6LOD

Cryo-EM structure of the air-oxidized photosynthetic alternative complex III from Roseiflexus castenholzii

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: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E	Cytochrome_CBB3	e6lodE1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrome_CBB3	ECOD (1.6)
F	F_UNCLASSIFIED	e6lodF2	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle (From Homology)	H: Transmembrane heme-binding four-helical bundle	T: Transmembrane di-heme cytochromes	F: F_UNCLASSIFIED	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF14522	Cytochrome c7 and related cytochrome c (Cytochrome_C7)	Cytochrome c7 and related cytochrome c	-	Family
B	PF01568	Molydopterin dinucleotide binding domain (Molydop_binding)	Molydopterin dinucleotide binding domain	This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entir ...	This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor [1]. This domain corresponds to the C-terminal domain IV in dimethyl sulfoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [2].	Domain
C	PF03916	Polysulphide reductase, NrfD (NrfD)	Polysulphide reductase, NrfD	-	Family
D	PF11821	Alternative complex III, ActD subunit (ActD)	Alternative complex III, ActD subunit	-	Family
E	PF13442	Cytochrome C oxidase, cbb3-type, subunit III (Cytochrome_CBB3)	Cytochrome C oxidase, cbb3-type, subunit III	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	MULTIHEME_CYTC domain-containing protein	-	-	cellular anatomical structure membrane
B	Fe-S-cluster-containing hydrogenase components 1-like protein	oxidoreductase activity catalytic activity binding organic cyclic compound binding molybdopterin cofactor binding	-	-
C	Polysulphide reductase NrfD	-	-	cell periphery cellular anatomical structure plasma membrane membrane
D	Uncharacterized protein ActD	-	-	cellular anatomical structure membrane
E	Cytochrome c domain-containing protein	binding organic cyclic compound binding tetrapyrrole binding heme binding electron transfer activity cation binding ion binding metal ion binding small molecule binding	-	cellular anatomical structure membrane
F	Uncharacterized protein ActF	-	-	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR029467	Cytochrome c7-like	Domain
A	IPR036280	Multiheme cytochrome superfamily	Homologous Superfamily
B	IPR006657	Molybdopterin dinucleotide-binding domain	Domain
B	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
B	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
B	IPR030948	TAT-variant-translocation signal domain	Domain
B	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
C	IPR005614	NrfD family	Family
D	IPR021776	Alternative complex III, ActD subunit	Family
E	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
E	IPR009056	Cytochrome c-like domain	Domain

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, C, D, E, F	OPM	Transmembrane	Alpha-helical polytopic	Electron transport chain complex II superfamily	Polysulfide reductase

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, C, D, E, F	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, C, D, E, F	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, C, D, E, F	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Complexes: Complex III (Cytochrome bc₁)	Alternative complex III (ACIII), dithionite reduced

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359

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.