3AJI

Structure of Gankyrin-S6ATPase photo-cross-linked site-specifically, and incoporated by genetic code expansion

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)
A	d3ajia_	Alpha and beta proteins (a+b)	beta-hairpin-alpha-hairpin repeat	Ankyrin repeat	Ankyrin repeat	26S proteasome non-ATPase regulatory subunit 10, gankyrin	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d3ajic_	Alpha and beta proteins (a+b)	beta-hairpin-alpha-hairpin repeat	Ankyrin repeat	Ankyrin repeat	26S proteasome non-ATPase regulatory subunit 10, gankyrin	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ankyrin repeat	8067324	3000154	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ankyrin repeat	8067324	3000154	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)
A	PF12796	e3ajiA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Ankyrin repeat (From Topology)	T: Ankyrin repeat	F: PF12796	ECOD (1.6)
C	PF12796	e3ajiC1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Ankyrin repeat (From Topology)	T: Ankyrin repeat	F: PF12796	ECOD (1.6)
B	PF17862	e3ajiB1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17862	ECOD (1.6)
D	PF17862	e3ajiD1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17862	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.25.40.20	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Ankyrin repeat-containing domain	CATH (4.3.0)
C	1.25.40.20	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Ankyrin repeat-containing domain	CATH (4.3.0)
B	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
D	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF12796	Ankyrin repeats (3 copies) (Ank_2)	Ankyrin repeats (3 copies)	-	Repeat
B, D	PF17862	AAA+ lid domain (AAA_lid_3)	AAA+ lid domain	This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	26S proteasome non-ATPase regulatory subunit 10	transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding binding DNA-binding transcription factor binding cytoskeletal protein binding protein-macromolecule adaptor activity molecular adaptor activity transmembrane transporter binding	protein localization regulation of cellular process regulation of primary metabolic process nucleobase-containing compound metabolic process negative regulation of NF-kappaB transcription factor activity DNA-templated transcription localization regulation of RNA metabolic process cellular macromolecule localization organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of biological process cellular metabolic process primary metabolic process protein localization regulation of cellular process regulation of primary metabolic process nucleobase-containing compound metabolic process negative regulation of NF-kappaB transcription factor activity DNA-templated transcription localization regulation of RNA metabolic process cellular macromolecule localization organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of biological process cellular metabolic process primary metabolic process regulation of cellular metabolic process maintenance of location regulation of molecular function organic cyclic compound metabolic process regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process cytoplasmic sequestering of transcription factor maintenance of protein location cellular localization cellular biosynthetic process negative regulation of DNA-binding transcription factor activity RNA metabolic process RNA biosynthetic process cytoplasmic sequestering of NF-kappaB nucleic acid biosynthetic process organic substance metabolic process cytoplasmic sequestering of protein regulation of RNA biosynthetic process regulation of biosynthetic process negative regulation of molecular function biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process macromolecule localization cellular process regulation of growth regulation of cellular component organization positive regulation of biological process growth positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular component organization or biogenesis positive regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death cellular response to stimulus response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of cellular response to stress regulation of signal transduction DNA damage response, signal transduction by p53 class mediator intracellular signal transduction negative regulation of cell communication cell communication cellular response to stress regulation of intracellular signal transduction response to stress regulation of response to stress regulation of signal transduction by p53 class mediator negative regulation of DNA damage response, signal transduction by p53 class mediator signal transduction regulation of DNA damage response, signal transduction by p53 class mediator negative regulation of signal transduction by p53 class mediator regulation of signaling negative regulation of response to stimulus signal transduction by p53 class mediator negative regulation of signal transduction regulation of response to stimulus DNA damage response regulation of cell communication signal transduction in response to DNA damage regulation of protein modification process positive regulation of protein metabolic process regulation of protein ubiquitination positive regulation of post-translational protein modification positive regulation of metabolic process positive regulation of protein modification process protein ubiquitination positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination organonitrogen compound metabolic process regulation of post-translational protein modification regulation of protein metabolic process macromolecule modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal protein localization to cell periphery protein localization to plasma membrane localization within membrane protein localization to membrane positive regulation of proteasomal protein catabolic process catabolic process proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process positive regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process modification-dependent macromolecule catabolic process proteolysis organonitrogen compound catabolic process proteasomal protein catabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process positive regulation of proteolysis regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process organic substance catabolic process regulation of protein catabolic process positive regulation of phosphorylation regulation of catalytic activity regulation of cyclin-dependent protein kinase activity regulation of transferase activity positive regulation of phosphate metabolic process positive regulation of protein serine/threonine kinase activity positive regulation of cyclin-dependent protein serine/threonine kinase activity regulation of phosphate metabolic process regulation of cyclin-dependent protein serine/threonine kinase activity phosphate-containing compound metabolic process cell cycle phosphorus metabolic process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation positive regulation of kinase activity regulation of kinase activity regulation of protein serine/threonine kinase activity regulation of phosphorus metabolic process regulation of protein phosphorylation positive regulation of cyclin-dependent protein kinase activity positive regulation of cellular metabolic process positive regulation of molecular function positive regulation of protein kinase activity regulation of cell cycle positive regulation of transferase activity positive regulation of catalytic activity regulation of protein kinase activity positive regulation of cell cycle regulation of phosphorylation cellular component biogenesis proteasome assembly cellular component assembly protein-containing complex organization protein-containing complex assembly proteasome regulatory particle assembly intracellular signaling cassette regulation of MAPK cascade MAPK cascade negative regulation of MAPK cascade apoptotic mitochondrial changes regulation of release of cytochrome c from mitochondria negative regulation of release of cytochrome c from mitochondria negative regulation of apoptotic signaling pathway mitochondrion organization negative regulation of cellular component organization regulation of organelle organization apoptotic signaling pathway organelle organization release of cytochrome c from mitochondria negative regulation of organelle organization regulation of mitochondrion organization regulation of apoptotic signaling pathway transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of macromolecule metabolic process negative regulation of biosynthetic process	protein-containing complex intracellular anatomical structure catalytic complex peptidase complex proteasome regulatory particle cellular anatomical entity proteasome accessory complex proteasome regulatory particle, base subcomplex proteasome complex endopeptidase complex intracellular protein-containing complex cytoplasm cytosol cell periphery protein-containing complex intracellular anatomical structure catalytic complex peptidase complex proteasome regulatory particle cellular anatomical entity proteasome accessory complex proteasome regulatory particle, base subcomplex proteasome complex endopeptidase complex intracellular protein-containing complex cytoplasm cytosol cell periphery plasma membrane membrane cell projection neuron projection plasma membrane bounded cell projection intracellular organelle cytoskeleton organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle intermediate filament cytoskeleton membrane-bounded organelle nucleus intracellular membrane-bounded organelle
B, D	Proteasome (Prosome, macropain) 26S subunit, ATPase, 4	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule 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 proteasome-activating activity	developmental process multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development anatomical structure development embryo development in utero embryonic development blastocyst development organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process developmental process multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development anatomical structure development embryo development in utero embryonic development blastocyst development organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process	proteasome accessory complex protein-containing complex intracellular anatomical structure catalytic complex peptidase complex proteasome complex endopeptidase complex cellular anatomical entity intracellular protein-containing complex proteasome regulatory particle proteasome regulatory particle, base subcomplex synapse cell junction cytoplasm proteasome accessory complex protein-containing complex intracellular anatomical structure catalytic complex peptidase complex proteasome complex endopeptidase complex cellular anatomical entity intracellular protein-containing complex proteasome regulatory particle proteasome regulatory particle, base subcomplex synapse cell junction cytoplasm cytosol inclusion body membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cytosolic proteasome complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A, C	IPR002110	Ankyrin repeat	Repeat
B, D	IPR041569	AAA ATPase, AAA+ lid domain	Domain
B, D	IPR032501	Proteasomal ATPase, second OB domain	Domain
B, D	IPR003960	ATPase, AAA-type, conserved site	Conserved Site
B, D	IPR003593	AAA+ ATPase domain	Domain
B, D	IPR003959	ATPase, AAA-type, core	Domain
B, D	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
B, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	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 R01GM133198.