8BED

Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI peripheral tip)


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
A [auth E]SCOP2B SuperfamilyThioredoxin-like 8101475 3000031 SCOP2B (2022-06-29)
E [auth Q]SCOP2B SuperfamilyNADH-ubiquinone oxidoreductase-like 8101739 3002258 SCOP2B (2022-06-29)
G [auth S]SCOP2B SuperfamilyThioredoxin-like 8101737 3000031 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
A [auth E]2Fe-2S_thioredx_Ne8bedE1 A: alpha bundlesX: NQO2 helical bundle domain (From Topology)H: NQO2 helical bundle domain (From Topology)T: NQO2 helical bundle domainF: 2Fe-2S_thioredx_NECOD (1.6)
A [auth E]2Fe-2S_thioredx_Ce8bedE2 A: a+b three layersX: Thioredoxin-likeH: Thioredoxin-like (From Topology)T: Thioredoxin-likeF: 2Fe-2S_thioredx_CECOD (1.6)
B [auth F]NADH_4Fe-4Se8bedF1 A: alpha bundlesX: Bromodomain-likeH: Nqo1C-terminal domain-like (From Topology)T: Nqo1C-terminal domain-likeF: NADH_4Fe-4SECOD (1.6)
B [auth F]SLBBe8bedF2 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Nqo1 middle domain-likeF: SLBBECOD (1.6)
B [auth F]Complex1_51Ke8bedF3 A: a/b three-layered sandwichesX: Nqo1 FMN-binding domain-like (From Topology)H: Nqo1 FMN-binding domain-like (From Topology)T: Nqo1 FMN-binding domain-likeF: Complex1_51KECOD (1.6)
C [auth G]PRK09129e8bedG3 A: a+b two layersX: 4Fe-4S ferredoxin (From Topology)H: 4Fe-4S ferredoxin (From Topology)T: 4Fe-4S ferredoxinF: PRK09129ECOD (1.6)
C [auth G]Fer2_4e8bedG2 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Ubiquitin-likeF: Fer2_4ECOD (1.6)
C [auth G]Molybdop_Fe4S4_1e8bedG4 A: a+b two layersX: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)H: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)T: Formate dehydrogenase/DMSO reductase, domain 1F: Molybdop_Fe4S4_1ECOD (1.6)
C [auth G]Molybdopterin_2nde8bedG6 A: a/b three-layered sandwichesX: Rossmann-likeH: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)T: Formate dehydrogenase/DMSO reductase, domains 2 and 3F: Molybdopterin_2ndECOD (1.6)
C [auth G]Molybdopterin_1ste8bedG5 A: a/b three-layered sandwichesX: Rossmann-likeH: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)T: Formate dehydrogenase/DMSO reductase, domains 2 and 3F: Molybdopterin_1stECOD (1.6)
C [auth G]NADH-G_4Fe-4S_3e8bedG1 A: extended segmentsX: iron-sulfur center-binding helical hairpin (From Topology)H: iron-sulfur center-binding helical hairpin (From Topology)T: iron-sulfur center-binding helical hairpinF: NADH-G_4Fe-4S_3ECOD (1.6)
E [auth Q]ETC_C1_NDUFA4e8bedQ1 A: a+b two layersX: Putative oxidoreductase (From Topology)H: Putative oxidoreductase (From Topology)T: Putative oxidoreductaseF: ETC_C1_NDUFA4ECOD (1.6)
F [auth R]zf-CHCCe8bedR1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Cytochrome c oxidase Subunit FF: zf-CHCCECOD (1.6)
G [auth S]L51_S25_CI-B8e8bedS1 A: a+b three layersX: Thioredoxin-likeH: Thioredoxin-like (From Topology)T: Thioredoxin-likeF: L51_S25_CI-B8ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth E]PF01257Thioredoxin-like [2Fe-2S] ferredoxin (2Fe-2S_thioredx)Thioredoxin-like [2Fe-2S] ferredoxin- Family
B [auth F]PF10531SLBB domain (SLBB)SLBB domain- Domain
B [auth F]PF22461SLBB domain (SLBB_2)SLBB domainThis entry represents a set of SLBB domains [5].Domain
B [auth F]PF01512Nuo51 FMN-binding domain (Complex1_51K)Respiratory-chain NADH dehydrogenase 51 Kd subunit- Family
B [auth F]PF10589NADH-ubiquinone oxidoreductase-F iron-sulfur binding region (NADH_4Fe-4S)NADH-ubiquinone oxidoreductase-F iron-sulfur binding region- Domain
C [auth G]PF00384Molybdopterin oxidoreductase (Molybdopterin)Molybdopterin oxidoreductase- Family
C [auth G]PF22151NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain (NDSU1_4Fe-4S)NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domainThis entry represents the 4Fe-4S domain of NADH-ubiquinone oxidoreductase NDUFS1 from mammals and NuoG from bacteria, which are part of respiratory chain complex I [1-5].Domain
C [auth G]PF22117NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain (Nqo3_Fer4)NADH-quinone oxidoreductase subunit 3, ferredoxin-like domainNADH-quinone oxidoreductase subunit 3 (Nqo3) is a component of respiratory complex I. This protein is located at the peripheral arm of the complex and consists of multiple domains. This entry represents the second ferredoxin-like domain which contain ...NADH-quinone oxidoreductase subunit 3 (Nqo3) is a component of respiratory complex I. This protein is located at the peripheral arm of the complex and consists of multiple domains. This entry represents the second ferredoxin-like domain which contains Fe4-S4 cluster, one of the redox centers of the complex [1-5].
Domain
C [auth G]PF135102Fe-2S iron-sulfur cluster binding domain (Fer2_4)2Fe-2S iron-sulfur cluster binding domainThe 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. Th ...The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This cluster appears within sarcosine oxidase proteins.
Domain
C [auth G]PF09326NADH-ubiquinone oxidoreductase subunit G, C-terminal (NADH_dhqG_C)NADH-ubiquinone oxidoreductase subunit G, C-terminal- Family
C [auth G]PF10588NADH-ubiquinone oxidoreductase-G iron-sulfur binding region (NADH-G_4Fe-4S_3)NADH-ubiquinone oxidoreductase-G iron-sulfur binding region- Domain
E [auth Q]PF04800NADH dehydrogenase ubiquinone Fe-S protein 4 (NDUS4)NADH dehydrogenase ubiquinone Fe-S protein 4- Family
F [auth R]PF10276Zinc-finger domain (zf-CHCC)Zinc-finger domainThis is a short zinc-finger domain conserved from fungi to humans. It is Cx8Hx14Cx2C.Domain
G [auth S]PF05047Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain (L51_S25_CI-B8)Mitochondrial ribosomal protein L51 / S25 / CI-B8 domainThe proteins in this family are located in the mitochondrion. The family includes ribosomal protein L51, and S25. This family also includes mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) EC:1.6.5.3. It is not known whether all member ...The proteins in this family are located in the mitochondrion. The family includes ribosomal protein L51, and S25. This family also includes mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) EC:1.6.5.3. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins. Structurally related to thioredoxin-fold.
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth E]NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial -
B [auth F]NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial -
C [auth G]NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial
D [auth I]NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial -
E [auth Q]NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
F [auth R]NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial-
G [auth S]NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2- -
H [auth W]NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6- -

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A [auth E]IPR042128NuoE domainDomain
A [auth E]IPR002023NADH-quinone oxidoreductase subunit E-likeFamily
A [auth E]IPR041921NADH-quinone oxidoreductase subunit E, N-terminalHomologous Superfamily
A [auth E]IPR036249Thioredoxin-like superfamilyHomologous Superfamily
B [auth F]IPR019575NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domainDomain
B [auth F]IPR054765SLBB domainDomain
B [auth F]IPR011537NADH ubiquinone oxidoreductase, F subunitFamily
B [auth F]IPR001949NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved siteConserved Site
B [auth F]IPR037225NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamilyHomologous Superfamily
B [auth F]IPR037207NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamilyHomologous Superfamily
B [auth F]IPR011538NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domainDomain
B [auth F]IPR050837Complex I 51 kDa subunitFamily
C [auth G]IPR006963Molybdopterin oxidoreductase, 4Fe-4S domainDomain
C [auth G]IPR015405NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial-likeDomain
C [auth G]IPR006656Molybdopterin oxidoreductaseDomain
C [auth G]IPR0360102Fe-2S ferredoxin-like superfamilyHomologous Superfamily
C [auth G]IPR0010412Fe-2S ferredoxin-type iron-sulfur binding domainDomain
C [auth G]IPR000283NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved siteConserved Site
C [auth G]IPR054351NADH-ubiquinone oxidoreductase, ferredoxin-like domainDomain
C [auth G]IPR010228NADH:ubiquinone oxidoreductase, subunit GFamily
C [auth G]IPR050123Prokaryotic molybdopterin-containing oxidoreductaseFamily
C [auth G]IPR019574NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur bindingDomain
D [auth I]IPR0179004Fe-4S ferredoxin, iron-sulphur binding, conserved siteConserved Site
D [auth I]IPR0178964Fe-4S ferredoxin-type, iron-sulphur binding domainDomain
D [auth I]IPR010226NADH-quinone oxidoreductase, chain IFamily
E [auth Q]IPR038532NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamilyHomologous Superfamily
E [auth Q]IPR006885NADH dehydrogenase ubiquinone Fe-S protein 4 mitochondrial-likeFamily
F [auth R]IPR019401Zinc finger, CHCC-typeDomain
F [auth R]IPR016668NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialFamily
G [auth S]IPR007741Ribosomal protein/NADH dehydrogenase domainDomain
G [auth S]IPR036249Thioredoxin-like superfamilyHomologous Superfamily
G [auth S]IPR016464NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2Family
H [auth W]IPR016488NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6Family
H [auth W]IPR045299NDUFA6, LYR domainDomain