6KKM | pdb_00006kkm

Crystal structure of RbcL-Raf1 complex from Anabaena sp. PCC 7120

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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 D]	d6kkmd2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	Anabaena sp. PCC 7120 (Nostoc sp. PCC 7120 = FACHB-418 ) [TaxId: 103690 ],	SCOPe (2.08)
H [auth D]	d6kkmd1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	Anabaena sp. PCC 7120 (Nostoc sp. PCC 7120 = FACHB-418 ) [TaxId: 103690 ],	SCOPe (2.08)
G [auth C]	d6kkmc2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	Anabaena sp. PCC 7120 (Nostoc sp. PCC 7120 = FACHB-418 ) [TaxId: 103690 ],	SCOPe (2.08)
G [auth C]	d6kkmc1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	Anabaena sp. PCC 7120 (Nostoc sp. PCC 7120 = FACHB-418 ) [TaxId: 103690 ],	SCOPe (2.08)
F [auth B]	d6kkmb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	Anabaena sp. PCC 7120 (Nostoc sp. PCC 7120 = FACHB-418 ) [TaxId: 103690 ],	SCOPe (2.08)
F [auth B]	d6kkmb1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	Anabaena sp. PCC 7120 (Nostoc sp. PCC 7120 = FACHB-418 ) [TaxId: 103690 ],	SCOPe (2.08)
E [auth A]	d6kkma2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	Anabaena sp. PCC 7120 (Nostoc sp. PCC 7120 = FACHB-418 ) [TaxId: 103690 ],	SCOPe (2.08)
E [auth A]	d6kkma1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	Anabaena sp. PCC 7120 (Nostoc sp. PCC 7120 = FACHB-418 ) [TaxId: 103690 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth H]	C1-set	e6kkmH1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
C [auth G]	C1-set	e6kkmG1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
B [auth F]	C1-set	e6kkmF1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
A [auth E]	C1-set	e6kkmE1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
H [auth D]	C1-set	e6kkmD1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
G [auth C]	C1-set	e6kkmC1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
F [auth B]	C1-set	e6kkmB1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
E [auth A]	C1-set	e6kkmA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H [auth D]	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (utative)
H [auth D]	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (utative)
G [auth C]	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (utative)
G [auth C]	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (utative)
F [auth B]	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (utative)
F [auth B]	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (utative)
E [auth A]	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (utative)
E [auth A]	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth E], B [auth F], C [auth G], D [auth H]	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
A [auth E], B [auth F], C [auth G], D [auth H]	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
A [auth E], B [auth F], C [auth G], D [auth H]	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
E [auth A], F [auth B], G [auth C], H [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
E [auth A], F [auth B], G [auth C], H [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
A [auth E], B [auth F], C [auth G], D [auth H]	All5250 protein	-	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
E [auth A], F [auth B], G [auth C], H [auth D]	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
A [auth E], B [auth F], C [auth G], D [auth H]	IPR037494	Rubisco accumulation factor 1	Family
A [auth E], B [auth F], C [auth G], D [auth H]	IPR040858	Rubisco accumulation factor 1, C-terminal	Domain
A [auth E], B [auth F], C [auth G], D [auth H]	IPR046382	Rubisco accumulation factor 1, cyanobacterial	Family
A [auth E], B [auth F], C [auth G], D [auth H]	IPR041358	Rubisco accumulation factor 1, alpha-helical domain	Domain
A [auth E], B [auth F], C [auth G], D [auth H]	IPR040781	Rubisco accumulation factor 1, helix turn helix domain	Domain
E [auth A], F [auth B], G [auth C], H [auth D]	IPR020888	Ribulose bisphosphate carboxylase large subunit, type I	Family
E [auth A], F [auth B], G [auth C], H [auth D]	IPR036376	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily	Homologous Superfamily
E [auth A], F [auth B], G [auth C], H [auth D]	IPR020878	Ribulose bisphosphate carboxylase, large chain, active site	Active Site
E [auth A], F [auth B], G [auth C], H [auth D]	IPR000685	Ribulose bisphosphate carboxylase, large subunit, C-terminal	Domain
E [auth A], F [auth B], G [auth C], H [auth D]	IPR033966	RuBisCO	Family
E [auth A], F [auth B], G [auth C], H [auth D]	IPR017443	Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal	Domain
E [auth A], F [auth B], G [auth C], H [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.