7XSD | pdb_00007xsd

Cryo-EM structure of RuBisCO assembly intermediate RbcL8Raf18RbcX16

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)
X [auth B]	RuBisCO_large_N	e7xsdB1	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)
X [auth B]	RuBisCO_large	e7xsdB2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: RuBisCO_large	ECOD (1.6)
W [auth A]	RuBisCO_large_N	e7xsdA1	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)
W [auth A]	RuBisCO_large	e7xsdA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: RuBisCO_large	ECOD (1.6)
P [auth F]	RuBisCO_large_N	e7xsdF2	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)
P [auth F]	RuBisCO_large	e7xsdF1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: RuBisCO_large	ECOD (1.6)
O [auth E]	RuBisCO_large_N	e7xsdE1	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)
O [auth E]	RuBisCO_large	e7xsdE2	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	e7xsdH2	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	e7xsdH1	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	e7xsdG1	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	e7xsdG2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: RuBisCO_large	ECOD (1.6)
FA [auth D]	RuBisCO_large_N	e7xsdD1	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)
FA [auth D]	RuBisCO_large	e7xsdD2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: RuBisCO_large	ECOD (1.6)
EA [auth C]	RuBisCO_large_N	e7xsdC2	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)
EA [auth C]	RuBisCO_large	e7xsdC1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: RuBisCO_large	ECOD (1.6)
Z [auth L]	EUF07884	e7xsdL2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: EUF07884	ECOD (1.6)
Z [auth L]	EUF07977	e7xsdL1	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)
Y [auth K]	EUF07884	e7xsdK1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: EUF07884	ECOD (1.6)
Y [auth K]	EUF07977	e7xsdK2	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)
R [auth J]	EUF07884	e7xsdJ1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: EUF07884	ECOD (1.6)
R [auth J]	EUF07977	e7xsdJ2	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)
Q [auth I]	EUF07884	e7xsdI1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: EUF07884	ECOD (1.6)
Q [auth I]	EUF07977	e7xsdI2	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	e7xsdN2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: EUF07884	ECOD (1.6)
N	EUF07977	e7xsdN1	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	e7xsdM1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: EUF07884	ECOD (1.6)
M	EUF07977	e7xsdM2	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)
F [auth P]	EUF07884	e7xsdP2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: EUF07884	ECOD (1.6)
F [auth P]	EUF07977	e7xsdP1	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)
E [auth O]	EUF07884	e7xsdO2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: EUF07884	ECOD (1.6)
E [auth O]	EUF07977	e7xsdO1	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)
V [auth T]	RcbX	e7xsdT1	A: alpha arrays	X: RbcX-like	H: RbcX-like (From Topology)	T: RbcX-like	F: RcbX	ECOD (1.6)
U [auth S]	RcbX	e7xsdS1	A: alpha arrays	X: RbcX-like	H: RbcX-like (From Topology)	T: RbcX-like	F: RcbX	ECOD (1.6)
T [auth R]	RcbX	e7xsdR1	A: alpha arrays	X: RbcX-like	H: RbcX-like (From Topology)	T: RbcX-like	F: RcbX	ECOD (1.6)
S [auth Q]	RcbX	e7xsdQ1	A: alpha arrays	X: RbcX-like	H: RbcX-like (From Topology)	T: RbcX-like	F: RcbX	ECOD (1.6)
L [auth 4]	RcbX	e7xsd41	A: alpha arrays	X: RbcX-like	H: RbcX-like (From Topology)	T: RbcX-like	F: RcbX	ECOD (1.6)
K [auth 3]	RcbX	e7xsd31	A: alpha arrays	X: RbcX-like	H: RbcX-like (From Topology)	T: RbcX-like	F: RcbX	ECOD (1.6)
J [auth 2]	RcbX	e7xsd21	A: alpha arrays	X: RbcX-like	H: RbcX-like (From Topology)	T: RbcX-like	F: RcbX	ECOD (1.6)
I [auth 1]	RcbX	e7xsd11	A: alpha arrays	X: RbcX-like	H: RbcX-like (From Topology)	T: RbcX-like	F: RcbX	ECOD (1.6)
DA [auth X]	RcbX	e7xsdX1	A: alpha arrays	X: RbcX-like	H: RbcX-like (From Topology)	T: RbcX-like	F: RcbX	ECOD (1.6)
D [auth 8]	RcbX	e7xsd81	A: alpha arrays	X: RbcX-like	H: RbcX-like (From Topology)	T: RbcX-like	F: RcbX	ECOD (1.6)
CA [auth W]	RcbX	e7xsdW1	A: alpha arrays	X: RbcX-like	H: RbcX-like (From Topology)	T: RbcX-like	F: RcbX	ECOD (1.6)
C [auth 7]	RcbX	e7xsd71	A: alpha arrays	X: RbcX-like	H: RbcX-like (From Topology)	T: RbcX-like	F: RcbX	ECOD (1.6)
BA [auth V]	RcbX	e7xsdV1	A: alpha arrays	X: RbcX-like	H: RbcX-like (From Topology)	T: RbcX-like	F: RcbX	ECOD (1.6)
B [auth 6]	RcbX	e7xsd61	A: alpha arrays	X: RbcX-like	H: RbcX-like (From Topology)	T: RbcX-like	F: RcbX	ECOD (1.6)
AA [auth U]	RcbX	e7xsdU1	A: alpha arrays	X: RbcX-like	H: RbcX-like (From Topology)	T: RbcX-like	F: RcbX	ECOD (1.6)
A [auth 5]	RcbX	e7xsd51	A: alpha arrays	X: RbcX-like	H: RbcX-like (From Topology)	T: RbcX-like	F: RcbX	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
EA [auth C], FA [auth D], G, H, O [auth E], EA [auth C], FA [auth D], G, H, O [auth E], P [auth F], W [auth A], X [auth B]	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
EA [auth C], FA [auth D], G, H, O [auth E], EA [auth C], FA [auth D], G, H, O [auth E], P [auth F], W [auth A], X [auth B]	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
E [auth O], F [auth P], M, N, Q [auth I], E [auth O], F [auth P], M, N, Q [auth I], R [auth J], Y [auth K], Z [auth L]	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
E [auth O], F [auth P], M, N, Q [auth I], E [auth O], F [auth P], M, N, Q [auth I], R [auth J], Y [auth K], Z [auth L]	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
EA [auth C], FA [auth D], G, H, O [auth E], EA [auth C], FA [auth D], G, H, O [auth E], P [auth F], W [auth A], X [auth B]	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
E [auth O], F [auth P], M, N, Q [auth I], E [auth O], F [auth P], M, N, Q [auth I], R [auth J], Y [auth K], Z [auth L]	RuBisCO accumulation factor 1	-	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 metabolic process carbon fixation	cellular anatomical structure intracellular anatomical structure cytoplasm
A [auth 5], AA [auth U], B [auth 6], BA [auth V], C [auth 7], A [auth 5], AA [auth U], B [auth 6], BA [auth V], C [auth 7], CA [auth W], D [auth 8], DA [auth X], I [auth 1], J [auth 2], K [auth 3], L [auth 4], S [auth Q], T [auth R], U [auth S], V [auth T]	RuBisCO chaperone RbcX	protein folding chaperone	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 metabolic process carbon fixation	intracellular organelle bacterial microcompartment cellular anatomical structure intracellular anatomical structure organelle carboxysome membraneless organelle intracellular membraneless organelle cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
EA [auth C], FA [auth D], G, H, O [auth E], EA [auth C], FA [auth D], G, H, O [auth E], P [auth F], W [auth A], X [auth B]	IPR020888	Ribulose bisphosphate carboxylase large subunit, type I	Family
EA [auth C], FA [auth D], G, H, O [auth E], EA [auth C], FA [auth D], G, H, O [auth E], P [auth F], W [auth A], X [auth B]	IPR036376	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily	Homologous Superfamily
EA [auth C], FA [auth D], G, H, O [auth E], EA [auth C], FA [auth D], G, H, O [auth E], P [auth F], W [auth A], X [auth B]	IPR020878	Ribulose bisphosphate carboxylase, large chain, active site	Active Site
EA [auth C], FA [auth D], G, H, O [auth E], EA [auth C], FA [auth D], G, H, O [auth E], P [auth F], W [auth A], X [auth B]	IPR000685	Ribulose bisphosphate carboxylase, large subunit, C-terminal	Domain
EA [auth C], FA [auth D], G, H, O [auth E], EA [auth C], FA [auth D], G, H, O [auth E], P [auth F], W [auth A], X [auth B]	IPR033966	RuBisCO	Family
EA [auth C], FA [auth D], G, H, O [auth E], EA [auth C], FA [auth D], G, H, O [auth E], P [auth F], W [auth A], X [auth B]	IPR017443	Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal	Domain
EA [auth C], FA [auth D], G, H, O [auth E], EA [auth C], FA [auth D], G, H, O [auth E], P [auth F], W [auth A], X [auth B]	IPR036422	RuBisCO large subunit, N-terminal domain superfamily	Homologous Superfamily
E [auth O], F [auth P], M, N, Q [auth I], E [auth O], F [auth P], M, N, Q [auth I], R [auth J], Y [auth K], Z [auth L]	IPR037494	Rubisco accumulation factor 1	Family
E [auth O], F [auth P], M, N, Q [auth I], E [auth O], F [auth P], M, N, Q [auth I], R [auth J], Y [auth K], Z [auth L]	IPR040858	Rubisco accumulation factor 1, C-terminal	Domain
E [auth O], F [auth P], M, N, Q [auth I], E [auth O], F [auth P], M, N, Q [auth I], R [auth J], Y [auth K], Z [auth L]	IPR046382	Rubisco accumulation factor 1, cyanobacterial	Family
E [auth O], F [auth P], M, N, Q [auth I], E [auth O], F [auth P], M, N, Q [auth I], R [auth J], Y [auth K], Z [auth L]	IPR041358	Rubisco accumulation factor 1, alpha-helical domain	Domain
E [auth O], F [auth P], M, N, Q [auth I], E [auth O], F [auth P], M, N, Q [auth I], R [auth J], Y [auth K], Z [auth L]	IPR040781	Rubisco accumulation factor 1, helix turn helix domain	Domain
A [auth 5], AA [auth U], B [auth 6], BA [auth V], C [auth 7], A [auth 5], AA [auth U], B [auth 6], BA [auth V], C [auth 7], CA [auth W], D [auth 8], DA [auth X], I [auth 1], J [auth 2], K [auth 3], L [auth 4], S [auth Q], T [auth R], U [auth S], V [auth T]	IPR046381	RuBisCO chaperone RbcX	Family
A [auth 5], AA [auth U], B [auth 6], BA [auth V], C [auth 7], A [auth 5], AA [auth U], B [auth 6], BA [auth V], C [auth 7], CA [auth W], D [auth 8], DA [auth X], I [auth 1], J [auth 2], K [auth 3], L [auth 4], S [auth Q], T [auth R], U [auth S], V [auth T]	IPR003435	Chaperonin-like RbcX	Family
A [auth 5], AA [auth U], B [auth 6], BA [auth V], C [auth 7], A [auth 5], AA [auth U], B [auth 6], BA [auth V], C [auth 7], CA [auth W], D [auth 8], DA [auth X], I [auth 1], J [auth 2], K [auth 3], L [auth 4], S [auth Q], T [auth R], U [auth S], V [auth T]	IPR038052	Chaperonin-like RbcX superfamily	Homologous Superfamily