8IO2 | pdb_00008io2

The Rubisco assembly intermidate of Arabidopsis thaliana Rubisco accumulation factor 1 (AtRaf1) and Rubisco large subunit (RbcL)

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8035453	3001258	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RuBisCo, C-terminal domain	8043701	3000552	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RuBisCo, C-terminal domain	8043701	3000552	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8035453	3001258	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RuBisCo, C-terminal domain	8043701	3000552	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8035453	3001258	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8035453	3001258	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RuBisCo, C-terminal domain	8043701	3000552	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8035453	3001258	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RuBisCo, C-terminal domain	8043701	3000552	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RuBisCo, C-terminal domain	8043701	3000552	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8035453	3001258	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8035453	3001258	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	RuBisCo, C-terminal domain	8043701	3000552	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8035453	3001258	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	RuBisCo, C-terminal domain	8043701	3000552	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)
K	Cullin_AB	e8io2K1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
L	Cullin_AB	e8io2L1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
M	Cullin_AB	e8io2M1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
N	Cullin_AB	e8io2N1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
P	Cullin_AB	e8io2P1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
Q	Cullin_AB	e8io2Q1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
O	Cullin_AB	e8io2O1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
J	Cullin_AB	e8io2J1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
I	Cullin_AB	e8io2I1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
A	Cullin_AB	e8io2A1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
B	Cullin_AB	e8io2B1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
C	Cullin_AB	e8io2C1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
D	Cullin_AB	e8io2D1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
E	Cullin_AB	e8io2E1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
F	Cullin_AB	e8io2F1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
H	Cullin_AB	e8io2H1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
G	Cullin_AB	e8io2G1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I, J, K, L, M I, J, K, L, M, N, O, P, Q	PF18087	Rubisco Assembly chaperone C-terminal domain (RuBisCo_chap_C)	Rubisco Assembly chaperone C-terminal domain	This is the C-terminal domain, also known as the beta domain, of Rubsico Assembly Chaperone protein (Raf1). Raf1 is necessary for rubisco to catalyze the rate-limiting step of carbon fixation through carboxylating the five-carbon sugar substrate rib ...	This is the C-terminal domain, also known as the beta domain, of Rubsico Assembly Chaperone protein (Raf1). Raf1 is necessary for rubisco to catalyze the rate-limiting step of carbon fixation through carboxylating the five-carbon sugar substrate ribulose-1,5-bisphosphate. The beta domains primary function is dimerization, which is critical for Raf1 to achieve the necessary avidity for complex formation with RbcL (the large complex sub-unbit of Rubsico) assembly intermediates. The beta domain is also involved, to a small extent, in binding to RbcL with use of the lustiness near the beta domain's conserved top surface [1].	Domain
I, J, K, L, M I, J, K, L, M, N, O, P, Q	PF18579	Rubisco accumulation factor 1 helix turn helix domain (Raf1_HTH)	Rubisco accumulation factor 1 helix turn helix domain	This is helix turn helix domain found in alpha helical region of Rubisco accumulation factor1 (Raf1). Raf1 from Arabidopsis thaliana consists of an N-terminal alpha-domain, a flexible linker segment and a C-terminal beta-sheet domain that mediates di ...	This is helix turn helix domain found in alpha helical region of Rubisco accumulation factor1 (Raf1). Raf1 from Arabidopsis thaliana consists of an N-terminal alpha-domain, a flexible linker segment and a C-terminal beta-sheet domain that mediates dimerization. The alpha-domains mediate the majority of functionally important contacts with RbcL (Rubisco large subunits) by bracketing each RbcL dimer at the top and bottom. The alpha-domain alone is essentially inactive [1].	Domain
I, J, K, L, M I, J, K, L, M, N, O, P, Q	PF18578	Rubisco accumulation factor 1 alpha helical domain (Raf1_N)	Rubisco accumulation factor 1 alpha helical domain	This is the N-terminal alpha helical domain found in Rubisco accumulation factor1 (Raf1). Raf1 from Arabidopsis thaliana consists of an N-terminal alpha-domain, a flexible linker segment and a C-terminal beta-sheet domain that mediates dimerization. ...	This is the N-terminal alpha helical domain found in Rubisco accumulation factor1 (Raf1). Raf1 from Arabidopsis thaliana consists of an N-terminal alpha-domain, a flexible linker segment and a C-terminal beta-sheet domain that mediates dimerization. The alpha-domains mediate the majority of functionally important contacts with RbcL (Rubisco large subunits) by bracketing each RbcL dimer at the top and bottom. The alpha-domain alone is essentially inactive [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I, J, K, L, M I, J, K, L, M, N, O, P, Q	Rubisco accumulation factor 1.2, chloroplastic	-	cellular component organization cellular component biogenesis cellular component assembly ribulose bisphosphate carboxylase complex assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle plastid organelle intracellular membrane-bounded organelle chloroplast plastid stroma chloroplast stroma
A, B, C, D, E A, B, C, D, E, F, G, H	Ribulose bisphosphate carboxylase large chain	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	intracellular organelle bacterial microcompartment cellular anatomical structure intracellular anatomical structure organelle carboxysome membraneless organelle intracellular membraneless organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I, J, K, L, M I, J, K, L, M, N, O, P, Q	IPR037494	Rubisco accumulation factor 1	Family
I, J, K, L, M I, J, K, L, M, N, O, P, Q	IPR040858	Rubisco accumulation factor 1, C-terminal	Domain
I, J, K, L, M I, J, K, L, M, N, O, P, Q	IPR041358	Rubisco accumulation factor 1, alpha-helical domain	Domain
I, J, K, L, M I, J, K, L, M, N, O, P, Q	IPR040781	Rubisco accumulation factor 1, helix turn helix domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR020888	Ribulose bisphosphate carboxylase large subunit, type I	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036376	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR020878	Ribulose bisphosphate carboxylase, large chain, active site	Active Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000685	Ribulose bisphosphate carboxylase, large subunit, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR033966	RuBisCO	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR017443	Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	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.