6SMH

Cryo-electron microscopy structure of a RbcL-Raf1 supercomplex from Synechococcus elongatus PCC 7942

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	RuBisCO_large_N	e6smhA1	A: a+b two layers	X: Alpha-beta plaits	H: RuBisCO, large subunit, small (N-terminal) domain (From Topology)	T: RuBisCO, large subunit, small (N-terminal) domain	F: RuBisCO_large_N	ECOD (1.6)
A	RuBisCO_large	e6smhA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: RuBisCO_large	ECOD (1.6)
B	RuBisCO_large_N	e6smhB1	A: a+b two layers	X: Alpha-beta plaits	H: RuBisCO, large subunit, small (N-terminal) domain (From Topology)	T: RuBisCO, large subunit, small (N-terminal) domain	F: RuBisCO_large_N	ECOD (1.6)
B	RuBisCO_large	e6smhB2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: RuBisCO_large	ECOD (1.6)
C	RuBisCO_large_N	e6smhC1	A: a+b two layers	X: Alpha-beta plaits	H: RuBisCO, large subunit, small (N-terminal) domain (From Topology)	T: RuBisCO, large subunit, small (N-terminal) domain	F: RuBisCO_large_N	ECOD (1.6)
C	RuBisCO_large	e6smhC2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: RuBisCO_large	ECOD (1.6)
D	RuBisCO_large_N	e6smhD2	A: a+b two layers	X: Alpha-beta plaits	H: RuBisCO, large subunit, small (N-terminal) domain (From Topology)	T: RuBisCO, large subunit, small (N-terminal) domain	F: RuBisCO_large_N	ECOD (1.6)
D	RuBisCO_large	e6smhD1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: RuBisCO_large	ECOD (1.6)
E	RuBisCO_large_N	e6smhE2	A: a+b two layers	X: Alpha-beta plaits	H: RuBisCO, large subunit, small (N-terminal) domain (From Topology)	T: RuBisCO, large subunit, small (N-terminal) domain	F: RuBisCO_large_N	ECOD (1.6)
E	RuBisCO_large	e6smhE1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: RuBisCO_large	ECOD (1.6)
F	RuBisCO_large_N	e6smhF1	A: a+b two layers	X: Alpha-beta plaits	H: RuBisCO, large subunit, small (N-terminal) domain (From Topology)	T: RuBisCO, large subunit, small (N-terminal) domain	F: RuBisCO_large_N	ECOD (1.6)
F	RuBisCO_large	e6smhF2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: RuBisCO_large	ECOD (1.6)
G	RuBisCO_large_N	e6smhG1	A: a+b two layers	X: Alpha-beta plaits	H: RuBisCO, large subunit, small (N-terminal) domain (From Topology)	T: RuBisCO, large subunit, small (N-terminal) domain	F: RuBisCO_large_N	ECOD (1.6)
G	RuBisCO_large	e6smhG2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: RuBisCO_large	ECOD (1.6)
H	RuBisCO_large_N	e6smhH1	A: a+b two layers	X: Alpha-beta plaits	H: RuBisCO, large subunit, small (N-terminal) domain (From Topology)	T: RuBisCO, large subunit, small (N-terminal) domain	F: RuBisCO_large_N	ECOD (1.6)
H	RuBisCO_large	e6smhH2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: RuBisCO_large	ECOD (1.6)
I	EUF07884	e6smhI1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: EUF07884	ECOD (1.6)
I	EUF07977	e6smhI2	A: alpha arrays	X: KorB C-terminal domain-like	H: Helical domain of Rubisco accumulation factor 1 (From Topology)	T: Helical domain of Rubisco accumulation factor 1	F: EUF07977	ECOD (1.6)
J	EUF07884	e6smhJ2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: EUF07884	ECOD (1.6)
J	EUF07977	e6smhJ1	A: alpha arrays	X: KorB C-terminal domain-like	H: Helical domain of Rubisco accumulation factor 1 (From Topology)	T: Helical domain of Rubisco accumulation factor 1	F: EUF07977	ECOD (1.6)
K	EUF07884	e6smhK2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: EUF07884	ECOD (1.6)
K	EUF07977	e6smhK1	A: alpha arrays	X: KorB C-terminal domain-like	H: Helical domain of Rubisco accumulation factor 1 (From Topology)	T: Helical domain of Rubisco accumulation factor 1	F: EUF07977	ECOD (1.6)
L	EUF07884	e6smhL2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: EUF07884	ECOD (1.6)
L	EUF07977	e6smhL1	A: alpha arrays	X: KorB C-terminal domain-like	H: Helical domain of Rubisco accumulation factor 1 (From Topology)	T: Helical domain of Rubisco accumulation factor 1	F: EUF07977	ECOD (1.6)
M	EUF07884	e6smhM1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: EUF07884	ECOD (1.6)
M	EUF07977	e6smhM2	A: alpha arrays	X: KorB C-terminal domain-like	H: Helical domain of Rubisco accumulation factor 1 (From Topology)	T: Helical domain of Rubisco accumulation factor 1	F: EUF07977	ECOD (1.6)
N	EUF07884	e6smhN1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: EUF07884	ECOD (1.6)
N	EUF07977	e6smhN2	A: alpha arrays	X: KorB C-terminal domain-like	H: Helical domain of Rubisco accumulation factor 1 (From Topology)	T: Helical domain of Rubisco accumulation factor 1	F: EUF07977	ECOD (1.6)
O	EUF07884	e6smhO2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: EUF07884	ECOD (1.6)
O	EUF07977	e6smhO1	A: alpha arrays	X: KorB C-terminal domain-like	H: Helical domain of Rubisco accumulation factor 1 (From Topology)	T: Helical domain of Rubisco accumulation factor 1	F: EUF07977	ECOD (1.6)
P	EUF07884	e6smhP1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: EUF07884	ECOD (1.6)
P	EUF07977	e6smhP2	A: alpha arrays	X: KorB C-terminal domain-like	H: Helical domain of Rubisco accumulation factor 1 (From Topology)	T: Helical domain of Rubisco accumulation factor 1	F: EUF07977	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	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, B, C, D, E A, B, C, D, E, F, G, H	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
I, J, K, L, M I, J, K, L, M, N, O, P	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	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
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	cellular metabolic process metabolic process cellular process cellular metabolic compound salvage photorespiration carbohydrate metabolic process photosynthesis carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process biosynthetic process reductive pentose-phosphate cycle carbon fixation	intracellular organelle bacterial microcompartment intracellular anatomical structure organelle carboxysome intracellular non-membrane-bounded organelle cellular anatomical entity non-membrane-bounded organelle
I, J, K, L, M I, J, K, L, M, N, O, P	Rubisco accumulation factor 1 (RAF1) peptide	-	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 photosynthesis cellular metabolic process metabolic process carbon fixation	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
I, J, K, L, M I, J, K, L, M, N, O, P	IPR037494	Rubisco accumulation factor 1	Family
I, J, K, L, M I, J, K, L, M, N, O, P	IPR040858	Rubisco accumulation factor 1, C-terminal	Domain
I, J, K, L, M I, J, K, L, M, N, O, P	IPR041358	Rubisco accumulation factor 1, alpha helical domain	Domain
I, J, K, L, M I, J, K, L, M, N, O, P	IPR046382	Rubisco accumulation factor 1, cyanobacterial	Family
I, J, K, L, M I, J, K, L, M, N, O, P	IPR040781	Rubisco accumulation factor 1, helix turn helix domain	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.

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6SMH

Cryo-electron microscopy structure of a RbcL-Raf1 supercomplex from Synechococcus elongatus PCC 7942

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage