4LCT | pdb_00004lct

Crystal Structure and Versatile Functional Roles of the COP9 Signalosome Subunit 1

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)
D	d4lctd2	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	C-terminal part of PCI (proteasome COP9/signalosome eIF3) domains (PINT motif)	COP9 signalosome complex subunit 1 (CSN1), C-terminal domain	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
D	d4lctd1	All alpha proteins	alpha-alpha superhelix	TPR-like	TPR-like repeats from PCI (proteasome / COP9 signalosome / eIF3) domains	COP9 signalosome complex subunit 1 (CSN1), N-terminal domain	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d4lctc2	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	C-terminal part of PCI (proteasome COP9/signalosome eIF3) domains (PINT motif)	COP9 signalosome complex subunit 1 (CSN1), C-terminal domain	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d4lctc1	All alpha proteins	alpha-alpha superhelix	TPR-like	TPR-like repeats from PCI (proteasome / COP9 signalosome / eIF3) domains	COP9 signalosome complex subunit 1 (CSN1), N-terminal domain	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d4lctb2	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	C-terminal part of PCI (proteasome COP9/signalosome eIF3) domains (PINT motif)	COP9 signalosome complex subunit 1 (CSN1), C-terminal domain	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d4lctb1	All alpha proteins	alpha-alpha superhelix	TPR-like	TPR-like repeats from PCI (proteasome / COP9 signalosome / eIF3) domains	COP9 signalosome complex subunit 1 (CSN1), N-terminal domain	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d4lcta2	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	C-terminal part of PCI (proteasome COP9/signalosome eIF3) domains (PINT motif)	COP9 signalosome complex subunit 1 (CSN1), C-terminal domain	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d4lcta1	All alpha proteins	alpha-alpha superhelix	TPR-like	TPR-like repeats from PCI (proteasome / COP9 signalosome / eIF3) domains	COP9 signalosome complex subunit 1 (CSN1), N-terminal domain	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	TPR-like	8057041	3001345	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	TPR-like	8057040	3001345	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TPR-like	8057041	3001345	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TPR-like	8057040	3001345	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TPR-like	8057040	3001345	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TPR-like	8057041	3001345	SCOP2B (2022-06-29)
A	SCOP2 Family	RPN7-like	8045189	4004342	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	TPR-like	8057041	3001345	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	TPR-like	8057040	3001345	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)
D	BSH_CusB	e4lctD1	A: a/b three-layered sandwiches	X: C-terminal domain in some PLP-dependent transferases	H: C-terminal domain in some PLP-dependent transferases	T: C-terminal domain in some PLP-dependent transferases	F: BSH_CusB	ECOD (v294.1)
C	LRR_adjacent	e4lctC1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: LRR_adjacent	ECOD (v294.1)
B	CBS	e4lctB1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: CBS	ECOD (v294.1)
A	CBS	e4lctA2	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: CBS	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.25.40.570	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
C	1.25.40.570	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
B	1.25.40.570	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
A	1.25.40.570	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF10602	26S proteasome subunit RPN7 (RPN7)	26S proteasome subunit RPN7	-	Repeat
A, B, C, D	PF01399	PCI domain (PCI)	PCI domain	This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	COP9 signalosome complex subunit 1	-	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis developmental process multicellular organismal process reproductive system development reproductive process embryo development developmental process involved in reproduction multicellular organism development cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis developmental process multicellular organismal process reproductive system development reproductive process embryo development developmental process involved in reproduction multicellular organism development fruit development embryo development ending in seed dormancy seed development anatomical structure development reproductive structure development post-embryonic development system development cellular response to stimulus response to light stimulus cellular response to red or far red light regulation of cellular process response to stimulus signaling response to red or far red light detection of abiotic stimulus cell communication cellular response to environmental stimulus cellular response to light stimulus signal transduction phototransduction detection of light stimulus detection of external stimulus regulation of biological process red or far-red light signaling pathway biological regulation response to external stimulus cellular response to radiation detection of stimulus red, far-red light phototransduction response to radiation response to abiotic stimulus cellular response to abiotic stimulus photomorphogenesis primary metabolic process protein deneddylation protein modification by small protein removal macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal response to light intensity response to absence of light response to osmotic stress response to stress response to salt stress hyperosmotic response	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex COP9 signalosome intracellular membrane-bounded organelle cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR048624	COP9 signalosome complex subunit 1, C-terminal helix	Domain
A, B, C, D	IPR019585	26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1	Family
A, B, C, D	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR000717	Proteasome component (PCI) domain	Domain
A, B, C, D	IPR045135	26S proteasome regulatory subunit Rpn7, N-terminal	Domain

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.