67

1

K → E in SDS. Ref.1

VAR_015392

Natural variant

87

1

I → S in SDS. Ref.1

VAR_015393

Natural variant

126

1

R → T in SDS; strongly reduced release of EIF6 from pre-60S ribosome subunits. Ref.1 Ref.14

VAR_015394

Natural variant

169

1

R → C in SDS. Ref.1

VAR_015395

Natural variant

212

1

I → T in SDS. Ref.1

VAR_015396

Experimental info

Mutagenesis

151

1

K → N: Strongly reduced release of EIF6 from pre-60S ribosome subunits. Ref.14

Sequence conflict

41 – 43

3

SGV → RAW in AAD34092. Ref.2

Sequence conflict

89

1

T → A in AAD34092. Ref.2

Sequence conflict

105

1

E → G in AAD34092. Ref.2

Sequence conflict

114

1

I → F in AAD34092. Ref.2

Sequence conflict

126

1

R → G in AAD34092. Ref.2

Sequence conflict

143

1

S → L in AAD34092. Ref.2

Sequence conflict

146

1

T → P in AAD34092. Ref.2

Secondary structure

1

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250

Helix Strand Turn

Details...

Turn

6 – 8

3

Beta strand

14 – 21

8

Beta strand

26 – 35

10

Helix

36 – 40

5

Helix

47 – 50

4

Beta strand

51 – 55

5

Beta strand

56 – 59

4

Turn

60 – 63

4

Beta strand

64 – 66

3

Helix

68 – 74

7

Helix

80 – 89

10

Beta strand

90 – 93

4

Beta strand

97 – 103

7

Helix

107 – 116

10

Turn

122 – 125

4

Helix

130 – 140

11

Helix

150 – 164

15

Beta strand

168 – 170

3

Beta strand

174 – 177

4

Helix

180 – 186

7

Turn

187 – 189

3

Helix

190 – 193

4

Beta strand

196 – 200

5

Beta strand

203 – 205

3

Beta strand

208 – 210

3

Helix

214 – 216

3

Helix

217 – 227

11

Turn

228 – 231

4

Beta strand

232 – 236

5

Beta strand

240 – 242

3

Sequences

	Sequence		Length	Mass (Da)
	Q9Y3A5 [UniParc]. Last modified January 23, 2007. Version 4. Checksum: D35C43003C05F5A7	FASTA	250	28,764
	10 20 30 40 50 60 MSIFTPTNQI RLTNVAVVRM KRAGKRFEIA CYKNKVVGWR SGVEKDLDEV LQTHSVFVNV 70 80 90 100 110 120 SKGQVAKKED LISAFGTDDQ TEICKQILTK GEVQVSDKER HTQLEQMFRD IATIVADKCV 130 140 150 160 170 180 NPETKRPYTV ILIERAMKDI HYSVKTNKST KQQALEVIKQ LKEKMKIERA HMRLRFILPV 190 200 210 220 230 240 NEGKKLKEKL KPLIKVIESE DYGQQLEIVC LIDPGCFREI DELIKKETKG KGSLEVLNLK 250 DVEEGDEKFE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Mutations in SBDS are associated with Shwachman-Diamond syndrome." Boocock G.R.B., Morrison J.A., Popovic M., Richards N., Ellis L., Durie P.R., Rommens J.M. Nat. Genet. 33:97-101(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANTS SDS LYS-8; GLY-44; GLU-67; SER-87; THR-126; CYS-169 AND THR-212.
[2]	"Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics." Lai C.-H., Chou C.-Y., Ch'ang L.-Y., Liu C.-S., Lin W.-C. Genome Res. 10:703-713(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[3]	"Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S. Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Brain cortex and Ovarian carcinoma.
[4]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: PNS.
[6]	Bienvenut W.V., Claeys D. Submitted (NOV-2005) to UniProtKB Cited for: PROTEIN SEQUENCE OF 2-19, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT SER-2, MASS SPECTROMETRY. Tissue: Platelet.
[7]	"The Shwachman-Diamond SBDS protein localizes to the nucleolus." Austin K.M., Leary R.J., Shimamura A. Blood 106:1253-1258(2005) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION.
[8]	"The human Shwachman-Diamond syndrome protein, SBDS, associates with ribosomal RNA." Ganapathi K.A., Austin K.M., Lee C.S., Dias A., Malsch M.M., Reed R., Shimamura A. Blood 110:1458-1465(2007) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH NPM1 AND THE 60S RIBOSOMAL SUBUNIT, SUBCELLULAR LOCATION.
[9]	"The Shwachman-Bodian-Diamond syndrome associated protein interacts with HsNip7 and its down-regulation affects gene expression at the transcriptional and translational levels." Hesling C., Oliveira C.C., Castilho B.A., Zanchin N.I. Exp. Cell Res. 313:4180-4195(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH NIP7.
[10]	"Shwachman-Bodian Diamond syndrome is a multi-functional protein implicated in cellular stress responses." Ball H.L., Zhang B., Riches J.J., Gandhi R., Li J., Rommens J.M., Myers J.S. Hum. Mol. Genet. 18:3684-3695(2009) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH RPA1; PRKDC AND THE 60S RIBOSOME SUBUNIT.
[11]	"SBDS expression and localization at the mitotic spindle in human myeloid progenitors." Orelio C., Verkuijlen P., Geissler J., van den Berg T.K., Kuijpers T.W. PLoS ONE 4:E7084-E7084(2009) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[12]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[13]	"Structure, dynamics, and RNA interaction analysis of the human SBDS protein." de Oliveira J.F., Sforca M.L., Blumenschein T.M., Goldfeder M.B., Guimaraes B.G., Oliveira C.C., Zanchin N.I., Zeri A.C. J. Mol. Biol. 396:1053-1069(2010) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR, RNA-BINDING.
[14]	"Uncoupling of GTP hydrolysis from eIF6 release on the ribosome causes Shwachman-Diamond syndrome." Finch A.J., Hilcenko C., Basse N., Drynan L.F., Goyenechea B., Menne T.F., Gonzalez Fernandez A., Simpson P., D'Santos C.S., Arends M.J., Donadieu J., Bellanne-Chantelot C., Costanzo M., Boone C., McKenzie A.N., Freund S.M., Warren A.J. Genes Dev. 25:917-929(2011) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR, FUNCTION, CHARACTERIZATION OF VARIANT SDS THR-126, MUTAGENESIS OF LYS-151.
+	Additional computationally mapped references.

Web resources

SBDSbase

SBDS mutation db

GeneReviews

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

IPI

IPI00427330.

RefSeq

NP_057122.2. NM_016038.2.

UniGene

Hs.110445.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2KDO	NMR	-	A	1-250	[»]
2L9N	NMR	-	A	1-250	[»]

ProteinModelPortal

Q9Y3A5.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q9Y3A5. 1 interaction.

STRING

9606.ENSP00000246868.

PTM databases

PhosphoSite

Q9Y3A5.

Polymorphism databases

DMDM

28380824.

Proteomic databases

PaxDb

Q9Y3A5.

PeptideAtlas

Q9Y3A5.

PRIDE

Q9Y3A5.

Protocols and materials databases

DNASU

51119.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000246868; ENSP00000246868; ENSG00000126524.

GeneID

51119.

KEGG

hsa:51119.

UCSC

uc003tvm.1. human.

Organism-specific databases

CTD

51119.

GeneCards

GC07M066452.

HGNC

HGNC:19440. SBDS.

HPA

HPA028891.

MIM

260400. phenotype.
607444. gene.

neXtProt

NX_Q9Y3A5.

Orphanet

88. Idiopathic aplastic anemia.
811. Shwachman-Diamond syndrome.

PharmGKB

PA134978742.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG1500.

HOGENOM

HOG000216685.

HOVERGEN

HBG039762.

InParanoid

Q9Y3A5.

KO

K14574.

OMA

DPYLARD.

OrthoDB

EOG40ZQZH.

PhylomeDB

Q9Y3A5.

Gene expression databases

ArrayExpress

Q9Y3A5.

Bgee

Q9Y3A5.

CleanEx

HS_SBDS.

Genevestigator

Q9Y3A5.

GermOnline

ENSG00000126524. Homo sapiens.

Family and domain databases

InterPro

IPR018978. Ribosome_mat_SBDS_C.
IPR018023. Ribosome_mat_SBDS_CS.
IPR019783. Ribosome_mat_SBDS_N.
IPR002140. Ribosome_maturation_pr_SBDS.
[Graphical view]

PANTHER

PTHR10927. PTHR10927. 1 hit.

Pfam

PF01172. SBDS. 1 hit.
PF09377. SBDS_C. 1 hit.
[Graphical view]

SUPFAM

SSF89895. Ribosome_mat_SBDS_N. 1 hit.

TIGRFAMs

TIGR00291. RNA_SBDS. 1 hit.

PROSITE

PS01267. UPF0023. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

ChiTaRS

SBDS. human.

EvolutionaryTrace

Q9Y3A5.

GenomeRNAi

51119.

NextBio

53897.

SOURCE

Search...

Entry information

Entry name

SBDS_HUMAN

Accession

Primary (citable) accession number: Q9Y3A5
Secondary accession number(s): A8K0P4, Q96FX0, Q9NV53

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 117 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.