2FNJ | pdb_00002fnj

Crystal structure of a B30.2/SPRY domain-containing protein GUSTAVUS in complex with Elongin B and Elongin C

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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)
C	d2fnjc_	Alpha and beta proteins (a+b)	POZ domain	POZ domain	BTB/POZ domain	Elongin C	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d2fnjb1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Elongin B	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d2fnja1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	SPRY domain	LD34464p	fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	POZ domain	8034753	3000894	SCOP2B (2022-06-29)
B	SCOP2 Family	Ubiquitin-related	8028798	4000962	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Ubiquitin-like	8041177	3000157	SCOP2 (2022-06-29)
A	SCOP2 Family	PRY/SPRY domain	8028795	4001665	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Concanavalin A-like lectins/glucanases	8041174	3000120	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	Skp1_POZ_1	e2fnjC1	A: a+b two layers	X: POZ domain (From Topology)	H: POZ domain (From Topology)	T: POZ domain	F: Skp1_POZ_1	ECOD (1.6)
B	ubiquitin_2	e2fnjB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_2	ECOD (1.6)
A	SPRY	e2fnjA1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: SPRY	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.30.710.10	Alpha Beta	2-Layer Sandwich	Potassium Channel Kv1.1	Chain A	CATH (4.3.0)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF03931	Skp1 family, tetramerisation domain (Skp1_POZ)	Skp1 family, tetramerisation domain		Domain
B	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain
A	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
A	PF07525	SOCS box (SOCS_box)	SOCS box	The SOCS box acts as a bridge between specific substrate- binding domains and more generic proteins that comprise a large family of E3 ubiquitin protein ligases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	Transcription elongation factor B polypeptide 1	transcription factor binding transcription coregulator binding transcription corepressor binding protein binding binding protein-containing complex binding	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 regulation of cellular process 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 regulation of cellular process negative regulation of biological process positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of macromolecule metabolic process miRNA metabolic process RNA catabolic process regulation of biological process negative regulation of metabolic process nucleobase-containing compound catabolic process miRNA-mediated post-transcriptional gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of miRNA-mediated gene silencing negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing nucleic acid catabolic process regulation of macromolecule biosynthetic process negative regulation of post-transcriptional gene silencing regulation of metabolic process positive regulation of biological process RNA metabolic process regulation of miRNA-mediated gene silencing negative regulation of post-transcriptional gene silencing by regulatory ncRNA regulation of gene silencing by regulatory ncRNA positive regulation of biosynthetic process negative regulation of cellular process regulation of post-transcriptional gene silencing by regulatory ncRNA positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of gene silencing by regulatory ncRNA biological regulation regulation of macromolecule metabolic process miRNA catabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated post-transcriptional gene silencing nucleic acid metabolic process target-directed miRNA degradation regulatory ncRNA-mediated gene silencing regulation of post-transcriptional gene silencing negative regulation of biosynthetic process positive regulation of gene expression nucleobase-containing compound biosynthetic process DNA-templated transcription initiation RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II transcription initiation at RNA polymerase II promoter transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II regulation of primary metabolic process regulation of RNA metabolic process positive regulation of DNA-templated transcription, elongation regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process DNA-templated transcription elongation positive regulation of RNA biosynthetic process regulation of DNA-templated transcription 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	membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle elongin complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle elongin complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen cytoplasm cytosol cytoplasmic ubiquitin ligase complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex VCB complex cullin-RING ubiquitin ligase complex Cul5-RING ubiquitin ligase complex
B	Transcription elongation factor B polypeptide 2	transcription factor binding transcription coregulator binding transcription corepressor binding protein binding binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding	regulation of cellular process negative regulation of biological process positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of macromolecule metabolic process miRNA metabolic process RNA catabolic process regulation of biological process negative regulation of metabolic process primary metabolic process nucleobase-containing compound catabolic process miRNA-mediated post-transcriptional gene silencing regulation of cellular process negative regulation of biological process positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of macromolecule metabolic process miRNA metabolic process RNA catabolic process regulation of biological process negative regulation of metabolic process primary metabolic process nucleobase-containing compound catabolic process miRNA-mediated post-transcriptional gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of miRNA-mediated gene silencing negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process negative regulation of post-transcriptional gene silencing regulation of metabolic process catabolic process positive regulation of biological process RNA metabolic process regulation of miRNA-mediated gene silencing macromolecule catabolic process negative regulation of post-transcriptional gene silencing by regulatory ncRNA regulation of gene silencing by regulatory ncRNA positive regulation of biosynthetic process negative regulation of cellular process regulation of post-transcriptional gene silencing by regulatory ncRNA positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of gene silencing by regulatory ncRNA biological regulation regulation of macromolecule metabolic process miRNA catabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated post-transcriptional gene silencing nucleic acid metabolic process target-directed miRNA degradation regulatory ncRNA-mediated gene silencing regulation of post-transcriptional gene silencing negative regulation of biosynthetic process positive regulation of gene expression cellular process nucleobase-containing compound biosynthetic process DNA-templated transcription initiation RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II transcription initiation at RNA polymerase II promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal	membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle elongin complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle elongin complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen cytoplasm cytosol cytoplasmic ubiquitin ligase complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex VCB complex cullin-RING ubiquitin ligase complex Cul5-RING ubiquitin ligase complex Cul2-RING ubiquitin ligase complex
A	CG2944-PF, isoform F	-	localization macromolecule localization intracellular protein localization sexual reproduction reproductive process multicellular organismal reproductive process germ cell migration cell migration cellular process cell motility gamete generation developmental process multicellular organismal process imaginal disc morphogenesis localization macromolecule localization intracellular protein localization sexual reproduction reproductive process multicellular organismal reproductive process germ cell migration cell migration cellular process cell motility gamete generation developmental process multicellular organismal process imaginal disc morphogenesis animal organ development wing disc development instar larval or pupal development metamorphosis multicellular organism development anatomical structure morphogenesis wing disc morphogenesis imaginal disc development instar larval or pupal morphogenesis anatomical structure development post-embryonic animal morphogenesis post-embryonic development animal organ morphogenesis cellular developmental process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction cell differentiation germ cell development blastoderm segmentation anterior/posterior pattern specification anterior/posterior axis specification, embryo segmentation pattern specification process female gamete generation embryo development oocyte development tripartite regional subdivision cellular component biogenesis cellular component organization embryonic axis specification cellular component assembly anterior/posterior axis specification cellular component organization or biogenesis cell maturation embryonic pattern specification oocyte axis specification oocyte construction oogenesis oocyte anterior/posterior axis specification cytoplasm organization developmental maturation regionalization pole plasm assembly anatomical structure maturation maternal determination of anterior/posterior axis, embryo oocyte differentiation axis specification regulation of cellular process catabolic process positive regulation of protein metabolic process positive regulation of biological process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biological process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process cuticle pattern formation cuticle development cellular component assembly involved in morphogenesis egg chorion assembly cellular anatomical entity morphogenesis anatomical structure formation involved in morphogenesis dorsal appendage formation external encapsulating structure organization cellular response to stimulus response to stimulus signaling signal transduction intracellular signal transduction cell communication	cell periphery cell cortex cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle protein-containing complex transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle elongin complex intracellular organelle lumen cell periphery cell cortex cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle protein-containing complex transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle elongin complex intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cullin-RING ubiquitin ligase complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex Cul5-RING ubiquitin ligase complex SCF ubiquitin ligase complex perinuclear region of cytoplasm pole plasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR016073	SKP1 component, POZ domain	Domain
C	IPR001232	S-phase kinase-associated protein 1-like	Family
C	IPR039948	Elongin-C	Family
C	IPR011333	SKP1/BTB/POZ domain superfamily	Homologous Superfamily
B	IPR000626	Ubiquitin-like domain	Domain
B	IPR039049	Elongin B	Family
B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A	IPR043136	B30.2/SPRY domain superfamily	Homologous Superfamily
A	IPR003877	SPRY domain	Domain
A	IPR001870	B30.2/SPRY domain	Domain
A	IPR036036	SOCS box-like domain superfamily	Homologous Superfamily
A	IPR001496	SOCS box domain	Domain
A	IPR050672	F-box/SPRY and SOCS box protein families	Family

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.