8B6G | pdb_00008b6g

Cryo-EM structure of succinate dehydrogenase complex (complex-II) in respiratory supercomplex of Tetrahymena thermophila

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: mpstruc

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth CB]	F_UNCLASSIFIED	e8b6gCB2	A: alpha arrays	X: alpha-helical ferredoxin-like	H: alpha-helical ferredoxin (From Topology)	T: alpha-helical ferredoxin	F: F_UNCLASSIFIED	ECOD (1.6)
F [auth CB]	F_UNCLASSIFIED	e8b6gCB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: F_UNCLASSIFIED	ECOD (1.6)
D [auth CA]	F_UNCLASSIFIED	e8b6gCA2	A: alpha bundles	X: Spectrin repeat-like	H: Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain (From Topology)	T: Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain	F: F_UNCLASSIFIED	ECOD (1.6)
D [auth CA]	F_UNCLASSIFIED	e8b6gCA3	A: a+b complex topology	X: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain (From Topology)	H: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain (From Topology)	T: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain	F: F_UNCLASSIFIED	ECOD (1.6)
D [auth CA]	F_UNCLASSIFIED	e8b6gCA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: F_UNCLASSIFIED	ECOD (1.6)
J [auth CE]	F_UNCLASSIFIED	e8b6gCE1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: F_UNCLASSIFIED	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
F [auth CB]	PF13085	2Fe-2S iron-sulfur cluster binding domain (Fer2_3)	2Fe-2S iron-sulfur cluster binding domain	The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which abeta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated.	Domain
F [auth CB]	PF13534	4Fe-4S dicluster domain (Fer4_17)	4Fe-4S dicluster domain	This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.	Domain
D [auth CA]	PF02910	Fumarate reductase flavoprotein C-term (Succ_DH_flav_C)	Fumarate reductase flavoprotein C-term	This family contains fumarate reductases, succinate dehydrogenases and L-aspartate oxidases.	Domain
D [auth CA]	PF00890	FAD binding domain (FAD_binding_2)	FAD binding domain	This family includes members that bind FAD. This family includes the flavoprotein subunits from succinate and fumarate dehydrogenase, aspartate oxidase and the alpha subunit of adenylylsulphate reductase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I [auth CK]	Transmembrane protein, putative	-	-	cellular anatomical structure membrane
H [auth CG]	SDHTT3	-	-	-
G [auth CF]	Transmembrane protein, putative	-	-	cellular anatomical structure membrane
F [auth CB]	Succinate dehydrogenase (quinone)	iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding 3 iron, 4 sulfur cluster binding oxidoreductase activity succinate dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor catalytic activity succinate dehydrogenase (quinone) activity 4 iron, 4 sulfur cluster binding electron transfer activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding 3 iron, 4 sulfur cluster binding oxidoreductase activity succinate dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor catalytic activity succinate dehydrogenase (quinone) activity 4 iron, 4 sulfur cluster binding electron transfer activity cation binding ion binding metal ion binding	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy respiratory electron transport chain electron transport chain	membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm organelle membrane
E [auth CI]	DUF4885 domain-containing protein	-	-	-
D [auth CA]	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity succinate dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor catalytic activity succinate dehydrogenase (quinone) activity flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity succinate dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor catalytic activity succinate dehydrogenase (quinone) activity electron transfer activity	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy mitochondrial electron transport, succinate to ubiquinone aerobic electron transport chain oxidative phosphorylation ATP synthesis coupled electron transport electron transport chain respiratory electron transport chain aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy mitochondrial electron transport, succinate to ubiquinone aerobic electron transport chain oxidative phosphorylation ATP synthesis coupled electron transport electron transport chain respiratory electron transport chain mitochondrial ATP synthesis coupled electron transport	membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm organelle membrane
C [auth CL]	Transposase	-	-	-
B [auth CM]	Transmembrane protein, putative	-	-	cellular anatomical structure membrane
O [auth CD]	SDHD	-	-	-
N [auth CO]	SDHTT11	-	-	-
M [auth CC]	Cytochrome b-c1 complex subunit 8	-	-	-
L [auth CN]	Transmembrane protein, putative	-	-	cellular anatomical structure membrane
K [auth CJ]	Transmembrane protein, putative	-	-	cellular anatomical structure membrane
J [auth CE]	NmrA domain-containing protein	-	-	-
A [auth CH]	Diphthamide synthesis protein	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F [auth CB]	IPR025192	Succinate dehydogenase/fumarate reductase N-terminal	Domain
F [auth CB]	IPR036010	2Fe-2S ferredoxin-like superfamily	Homologous Superfamily
F [auth CB]	IPR006058	2Fe-2S ferredoxin, iron-sulphur binding site	Binding Site
F [auth CB]	IPR004489	Succinate dehydrogenase/fumarate reductase iron-sulphur protein	Family
F [auth CB]	IPR009051	Alpha-helical ferredoxin	Homologous Superfamily
F [auth CB]	IPR050573	Succinate Dehydrogenase/Fumarate Reductase Iron-Sulfur	Family
F [auth CB]	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
F [auth CB]	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
F [auth CB]	IPR012675	Beta-grasp domain superfamily	Homologous Superfamily
D [auth CA]	IPR003953	FAD-dependent oxidoreductase 2, FAD-binding domain	Domain
D [auth CA]	IPR015939	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal	Domain
D [auth CA]	IPR003952	Fumarate reductase/succinate dehydrogenase, FAD-binding site	Binding Site
D [auth CA]	IPR037099	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily	Homologous Superfamily
D [auth CA]	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
D [auth CA]	IPR030664	FAD-dependent oxidoreductase SdhA/FrdA/AprA	Family
D [auth CA]	IPR027477	Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily	Homologous Superfamily
D [auth CA]	IPR014006	Succinate dehydrogenase/fumarate reductase, flavoprotein subunit	Family
D [auth CA]	IPR011281	Succinate dehydrogenase, flavoprotein subunit	Family
J [auth CE]	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
B [auth CM], D [auth CA], G [auth CF], I [auth CK], K [auth CJ] B [auth CM], D [auth CA], G [auth CF], I [auth CK], K [auth CJ], L [auth CN]	OPM	Transmembrane	Alpha-helical polytopic	Electron transport chain complex II superfamily	Succinate dehydrogenase/fumarate reductase

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
B [auth CM], D [auth CA], G [auth CF], I [auth CK], K [auth CJ] B [auth CM], D [auth CA], G [auth CF], I [auth CK], K [auth CJ], L [auth CN]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Supercomplexes (Respirasome)	Respiratory chain super-complex, I-II-III₂-IV₂

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.