4RUB | pdb_00004rub

A CRYSTAL FORM OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE FROM NICOTIANA TABACUM IN THE ACTIVATED STATE

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)
H [auth V]	d4rubv_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	RuBisCO, small subunit	Ribulose 1,5-bisphosphate carboxylase-oxygenase	common tobacco (Nicotiana tabacum ) [TaxId: 4097 ],	SCOPe (2.08)
F [auth U]	d4rubu_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	RuBisCO, small subunit	Ribulose 1,5-bisphosphate carboxylase-oxygenase	common tobacco (Nicotiana tabacum ) [TaxId: 4097 ],	SCOPe (2.08)
D [auth T]	d4rubt_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	RuBisCO, small subunit	Ribulose 1,5-bisphosphate carboxylase-oxygenase	common tobacco (Nicotiana tabacum ) [TaxId: 4097 ],	SCOPe (2.08)
B [auth S]	d4rubs_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	RuBisCO, small subunit	Ribulose 1,5-bisphosphate carboxylase-oxygenase	common tobacco (Nicotiana tabacum ) [TaxId: 4097 ],	SCOPe (2.08)
G [auth D]	d4rubd1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	Ribulose 1,5-bisphosphate carboxylase-oxygenase	common tobacco (Nicotiana tabacum ) [TaxId: 4097 ],	SCOPe (2.08)
G [auth D]	d4rubd2	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	Ribulose 1,5-bisphosphate carboxylase-oxygenase	Ribulose 1,5-bisphosphate carboxylase-oxygenase	common tobacco (Nicotiana tabacum ) [TaxId: 4097 ],	SCOPe (2.08)
E [auth C]	d4rubc1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	Ribulose 1,5-bisphosphate carboxylase-oxygenase	common tobacco (Nicotiana tabacum ) [TaxId: 4097 ],	SCOPe (2.08)
E [auth C]	d4rubc2	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	Ribulose 1,5-bisphosphate carboxylase-oxygenase	Ribulose 1,5-bisphosphate carboxylase-oxygenase	common tobacco (Nicotiana tabacum ) [TaxId: 4097 ],	SCOPe (2.08)
C [auth B]	d4rubb1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	Ribulose 1,5-bisphosphate carboxylase-oxygenase	common tobacco (Nicotiana tabacum ) [TaxId: 4097 ],	SCOPe (2.08)
C [auth B]	d4rubb2	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	Ribulose 1,5-bisphosphate carboxylase-oxygenase	Ribulose 1,5-bisphosphate carboxylase-oxygenase	common tobacco (Nicotiana tabacum ) [TaxId: 4097 ],	SCOPe (2.08)
A	d4ruba1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	Ribulose 1,5-bisphosphate carboxylase-oxygenase	common tobacco (Nicotiana tabacum ) [TaxId: 4097 ],	SCOPe (2.08)
A	d4ruba2	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	Ribulose 1,5-bisphosphate carboxylase-oxygenase	Ribulose 1,5-bisphosphate carboxylase-oxygenase	common tobacco (Nicotiana tabacum ) [TaxId: 4097 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H [auth V]	SCOP2B Superfamily	RuBisCO, small subunit	8035797	3001622	SCOP2B (2022-06-29)
F [auth U]	SCOP2B Superfamily	RuBisCO, small subunit	8035797	3001622	SCOP2B (2022-06-29)
D [auth T]	SCOP2B Superfamily	RuBisCO, small subunit	8035797	3001622	SCOP2B (2022-06-29)
B [auth S]	SCOP2B Superfamily	RuBisCO, small subunit	8035797	3001622	SCOP2B (2022-06-29)
G [auth D]	SCOP2B Superfamily	RuBisCo, C-terminal domain	8043670	3000552	SCOP2B (2022-06-29)
G [auth D]	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8035389	3001258	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	RuBisCo, C-terminal domain	8043670	3000552	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8035389	3001258	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	RuBisCo, C-terminal domain	8043670	3000552	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8035389	3001258	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RuBisCo, C-terminal domain	8043670	3000552	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8035389	3001258	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)
H [auth V]	OKR_DC_1_C	e4rubV1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: OKR_DC_1_C	ECOD (v294.1)
F [auth U]	OKR_DC_1_C	e4rubU1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: OKR_DC_1_C	ECOD (v294.1)
D [auth T]	OKR_DC_1_C	e4rubT1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: OKR_DC_1_C	ECOD (v294.1)
B [auth S]	OKR_DC_1_C	e4rubS1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: OKR_DC_1_C	ECOD (v294.1)
G [auth D]	RNase_P_Rpp14	e4rubD1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (v294.1)
G [auth D]	DUF711	e4rubD2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (v294.1)
E [auth C]	RNase_P_Rpp14	e4rubC1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (v294.1)
E [auth C]	DUF711	e4rubC2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (v294.1)
C [auth B]	RNase_P_Rpp14	e4rubB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (v294.1)
C [auth B]	DUF711	e4rubB2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (v294.1)
A	RNase_P_Rpp14	e4rubA1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (v294.1)
A	DUF711	e4rubA2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H [auth V]	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
F [auth U]	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
D [auth T]	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
B [auth S]	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
G [auth D]	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
G [auth D]	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
E [auth C]	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
E [auth C]	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
C [auth B]	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
C [auth B]	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
A	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
A	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth S], D [auth T], F [auth U], H [auth V]	PF00101	Ribulose bisphosphate carboxylase, small chain (RuBisCO_small)	Ribulose bisphosphate carboxylase, small chain		Domain
A, C [auth B], E [auth C], G [auth D]	PF02788	Ribulose bisphosphate carboxylase large chain, N-terminal domain (RuBisCO_large_N)	Ribulose bisphosphate carboxylase large chain, N-terminal domain	The N-terminal domain of RuBisCO large chain adopts a ferredoxin-like fold.	Domain
A, C [auth B], E [auth C], G [auth D]	PF00016	Ribulose bisphosphate carboxylase large chain, catalytic domain (RuBisCO_large)	Ribulose bisphosphate carboxylase large chain, catalytic domain	The C-terminal domain of RuBisCO large chain is the catalytic domain adopting a TIM barrel fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth S], D [auth T], F [auth U], H [auth V]	RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)	ribulose-bisphosphate carboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	metabolic compound salvage biosynthetic process metabolic process cellular process photorespiration biological process involved in interspecies interaction between organisms defense response to virus response to stimulus defense response response to other organism response to stress response to external stimulus response to external biotic stimulus response to virus metabolic compound salvage biosynthetic process metabolic process cellular process photorespiration biological process involved in interspecies interaction between organisms defense response to virus response to stimulus defense response response to other organism response to stress response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus carbohydrate metabolic process photosynthesis reductive pentose-phosphate cycle carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process carbon fixation	cell-cell junction cellular anatomical structure symplast anchoring junction cell junction plasmodesma membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle chloroplast
A, C [auth B], E [auth C], G [auth D]	RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding ribulose-bisphosphate carboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity monooxygenase activity oxidoreductase activity	metabolic compound salvage biosynthetic process metabolic process cellular process photorespiration carbohydrate metabolic process photosynthesis reductive pentose-phosphate cycle carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process carbon fixation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth S], D [auth T], F [auth U], H [auth V]	IPR024680	Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal	Domain
B [auth S], D [auth T], F [auth U], H [auth V]	IPR036385	Ribulose bisphosphate carboxylase, small subunit superfamily	Homologous Superfamily
B [auth S], D [auth T], F [auth U], H [auth V]	IPR024681	Ribulose bisphosphate carboxylase, small subunit	Family
B [auth S], D [auth T], F [auth U], H [auth V]	IPR000894	Ribulose bisphosphate carboxylase small subunit, domain	Domain
A, C [auth B], E [auth C], G [auth D]	IPR020888	Ribulose bisphosphate carboxylase large subunit, type I	Family
A, C [auth B], E [auth C], G [auth D]	IPR036376	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D]	IPR020878	Ribulose bisphosphate carboxylase, large chain, active site	Active Site
A, C [auth B], E [auth C], G [auth D]	IPR000685	Ribulose bisphosphate carboxylase, large subunit, C-terminal	Domain
A, C [auth B], E [auth C], G [auth D]	IPR033966	RuBisCO	Family
A, C [auth B], E [auth C], G [auth D]	IPR017443	Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal	Domain
A, C [auth B], E [auth C], G [auth D]	IPR036422	RuBisCO large subunit, 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.