3F2O | pdb_00003f2o

Crystal Structure of human splA/ryanodine receptor domain and SOCS box containing 1 (SPSB1) in complex with a 20-residue VASA peptide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8059599	3000120	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8059599	3000120	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	SPRY	e3f2oB1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: SPRY	ECOD (1.6)
A	SPRY	e3f2oA1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: SPRY	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00622	SPRY domain (SPRY)	SPRY domain	SPRY Domain is named from SPla and the RYanodine Receptor and it is found in many eukaryotic proteins with a wide range of functions. It is a protein-interaction module involved in many important signalling pathways like RNA processing, regulation of ...	SPRY Domain is named from SPla and the RYanodine Receptor and it is found in many eukaryotic proteins with a wide range of functions. It is a protein-interaction module involved in many important signalling pathways like RNA processing, regulation of histone H3 methylation, innate immunity or embryonic development [1,2,3,4]. It can be divided into 11 subfamilies based on amino acid sequence similarity or the presence of additional protein domains. The greater SPRY family is divided into the SPRY/B30.2 (which contains a PRY extension at the N-terminal) and SPRY-only sub-families which are preceded by a subdomain that is structurally similar to the PRY region [2]. SPRY/B30.2 structures revealed a bent beta-sandwich fold comprised of two beta-sheets. Distant homologues are domains in butyrophilin/ marenostrin/pyrin [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	20-mer peptide from ATP-dependent RNA helicase vasa	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding RNA binding nucleic acid binding mRNA binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity	developmental process cellular developmental process cell differentiation cellular process sexual reproduction reproductive process multicellular organismal reproductive process gamete generation oogenesis cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction female gamete generation anatomical structure development developmental process cellular developmental process cell differentiation cellular process sexual reproduction reproductive process multicellular organismal reproductive process gamete generation oogenesis cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction female gamete generation anatomical structure development germ cell development localization macromolecule localization intracellular protein localization regulation of cellular process piRNA processing negative regulation of biological process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process negative regulation of cellular process RNA processing negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process secondary piRNA processing negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process regulatory ncRNA processing regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process	intracellular anatomical structure P granule cytoplasmic ribonucleoprotein granule germ plasm intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle pole plasm membraneless organelle cytoplasm supramolecular complex membrane-bounded organelle intracellular anatomical structure P granule cytoplasmic ribonucleoprotein granule germ plasm intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle pole plasm membraneless organelle cytoplasm supramolecular complex membrane-bounded organelle nucleus germ cell nucleus intracellular membrane-bounded organelle perinuclear region of cytoplasm cell periphery cell cortex posterior cell cortex cell cortex region cytoplasmic region
A, B	SPRY domain-containing SOCS box protein 1	ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process protein ubiquitination catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR044763	Ded1/Dbp1, DEAD-box helicase domain	Domain
C, D	IPR001650	Helicase, C-terminal domain-like	Domain
C, D	IPR000629	ATP-dependent RNA helicase DEAD-box, conserved site	Conserved Site
C, D	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
C, D	IPR014014	RNA helicase, DEAD-box type, Q motif	Domain
C, D	IPR011545	DEAD/DEAH-box helicase domain	Domain
C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, B	IPR001496	SOCS box domain	Domain
A, B	IPR050672	F-box/SPRY and SOCS box protein families	Family
A, B	IPR001870	B30.2/SPRY domain	Domain
A, B	IPR043136	B30.2/SPRY domain superfamily	Homologous Superfamily
A, B	IPR003877	SPRY domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q96BD6	allergic rhinitis glioblastoma malignant glioma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm tuberculosis atypical teratoid rhabdoid tumor large cell medulloblastoma malignant pancreatic neoplasm pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia gastric carcinoma malignant ependymoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma allergic rhinitis glioblastoma malignant glioma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm tuberculosis atypical teratoid rhabdoid tumor large cell medulloblastoma malignant pancreatic neoplasm pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia gastric carcinoma malignant ependymoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma

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.