6RFR
Cryo-EM structure of respiratory complex I from Yarrowia lipolytica at 3.2 A resolution
External Resource: Annotation
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
C | SCOP2 Family | Nqo4-like | 8097757 | 4000433 | SCOP2 (2022-06-29) |
C | SCOP2 Superfamily | HydB/Nqo4-like | 8097758 | 3001849 | SCOP2 (2022-06-29) |
L | SCOP2B Superfamily | NADH-quinone oxidoreductase subunit 11-like | 8053510 | 3002200 | SCOP2B (2022-06-29) |
P [auth Q] | SCOP2B Superfamily | ACP-like | 8099778 | 3001805 | SCOP2B (2022-06-29) |
V [auth Y] | SCOP2B Superfamily | NADH-ubiquinone oxidoreductase-like | 8099784 | 3002258 | SCOP2B (2022-06-29) |
NA [auth 6] | SCOP2B Superfamily | NADH-quinone oxidoreductase subunit 11-like | 8053517 | 3002200 | SCOP2B (2022-06-29) |
N [auth O] | SCOP2B Superfamily | ACP-like | 8099780 | 3001805 | SCOP2B (2022-06-29) |
CA [auth f] | SCOP2B Superfamily | Thioredoxin-like | 8096526 | 3000031 | SCOP2B (2022-06-29) |
IA [auth 1] | SCOP2B Superfamily | Antiporter subunits half-channel-like | 8067553 | 3002280 | SCOP2B (2022-06-29) |
KA [auth 3] | SCOP2B Superfamily | NADH-quinone oxidoreductase subunit 11-like | 8106708 | 3002200 | SCOP2B (2022-06-29) |
LA [auth 4] | SCOP2B Superfamily | Antiporter subunits half-channel-like | 8071762 | 3002280 | SCOP2B (2022-06-29) |
LA [auth 4] | SCOP2B Superfamily | Antiporter subunits half-channel-like | 8093347 | 3002280 | SCOP2B (2022-06-29) |
H | SCOP2 Family | NQO2-like | 8097759 | 4002945 | SCOP2 (2022-06-29) |
H | SCOP2 Superfamily | Thioredoxin-like | 8097760 | 3000031 | 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) |
---|---|---|---|---|---|---|---|---|
B | PF10589 | e6rfrB3 | A: alpha bundles | X: Bromodomain-like | H: Nqo1C-terminal domain-like (From Topology) | T: Nqo1C-terminal domain-like | F: PF10589 | ECOD (1.6) |
B | PF22461 | e6rfrB1 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Nqo1 middle domain-like | F: PF22461 | ECOD (1.6) |
B | PF01512 | e6rfrB2 | A: a/b three-layered sandwiches | X: Nqo1 FMN-binding domain-like (From Topology) | H: Nqo1 FMN-binding domain-like (From Topology) | T: Nqo1 FMN-binding domain-like | F: PF01512 | ECOD (1.6) |
E | PF01370 | e6rfrE1 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: NAD(P)-binding Rossmann-fold domains | F: PF01370 | ECOD (1.6) |
K | PF01058 | e6rfrK1 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Class I glutamine amidotransferase-like | T: CheY-like | F: PF01058 | ECOD (1.6) |
L | PF00420 | e6rfrL1 | A: alpha complex topology | X: NADH-quinone oxidoreductase subunit K (From Topology) | H: NADH-quinone oxidoreductase subunit K (From Topology) | T: NADH-quinone oxidoreductase subunit K | F: PF00420 | ECOD (1.6) |
O [auth P] | PF05347 | e6rfrP1 | A: alpha bundles | X: LYR protein (From Topology) | H: LYR protein (From Topology) | T: LYR protein | F: PF05347 | ECOD (1.6) |
P [auth Q] | PF00550 | e6rfrQ1 | A: alpha bundles | X: ACP-like | H: Acyl-carrier protein (ACP) (From Topology) | T: Acyl-carrier protein (ACP) | F: PF00550 | ECOD (1.6) |
Q [auth R] | F_UNCLASSIFIED | e6rfrR1 | A: alpha bundles | X: LYR protein (From Topology) | H: LYR protein (From Topology) | T: LYR protein | F: F_UNCLASSIFIED | ECOD (1.6) |
V [auth Y] | PF04800 | e6rfrY1 | A: a+b two layers | X: Putative oxidoreductase (From Topology) | H: Putative oxidoreductase (From Topology) | T: Putative oxidoreductase | F: PF04800 | ECOD (1.6) |
NA [auth 6] | PF00499 | e6rfr61 | A: extended segments | X: NADH-quinone oxidoreductase subunit J (From Topology) | H: NADH-quinone oxidoreductase subunit J (From Topology) | T: NADH-quinone oxidoreductase subunit J | F: PF00499 | ECOD (1.6) |
A | PF22117 | e6rfrA5 | A: a+b two layers | X: 4Fe-4S ferredoxin (From Topology) | H: 4Fe-4S ferredoxin (From Topology) | T: 4Fe-4S ferredoxin | F: PF22117 | ECOD (1.6) |
A | PF13510 | e6rfrA6 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Ubiquitin-like | F: PF13510 | ECOD (1.6) |
A | PF22151 | e6rfrA4 | A: a+b two layers | X: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology) | H: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology) | T: Formate dehydrogenase/DMSO reductase, domain 1 | F: PF22151 | ECOD (1.6) |
A | PF00384 | e6rfrA1 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology) | T: Formate dehydrogenase/DMSO reductase, domains 2 and 3 | F: PF00384 | ECOD (1.6) |
A | PF00384,PF09326 | e6rfrA3 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology) | T: Formate dehydrogenase/DMSO reductase, domains 2 and 3 | F: PF00384,PF09326 | ECOD (1.6) |
A | PF10588 | e6rfrA2 | A: extended segments | X: iron-sulfur center-binding helical hairpin (From Topology) | H: iron-sulfur center-binding helical hairpin (From Topology) | T: iron-sulfur center-binding helical hairpin | F: PF10588 | ECOD (1.6) |
M | PF10276 | e6rfrM1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Cytochrome c oxidase Subunit F | F: PF10276 | ECOD (1.6) |
N [auth O] | PF00550 | e6rfrO1 | A: alpha bundles | X: ACP-like | H: Acyl-carrier protein (ACP) (From Topology) | T: Acyl-carrier protein (ACP) | F: PF00550 | ECOD (1.6) |
S [auth U] | PF06747 | e6rfrU1 | A: few secondary structure elements | X: p8-MTCP1-related (From Topology) | H: p8-MTCP1-related (From Topology) | T: p8-MTCP1-related | F: PF06747 | ECOD (1.6) |
T [auth W] | PF06212 | e6rfrW1 | A: extended segments | X: Mitochondrial complex I, B16.6 subunit (From Topology) | H: Mitochondrial complex I, B16.6 subunit (From Topology) | T: Mitochondrial complex I, B16.6 subunit | F: PF06212 | ECOD (1.6) |
CA [auth f] | PF05047 | e6rfrf1 | A: a+b three layers | X: Thioredoxin-like | H: Thioredoxin-like (From Topology) | T: Thioredoxin-like | F: PF05047 | ECOD (1.6) |
EA [auth h] | PF05071 | e6rfrh1 | A: a+b three layers | X: Mitochondrial complex I, B17.2 subunit (From Topology) | H: Mitochondrial complex I, B17.2 subunit (From Topology) | T: Mitochondrial complex I, B17.2 subunit | F: PF05071 | ECOD (1.6) |
IA [auth 1] | PF00146 | e6rfr11 | A: alpha complex topology | X: Sodium/proton antiporter subunits-like (From Homology) | H: Sodium/proton antiporter subunits-like | T: NADH-quinone oxidoreductase subunit 8 (Nqo8)-related | F: PF00146 | ECOD (1.6) |
JA [auth 2] | PF00361 | e6rfr21 | A: alpha complex topology | X: Sodium/proton antiporter subunits-like (From Homology) | H: Sodium/proton antiporter subunits-like | T: NADH-quinone oxidoreductase subunit L (NuoL)-related | F: PF00361 | ECOD (1.6) |
KA [auth 3] | PF00507 | e6rfr31 | A: extended segments | X: NADH-quinone oxidoreductase subunit A (From Topology) | H: NADH-quinone oxidoreductase subunit A (From Topology) | T: NADH-quinone oxidoreductase subunit A | F: PF00507 | ECOD (1.6) |
LA [auth 4] | PF00361 | e6rfr41 | A: alpha complex topology | X: Sodium/proton antiporter subunits-like (From Homology) | H: Sodium/proton antiporter subunits-like | T: NADH-quinone oxidoreductase subunit L (NuoL)-related | F: PF00361 | ECOD (1.6) |
MA [auth 5] | PF00361,PF00662 | e6rfr51 | A: alpha complex topology | X: Sodium/proton antiporter subunits-like (From Homology) | H: Sodium/proton antiporter subunits-like | T: NADH-quinone oxidoreductase subunit L (NuoL)-related | F: PF00361,PF00662 | ECOD (1.6) |
D | PF15879 | e6rfrD1 | A: extended segments | X: Mitochondrial complex I, MWFE subunit (From Topology) | H: Mitochondrial complex I, MWFE subunit (From Topology) | T: Mitochondrial complex I, MWFE subunit | F: PF15879 | ECOD (1.6) |
PA [auth 9] | PF10200 | e6rfr91 | A: alpha bundles | X: cytochrome bc1 complex 11 kDa protein-like | H: CHCH domain (From Topology) | T: CHCH domain | F: PF10200 | ECOD (1.6) |
F | PF04716 | e6rfrF1 | A: extended segments | X: FATC domain (From Topology) | H: FATC domain (From Topology) | T: FATC domain | F: PF04716 | ECOD (1.6) |
G | PF00329 | e6rfrG1 | A: a+b two layers | X: Nqo5-like | H: Nqo5-like (From Topology) | T: Nqo5-like | F: PF00329 | ECOD (1.6) |
H | PF01257 | e6rfrH2 | A: alpha bundles | X: NQO2 helical bundle domain (From Topology) | H: NQO2 helical bundle domain (From Topology) | T: NQO2 helical bundle domain | F: PF01257 | ECOD (1.6) |
H | PF01257 | e6rfrH1 | A: a+b three layers | X: Thioredoxin-like | H: Thioredoxin-like (From Topology) | T: Thioredoxin-like | F: PF01257 | ECOD (1.6) |
I | PF00037 | e6rfrI1 | A: a+b two layers | X: 4Fe-4S ferredoxin (From Topology) | H: 4Fe-4S ferredoxin (From Topology) | T: 4Fe-4S ferredoxin | F: PF00037 | ECOD (1.6) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF10531 | SLBB domain (SLBB) | SLBB domain | - | Domain | |
PF01512 | Respiratory-chain NADH dehydrogenase 51 Kd subunit (Complex1_51K) | Respiratory-chain NADH dehydrogenase 51 Kd subunit | - | Family | |
PF10589 | NADH-ubiquinone oxidoreductase-F iron-sulfur binding region (NADH_4Fe-4S) | NADH-ubiquinone oxidoreductase-F iron-sulfur binding region | - | Domain | |
PF00346 | Respiratory-chain NADH dehydrogenase, 49 Kd subunit (Complex1_49kDa) | Respiratory-chain NADH dehydrogenase, 49 Kd subunit | - | Family | |
PF01370 | NAD dependent epimerase/dehydratase family (Epimerase) | NAD dependent epimerase/dehydratase family | - | Family | |
PF01058 | NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6) | NADH ubiquinone oxidoreductase, 20 Kd subunit | - | Family | |
PF00420 | NADH-ubiquinone/plastoquinone oxidoreductase chain 4L (Oxidored_q2) | NADH-ubiquinone/plastoquinone oxidoreductase chain 4L | - | Family | |
O [auth P] | PF13233 | Complex1_LYR-like (Complex1_LYR_2) | Complex1_LYR-like | - | Family |
P [auth Q] | 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 |
V [auth Y] | PF04800 | NADH dehydrogenase ubiquinone Fe-S protein 4 (NDUS4) | NADH dehydrogenase ubiquinone Fe-S protein 4 | - | Family |
X [auth a] | PF05821 | NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) (NDUF_B8) | NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) | - | Family |
AA [auth d] | PF10249 | NADH-ubiquinone oxidoreductase subunit 10 (NDUFB10) | NADH-ubiquinone oxidoreductase subunit 10 | - | Family |
NA [auth 6] | PF00499 | NADH-ubiquinone/plastoquinone oxidoreductase chain 6 (Oxidored_q3) | NADH-ubiquinone/plastoquinone oxidoreductase chain 6 | - | Family |
OA [auth 8] | PF05676 | NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) (NDUF_B7) | NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) | - | Family |
PF00384 | Molybdopterin oxidoreductase (Molybdopterin) | Molybdopterin oxidoreductase | - | Family | |
PF09326 | NADH-ubiquinone oxidoreductase subunit G, C-terminal (NADH_dhqG_C) | NADH-ubiquinone oxidoreductase subunit G, C-terminal | - | Family | |
PF13510 | 2Fe-2S iron-sulfur cluster binding domain (Fer2_4) | 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 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 ... | Domain | |
PF10588 | NADH-ubiquinone oxidoreductase-G iron-sulfur binding region (NADH-G_4Fe-4S_3) | NADH-ubiquinone oxidoreductase-G iron-sulfur binding region | - | Domain | |
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 | |
N [auth O] | 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 |
S [auth U] | PF06747 | CHCH domain (CHCH) | CHCH domain | we have identified a conserved motif in the LOC118487 protein that we have called the CHCH motif. Alignment of this protein with related members showed the presence of three subgroups of proteins, which are called the S (Small), N (N-terminal extende ... | Domain |
T [auth W] | PF06212 | GRIM-19 protein (GRIM-19) | GRIM-19 protein | - | Family |
U [auth X] | PF12853 | C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit (NADH_u_ox_C) | C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit | This family is the C-terminal domain of NADH-ubiquinone oxidoreductase 21 kDa subunits from fungi. | Domain |
U [auth X] | 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 |
Z [auth c] | PF08122 | NADH-ubiquinone oxidoreductase B12 subunit family (NDUF_B12) | NADH-ubiquinone oxidoreductase B12 subunit family | - | Family |
CA [auth f] | 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 |
EA [auth h] | PF05071 | NADH ubiquinone oxidoreductase subunit NDUFA12 (NDUFA12) | NADH ubiquinone oxidoreductase subunit NDUFA12 | - | Family |
IA [auth 1] | PF00146 | NADH dehydrogenase (NADHdh) | NADH dehydrogenase | - | Family |
JA [auth 2] | PF00361 | Proton-conducting membrane transporter (Proton_antipo_M) | Proton-conducting membrane transporter | - | Family |
KA [auth 3] | PF00507 | NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 (Oxidored_q4) | NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 | - | Family |
LA [auth 4] | PF00361 | Proton-conducting membrane transporter (Proton_antipo_M) | Proton-conducting membrane transporter | - | Family |
MA [auth 5] | PF00361 | Proton-conducting membrane transporter (Proton_antipo_M) | Proton-conducting membrane transporter | - | Family |
MA [auth 5] | PF00662 | NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus (Proton_antipo_N) | NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus | - | Family |
PF15879 | NADH-ubiquinone oxidoreductase MWFE subunit (MWFE) | NADH-ubiquinone oxidoreductase MWFE subunit | - | Family | |
PA [auth 9] | PF10200 | NADH:ubiquinone oxidoreductase, NDUFS5-15kDa (Ndufs5) | NADH:ubiquinone oxidoreductase, NDUFS5-15kDa | - | Family |
PF04716 | ETC complex I subunit conserved region (ETC_C1_NDUFA5) | ETC complex I subunit conserved region | - | Family | |
PF00329 | Respiratory-chain NADH dehydrogenase, 30 Kd subunit (Complex1_30kDa) | Respiratory-chain NADH dehydrogenase, 30 Kd subunit | - | Family | |
PF01257 | Thioredoxin-like [2Fe-2S] ferredoxin (2Fe-2S_thioredx) | Thioredoxin-like [2Fe-2S] ferredoxin | - | Family | |
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 |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Membrane Protein Annotation: OPM OPM Database Homepage
Chains | External Link | Type | Class | Superfamily | Family |
---|---|---|---|---|---|
OPM | Transmembrane | Alpha-helical polytopic | Electron transport chain complex I (NADH dehydrogenase) and supercomplexes | H+ or Na+ translocating NADH dehydrogenase |
Membrane Protein Annotation: PDBTM PDBTM Database Homepage
Chains | External Link | Comment |
---|---|---|
PDBTM | Annotated as membrane protein by PDBTM |
Membrane Protein Annotation: mpstruc mpstruc Database Homepage
Chains | Resource Link | Group | Subgroup | Protein |
---|---|---|---|---|
mpstruc | TRANSMEMBRANE PROTEINS: ALPHA-HELICAL | Electron Transport Chain Complexes: Complex I | Mitochondrial Complex I |