Cryo-EM structure of respiratory super-complex CI+III2 from Tetrahymena thermophila
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
| Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
|---|---|---|---|---|---|
| MB [auth S7] | SCOP2 Family | Nq06/HydA N-terminal domain-like | 8107321 | 4007641 | SCOP2 (2022-06-29) |
| MB [auth S7] | SCOP2 Superfamily | Nqo6/HydA N-terminal domain-like | 8107322 | 3002291 | SCOP2 (2022-06-29) |
| IB [auth S2] | SCOP2 Family | Nqo4-like | 8107319 | 4000433 | SCOP2 (2022-06-29) |
| IB [auth S2] | SCOP2 Superfamily | HydB/Nqo4-like | 8107320 | 3001849 | SCOP2 (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
| Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
|---|---|---|---|---|---|---|---|---|
| I [auth 3D] | Complex1_49kDa | e7tgh3D01 | A: a/b three-layered sandwiches | X: Rossmann-like | H: all-alpha NTP pyrophosphatases | T: Hypothetical protein AF_0060 | F: Complex1_49kDa | ECOD (v294.1) |
| H [auth 3C] | Complex1_49kDa | e7tgh3C01 | A: a/b three-layered sandwiches | X: Rossmann-like | H: all-alpha NTP pyrophosphatases | T: Hypothetical protein AF_0060 | F: Complex1_49kDa | ECOD (v294.1) |
| GC [auth S5] | C1-set | e7tghS51 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: C1-set | ECOD (v294.1) |
| G [auth 3B] | SLBB | e7tgh3B1 | A: a/b three-layered sandwiches | X: RNase A-like | H: RNase A-like | T: RNase A-like | F: SLBB | ECOD (v294.1) |
| TB [auth V2] | PF31221 | e7tghV201 | A: a/b three-layered sandwiches | X: Rossmann-like | H: all-alpha NTP pyrophosphatases | T: Hypothetical protein AF_0060 | F: PF31221 | ECOD (v294.1) |
| SB [auth V1] | NADH_4Fe-4S | e7tghV11 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: NADH_4Fe-4S | ECOD (v294.1) |
| F [auth 3A] | Complex1_49kDa | e7tgh3A01 | A: a/b three-layered sandwiches | X: Rossmann-like | H: all-alpha NTP pyrophosphatases | T: Hypothetical protein AF_0060 | F: Complex1_49kDa | ECOD (v294.1) |
| PB [auth TX] | NADH_4Fe-4S | e7tghTX1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: NADH_4Fe-4S | ECOD (v294.1) |
| NB [auth S8] | PF31221 | e7tghS801 | A: a/b three-layered sandwiches | X: Rossmann-like | H: all-alpha NTP pyrophosphatases | T: Hypothetical protein AF_0060 | F: PF31221 | ECOD (v294.1) |
| MB [auth S7] | NADH_4Fe-4S | e7tghS71 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: NADH_4Fe-4S | ECOD (v294.1) |
| LB [auth S6] | PF31221 | e7tghS601 | A: a/b three-layered sandwiches | X: Rossmann-like | H: all-alpha NTP pyrophosphatases | T: Hypothetical protein AF_0060 | F: PF31221 | ECOD (v294.1) |
| KB [auth S4] | PF31221 | e7tghS401 | A: a/b three-layered sandwiches | X: Rossmann-like | H: all-alpha NTP pyrophosphatases | T: Hypothetical protein AF_0060 | F: PF31221 | ECOD (v294.1) |
| JB [auth S3] | NADH_4Fe-4S | e7tghS31 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: NADH_4Fe-4S | ECOD (v294.1) |
| IB [auth S2] | Complex1_49kDa | e7tghS201 | A: a/b three-layered sandwiches | X: Rossmann-like | H: all-alpha NTP pyrophosphatases | T: Hypothetical protein AF_0060 | F: Complex1_49kDa | ECOD (v294.1) |
| HB [auth S1] | NADH_4Fe-4S | e7tghS11 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: NADH_4Fe-4S | ECOD (v294.1) |
| E [auth 3] | Complex1_49kDa | e7tgh301 | A: a/b three-layered sandwiches | X: Rossmann-like | H: all-alpha NTP pyrophosphatases | T: Hypothetical protein AF_0060 | F: Complex1_49kDa | ECOD (v294.1) |
| BB [auth T1] | e7tghT11 | A: a/b three-layered sandwiches | X: RNase A-like | H: RNase A-like | T: RNase A-like | F: | ECOD (v294.1) | |
| ZA [auth FX] | NADH_4Fe-4S | e7tghFX1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: NADH_4Fe-4S | ECOD (v294.1) |
| WA [auth C3] | Complex1_49kDa | e7tghC301 | A: a/b three-layered sandwiches | X: Rossmann-like | H: all-alpha NTP pyrophosphatases | T: Hypothetical protein AF_0060 | F: Complex1_49kDa | ECOD (v294.1) |
| VA [auth C2] | Complex1_49kDa | e7tghC201 | A: a/b three-layered sandwiches | X: Rossmann-like | H: all-alpha NTP pyrophosphatases | T: Hypothetical protein AF_0060 | F: Complex1_49kDa | ECOD (v294.1) |
| UA [auth C1] | Complex1_49kDa | e7tghC101 | A: a/b three-layered sandwiches | X: Rossmann-like | H: all-alpha NTP pyrophosphatases | T: Hypothetical protein AF_0060 | F: Complex1_49kDa | ECOD (v294.1) |
| OA [auth AL] | Complex1_49kDa | e7tghAL01 | A: a/b three-layered sandwiches | X: Rossmann-like | H: all-alpha NTP pyrophosphatases | T: Hypothetical protein AF_0060 | F: Complex1_49kDa | ECOD (v294.1) |
| NA [auth AC] | Complex1_49kDa | e7tghAC01 | A: a/b three-layered sandwiches | X: Rossmann-like | H: all-alpha NTP pyrophosphatases | T: Hypothetical protein AF_0060 | F: Complex1_49kDa | ECOD (v294.1) |
| MA [auth AB] | Complex1_49kDa | e7tghAB01 | A: a/b three-layered sandwiches | X: Rossmann-like | H: all-alpha NTP pyrophosphatases | T: Hypothetical protein AF_0060 | F: Complex1_49kDa | ECOD (v294.1) |
| LA [auth A9] | G-alpha | e7tghA91 | A: a/b three-layered sandwiches | X: RNase A-like | H: Cytochrome P450 | T: Cytochrome P450 | F: G-alpha | ECOD (v294.1) |
| JA [auth A6] | Complex1_49kDa | e7tghA601 | A: a/b three-layered sandwiches | X: Rossmann-like | H: all-alpha NTP pyrophosphatases | T: Hypothetical protein AF_0060 | F: Complex1_49kDa | ECOD (v294.1) |
| IA [auth A5] | Complex1_49kDa | e7tghA501 | A: a/b three-layered sandwiches | X: Rossmann-like | H: all-alpha NTP pyrophosphatases | T: Hypothetical protein AF_0060 | F: Complex1_49kDa | ECOD (v294.1) |
| HA [auth A2] | NADH_4Fe-4S | e7tghA21 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: NADH_4Fe-4S | ECOD (v294.1) |
| EA [auth 5] | NADH_4Fe-4S | e7tgh51 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: NADH_4Fe-4S | ECOD (v294.1) |
| DA [auth 4L] | NADH_4Fe-4S | e7tgh4L1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: NADH_4Fe-4S | ECOD (v294.1) |
| CA [auth 4] | Proton_antipo_M | e7tgh41 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Proton_antipo_M | ECOD (v294.1) |
| V [auth 3f] | Proton_antipo_M | e7tgh3f1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Proton_antipo_M | ECOD (v294.1) |
| K [auth 3F] | Proton_antipo_M | e7tgh3F1 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Proton_antipo_M | ECOD (v294.1) |
| J [auth 3E] | Complex1_49kDa | e7tgh3E01 | A: a/b three-layered sandwiches | X: Rossmann-like | H: all-alpha NTP pyrophosphatases | T: Hypothetical protein AF_0060 | F: Complex1_49kDa | ECOD (v294.1) |
| A [auth 1] | Proton_antipo_M | e7tgh11 | A: a/b three-layered sandwiches | X: RNase A-like | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: Proton_antipo_M | ECOD (v294.1) |
Protein Family Annotation Pfam Database Homepage
| Chains | Accession | Name | Description | Comments | Source |
|---|---|---|---|---|---|
| I [auth 3D], T [auth 3d] | PF02167 | Cytochrome C1 family (Cytochrom_C1) | Cytochrome C1 family | - | Family |
| G [auth 3B], R [auth 3b] | PF05193 | Peptidase M16 inactive domain (Peptidase_M16_C) | Peptidase M16 inactive domain | Peptidase M16 consists of two structurally related domains. One is the active peptidase, whereas the other is inactive. The two domains hold the substrate like a clamp [1]. | Domain |
| G [auth 3B], R [auth 3b] | PF00675 | Insulinase (Peptidase family M16) (Peptidase_M16) | Insulinase (Peptidase family M16) | - | Family |
| TB [auth V2] | PF01257 | Thioredoxin-like [2Fe-2S] ferredoxin (2Fe-2S_thioredx) | Thioredoxin-like [2Fe-2S] ferredoxin | - | Family |
| SB [auth V1] | PF22461 | SLBB domain (SLBB_2) | SLBB domain | This entry represents a set of SLBB domains [5]. | Domain |
| SB [auth V1] | PF01512 | Nuo51 FMN-binding domain (Complex1_51K) | Nuo51 FMN-binding domain | This entry represents the FMN-binding domain of NADH-ubiquinone oxidoreductase 51kDa subunit from NADH:ubiquinone oxidoreductase. | Domain |
| SB [auth V1] | PF10589 | NADH-ubiquinone oxidoreductase-F iron-sulfur binding region (NADH_4Fe-4S) | NADH-ubiquinone oxidoreductase-F iron-sulfur binding region | Domain | |
| F [auth 3A], Q [auth 3a] | PF05193 | Peptidase M16 inactive domain (Peptidase_M16_C) | Peptidase M16 inactive domain | Peptidase M16 consists of two structurally related domains. One is the active peptidase, whereas the other is inactive. The two domains hold the substrate like a clamp [1]. | Domain |
| PB [auth TX] | PF00085 | Thioredoxin (Thioredoxin) | Thioredoxin | Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond. Some members with only the active site are not separated from the noise. | Domain |
| NB [auth S8] | PF12838 | 4Fe-4S dicluster domain (Fer4_7) | 4Fe-4S dicluster domain | Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contai ... | Domain |
| LB [auth S6] | PF10276 | Zinc-finger domain (zf-CHCC) | Zinc-finger domain | This is a short zinc-finger domain conserved from fungi to humans. It is Cx8Hx14Cx2C. | Domain |
| KB [auth S4] | PF04800 | NADH dehydrogenase ubiquinone Fe-S protein 4 (NDUS4) | NADH dehydrogenase ubiquinone Fe-S protein 4 | - | Family |
| HB [auth S1] | PF00384 | Molybdopterin oxidoreductase (Molybdopterin) | Molybdopterin oxidoreductase | Domain | |
| HB [auth S1] | PF22151 | NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain (Fer4_NDSU1) | NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain | This 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 |
| HB [auth S1] | PF09326 | NADH-ubiquinone oxidoreductase subunit G, C-terminal (NADH_dhqG_C) | NADH-ubiquinone oxidoreductase subunit G, C-terminal | - | Family |
| HB [auth S1] | PF22117 | NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain (Fer4_Nqo3) | NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain | 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 contain ... | Domain |
| HB [auth S1] | PF10588 | NADH-ubiquinone oxidoreductase-G iron-sulfur binding region (NADH-G_4Fe-4S_3) | NADH-ubiquinone oxidoreductase-G iron-sulfur binding region | Domain | |
| DB [auth X1] | PF10785 | NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit (NADH-u_ox-rdase) | NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit | This family is the N-terminal domain of NADH-ubiquinone oxidoreductase 21 kDa subunits from fungi, lower metazoa and plants. | Domain |
| BB [auth T1] | PF02684 | Lipid-A-disaccharide synthetase (LpxB) | Lipid-A-disaccharide synthetase | - | Family |
| AB [auth T2] | PF00501 | AMP-binding enzyme (AMP-binding) | AMP-binding enzyme | - | Family |
| ZA [auth FX] | PF00111 | 2Fe-2S iron-sulfur cluster binding domain (Fer2) | 2Fe-2S iron-sulfur cluster binding domain | Domain | |
| YA [auth J1] | PF00226 | DnaJ domain (DnaJ) | DnaJ domain | DnaJ domains (J-domains) are associated with hsp70 heat-shock system and it is thought that this domain mediates the interaction. DnaJ-domain is therefore part of a chaperone (protein folding) system. The T-antigens, although not in Prosite are conf ... | Domain |
| WA [auth C3] | PF00132 | Bacterial transferase hexapeptide (six repeats) (Hexapep) | Bacterial transferase hexapeptide (six repeats) | - | Repeat |
| VA [auth C2] | PF21711 | Dynactin subunit 5 (DCTN5) | Dynactin subunit 5 | - | Repeat |
| UA [auth C1] | PF00132 | Bacterial transferase hexapeptide (six repeats) (Hexapep) | Bacterial transferase hexapeptide (six repeats) | - | Repeat |
| OA [auth AL] | PF05071 | NADH ubiquinone oxidoreductase subunit NDUFA12 (NDUFA12) | NADH ubiquinone oxidoreductase subunit NDUFA12 | - | Family |
| NA [auth AC] | PF00550 | Phosphopantetheine attachment site (PP-binding) | Phosphopantetheine attachment site | A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes memb ... | Domain |
| MA [auth AB] | PF00550 | Phosphopantetheine attachment site (PP-binding) | Phosphopantetheine attachment site | A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes memb ... | Domain |
| LA [auth A9] | PF01370 | NAD dependent epimerase/dehydratase family (Epimerase) | NAD dependent epimerase/dehydratase family | - | Family |
| IA [auth A5] | PF04716 | ETC complex I subunit conserved region (ETC_C1_NDUFA5) | ETC complex I subunit conserved region | - | Family |
| HA [auth A2] | PF05047 | Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain (L51_S25_CI-B8) | Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain | 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 member ... | Domain |
| K [auth 3F], V [auth 3f] | PF02320 | Ubiquinol-cytochrome C reductase hinge protein (UCR_hinge) | Ubiquinol-cytochrome C reductase hinge protein | The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multienzyme complex [1]. This Pfam family represents the 'hinge' protein of the complex which is thought to mediate formation of the cytochrome c1 and cytochrome c ... | Domain |
| J [auth 3E], U [auth 3e] | PF00355 | Rieske [2Fe-2S] domain (Rieske) | Rieske [2Fe-2S] domain | The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in ... | Domain |
