2WBM

Crystal structure of mthSBDS, the homologue of the Shwachman-Bodian- Diamond syndrome protein in the euriarchaeon Methanothermobacter thermautotrophicus

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2wbma2	All alpha proteins	RuvA C-terminal domain-like	Hypothetical protein AF0491, middle domain	automated matches	automated matches	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
A	d2wbma3	Alpha and beta proteins (a+b)	Ferredoxin-like	EF-G C-terminal domain-like	automated matches	automated matches	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
A	d2wbma1	Alpha and beta proteins (a+b)	FYSH domain	FYSH domain	automated matches	automated matches	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
A	d2wbma4	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
B	d2wbmb2	All alpha proteins	RuvA C-terminal domain-like	Hypothetical protein AF0491, middle domain	automated matches	automated matches	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
B	d2wbmb3	Alpha and beta proteins (a+b)	Ferredoxin-like	EF-G C-terminal domain-like	automated matches	automated matches	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
B	d2wbmb1	Alpha and beta proteins (a+b)	FYSH domain	FYSH domain	automated matches	automated matches	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	SBDS_C_N	e2wbmA1	A: alpha arrays	X: RuvA-C	H: Hypothetical protein AF0491, middle domain (From Topology)	T: Hypothetical protein AF0491, middle domain	F: SBDS_C_N	ECOD (1.6)
A	SBDS	e2wbmA3	A: a+b two layers	X: FYSH domain (From Topology)	H: FYSH domain (From Topology)	T: FYSH domain	F: SBDS	ECOD (1.6)
A	SBDS_C_C	e2wbmA2	A: a+b two layers	X: Alpha-beta plaits	H: EF-G C-terminal domain-like (From Topology)	T: EF-G C-terminal domain-like	F: SBDS_C_C	ECOD (1.6)
B	SBDS_C_N	e2wbmB1	A: alpha arrays	X: RuvA-C	H: Hypothetical protein AF0491, middle domain (From Topology)	T: Hypothetical protein AF0491, middle domain	F: SBDS_C_N	ECOD (1.6)
B	SBDS	e2wbmB3	A: a+b two layers	X: FYSH domain (From Topology)	H: FYSH domain (From Topology)	T: FYSH domain	F: SBDS	ECOD (1.6)
B	SBDS_C_C	e2wbmB2	A: a+b two layers	X: Alpha-beta plaits	H: EF-G C-terminal domain-like (From Topology)	T: EF-G C-terminal domain-like	F: SBDS_C_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.1250.10	Alpha Beta	2-Layer Sandwich	Hypothetical 12.0 Kda Protein In Nam8-gar1 Intergenic Region	Chain: A	CATH (4.3.0)
A	1.10.10.900	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	SBDS protein C-terminal domain, subdomain 1	CATH (4.3.0)
A	3.30.70.240	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	3.30.1250.10	Alpha Beta	2-Layer Sandwich	Hypothetical 12.0 Kda Protein In Nam8-gar1 Intergenic Region	Chain: A	CATH (4.3.0)
B	1.10.10.900	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	SBDS protein C-terminal domain, subdomain 1	CATH (4.3.0)
B	3.30.70.240	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF09377	SBDS protein, domain II (SBDS_domain_II)	SBDS protein, domain II	Members containing this domain are highly conserved in species ranging from archaea to vertebrates and plants [1], including several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autoso ...	Members containing this domain are highly conserved in species ranging from archaea to vertebrates and plants [1], including several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. These proteins play a role in RNA metabolism [2,3]. In yeast Sdo1 is involved in the biogenesis of the 60S ribosomal subunit and translational activation of ribosomes [4]. SBDS protein is composed of three domains. The N-terminal (Pfam:PF01172) (FYSH) domain (domain I) is the most frequent target for disease mutations and contains a novel mixed alpha/beta-fold, the central domain (domain II) represented in this entry consists of a three-helical bundle and the C-terminal domain that has a ferredoxin-like fold [3,5].	Domain
A, B	PF01172	Shwachman-Bodian-Diamond syndrome (SBDS) N-terminal domain (SBDS_N)	Shwachman-Bodian-Diamond syndrome (SBDS) N-terminal domain	This entry represents the N-terminal domain of proteins that are highly conserved in species ranging from archaea to vertebrates and plants [1], including several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman ...	This entry represents the N-terminal domain of proteins that are highly conserved in species ranging from archaea to vertebrates and plants [1], including several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. It is characterised by bone marrow failure and leukemia predisposition. Members of this entry play a role in RNA metabolism [2][3]. In yeast these proteins have been shown to be critical for the release and recycling of the nucleolar shuttling factor Tif6 from pre-60S ribosomes, a key step in 60S maturation and translational activation of ribosomes [4]. This data links defective late 60S subunit maturation to an inherited bone marrow failure syndrome associated with leukemia predisposition [4].	Domain
A, B	PF20268	SBDS protein, C-terminal domain (SBDS_C)	SBDS protein, C-terminal domain	Members containing this domain are highly conserved in species ranging from archaea to vertebrates and plants [1], including several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autoso ...	Members containing this domain are highly conserved in species ranging from archaea to vertebrates and plants [1], including several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. These proteins play a role in RNA metabolism [2,3]. In yeast Sdo1 is involved in the biogenesis of the 60S ribosomal subunit and translational activation of ribosomes [4]. The SBDS protein is composed of three domains. The N-terminal (Pfam:PF01172) (FYSH) domain (domain I) is the most frequent target for disease mutations and contains a novel mixed alpha/beta-fold, the central domain (domain II, Pfam:PF09377) consists of a three-helical bundle and this C-terminal domain which has a ferredoxin-like fold [3,5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	RIBOSOME MATURATION PROTEIN SDO1 HOMOLOG	-	ribonucleoprotein complex biogenesis organelle assembly membraneless organelle assembly cellular component biogenesis cellular component organization ribosome biogenesis organelle organization cellular component assembly cytosolic ribosome assembly cellular process cellular component organization or biogenesis ribosome assembly	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR002140	Ribosome maturation protein Sdo1/SBDS	Family
A, B	IPR037188	Ribosome maturation protein Sdo1/SBDS, central domain superfamily	Homologous Superfamily
A, B	IPR018023	Ribosome maturation protein SBDS, conserved site	Conserved Site
A, B	IPR035647	EF-G domain III/V-like	Homologous Superfamily
A, B	IPR018978	Ribosome maturation protein SDO1/SBDS, central domain	Domain
A, B	IPR046928	Ribosome maturation protein SDO1/SBDS, C-terminal domain	Domain
A, B	IPR039100	Ribosome maturation protein Sdo1/SBDS-like	Family
A, B	IPR019783	Ribosome maturation protein SDO1/SBDS, N-terminal	Domain
A, B	IPR036786	Ribosome maturation protein SBDS, N-terminal domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.