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 6GCS | pdb_00006gcs

Cryo-EM structure of respiratory complex I from Yarrowia lipolytica


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
HSCOP2 FamilyNQO2-like 8085744 4002945 SCOP2 (2022-06-29)
HSCOP2 SuperfamilyThioredoxin-like 8085745 3000031 SCOP2 (2022-06-29)
LA [auth 4]SCOP2 FamilyND4 antiporter-like subunits 8071761 4005749 SCOP2 (2022-06-29)
LA [auth 4]SCOP2 SuperfamilyAntiporter subunits half-channel-like 8093347 3002280 SCOP2 (2022-06-29)
LA [auth 4]SCOP2 SuperfamilyAntiporter subunits half-channel-like 8071762 3002280 SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
IPP-bindinge6gcsI1 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: PP-bindingECOD (v295.2)
HPP-bindinge6gcsH1 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: PP-bindingECOD (v295.2)
GLlgE_F_G_D1e6gcsG1 A: alpha arraysX: Hypothetical protein YqbG-likeH: Hypothetical protein YqbG-likeT: alpha/beta-HydrolasesF: LlgE_F_G_D1ECOD (v295.2)
FPP-bindinge6gcsF1 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: PP-bindingECOD (v295.2)
EPP-bindinge6gcsE1 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: PP-bindingECOD (v295.2)
PA [auth 9]LlgE_F_G_D1e6gcs91 A: alpha arraysX: Hypothetical protein YqbG-likeH: Hypothetical protein YqbG-likeT: alpha/beta-HydrolasesF: LlgE_F_G_D1ECOD (v295.2)
NA [auth 6]LlgE_F_G_D1e6gcs61 A: alpha arraysX: Hypothetical protein YqbG-likeH: Hypothetical protein YqbG-likeT: alpha/beta-HydrolasesF: LlgE_F_G_D1ECOD (v295.2)
DPP-bindinge6gcsD1 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: PP-bindingECOD (v295.2)
MA [auth 5]EamAe6gcs51 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: EamAECOD (v295.2)
LA [auth 4]EamAe6gcs41 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: EamAECOD (v295.2)
KA [auth 3]LlgE_F_G_D1e6gcs31 A: alpha arraysX: Hypothetical protein YqbG-likeH: Hypothetical protein YqbG-likeT: alpha/beta-HydrolasesF: LlgE_F_G_D1ECOD (v295.2)
JA [auth 2]EamAe6gcs21 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: EamAECOD (v295.2)
IA [auth 1]EamAe6gcs11 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: EamAECOD (v295.2)
EA [auth h]EamAe6gcsh1 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: EamAECOD (v295.2)
CLlgE_F_G_D1e6gcsC1 A: alpha arraysX: Hypothetical protein YqbG-likeH: Hypothetical protein YqbG-likeT: alpha/beta-HydrolasesF: LlgE_F_G_D1ECOD (v295.2)
CA [auth f]EamAe6gcsf1 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: EamAECOD (v295.2)
V [auth Y]EamAe6gcsY1 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: EamAECOD (v295.2)
T [auth W]EamAe6gcsW1 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: EamAECOD (v295.2)
BPP-bindinge6gcsB1 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: PP-bindingECOD (v295.2)
S [auth U]EamAe6gcsU1 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: EamAECOD (v295.2)
Q [auth R]EamAe6gcsR1 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: EamAECOD (v295.2)
P [auth Q]PP-bindinge6gcsQ1 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: PP-bindingECOD (v295.2)
O [auth P]PP-bindinge6gcsP1 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: PP-bindingECOD (v295.2)
N [auth O]PP-bindinge6gcsO1 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: PP-bindingECOD (v295.2)
MPP-bindinge6gcsM1 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: PP-bindingECOD (v295.2)
LPP-bindinge6gcsL1 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: PP-bindingECOD (v295.2)
KPP-bindinge6gcsK1 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: PP-bindingECOD (v295.2)
APP-bindinge6gcsA1 A: alpha arraysX: fingers domain in bacteriophage RB69-like DNA polymerase IH: fingers domain in bacteriophage RB69-like DNA polymerase IT: fingers domain in bacteriophage RB69-like DNA polymerase IF: PP-bindingECOD (v295.2)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
TYKY SUBUNIT (NUIM)
24-KDA SUBUNIT (NUHM)
30-KDA PROTEIN (NUGM) -
NUFM SUBUNIT-
NUEM SUBUNIT -
PA [auth 9]NIPM SUBUNIT-
OA [auth 8]NB8M SUBUNIT- -
NA [auth 6]ND6 SUBUNIT (NU6M) -
NIMM SUBUNIT- -
MA [auth 5]ND5 SUBUNIT (NU5M)
LA [auth 4]ND4 SUBUNIT (NU4M)
KA [auth 3]ND3 SUBUNIT (NU3M) -
JA [auth 2]ND2 SUBUNIT (NU2M)
IA [auth 1]ND1 SUBUNIT (NU1M)
HA [auth n]NUNM SUBUNIT---
GA [auth j]NB5M SUBUNIT- - -
FA [auth i]UNKNOWN SUBUNIT---
EA [auth h]N7BM SUBUNIT- -
DA [auth g]NI9M SUBUNIT- - -
49-KDA PROTEIN (NUCM)
CA [auth f]NI8M SUBUNIT- -
BA [auth e]NUUM SUBUNIT---
AA [auth d]NIDM SUBUNIT- -
Z [auth c]NB2M SUBUNIT-
Y [auth b]NEBM SUBUNIT---
X [auth a]NIAM SUBUNIT---
W [auth Z]NUZM SUBUNIT---
V [auth Y]NUYM SUBUNIT-
U [auth X]NUXM SUBUNIT- - -
T [auth W]NB6M SUBUNIT- -
51-KDA PROTEIN (NUBM) -
S [auth U]NUPM SUBUNIT-
R [auth S]NESM SUBUNIT---
Q [auth R]NI2M SUBUNIT-
P [auth Q]ACPM2 SUBUNIT -
O [auth P]NB4M SUBUNIT-
N [auth O]ACPM1 SUBUNIT -
NUMM SUBUNIT-
ND4L SUBUNIT (NULM)
PSST SUBUNIT (NUKM)
NUJM SUBUNIT-
75-KDA PROTEIN (NUAM)

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR0179004Fe-4S ferredoxin, iron-sulphur binding, conserved siteConserved Site
IPR0178964Fe-4S ferredoxin-type, iron-sulphur binding domainDomain
IPR010226NADH-quinone oxidoreductase, chain IFamily
IPR042128NuoE domainDomain
IPR002023NADH-quinone oxidoreductase subunit E-likeFamily
IPR041921NADH-quinone oxidoreductase subunit E, N-terminalHomologous Superfamily
IPR036249Thioredoxin-like superfamilyHomologous Superfamily
IPR037232NADH:ubiquinone oxidoreductase, 30kDa subunit superfamilyHomologous Superfamily
IPR001268NADH:ubiquinone oxidoreductase, 30kDa subunitDomain
IPR020396NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved siteConserved Site
IPR010218NADH dehydrogenase, subunit CFamily
IPR006806NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5Family
IPR051207Mitochondrial Complex I NDUFA9 SubunitFamily
IPR036291NAD(P)-binding domain superfamilyHomologous Superfamily
IPR001509NAD-dependent epimerase/dehydrataseDomain
PA [auth 9]IPR019342NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5Family
OA [auth 8]IPR008698NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7Family
NA [auth 6]IPR042106NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJHomologous Superfamily
NA [auth 6]IPR001457NADH:ubiquinone/plastoquinone oxidoreductase, chain 6Family
IPR017384NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1Family
MA [auth 5]IPR003945NADH-quinone oxidoreductase, chain 5-likeFamily
MA [auth 5]IPR001516NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminalDomain
MA [auth 5]IPR001750NADH:quinone oxidoreductase/Mrp antiporter, transmembrane domainDomain
MA [auth 5]IPR018393NADH-plastoquinone oxidoreductase, chain 5 subgroupFamily
LA [auth 4]IPR003918NADH:ubiquinone oxidoreductaseFamily
LA [auth 4]IPR010227NADH-quinone oxidoreductase, chain M/4Family
LA [auth 4]IPR001750NADH:quinone oxidoreductase/Mrp antiporter, transmembrane domainDomain
KA [auth 3]IPR000440NADH:ubiquinone/plastoquinone oxidoreductase, chain 3Family
KA [auth 3]IPR038430NADH:ubiquinone oxidoreductase, subunit 3 superfamilyHomologous Superfamily
JA [auth 2]IPR001750NADH:quinone oxidoreductase/Mrp antiporter, transmembrane domainDomain
IA [auth 1]IPR001694NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit HFamily
IA [auth 1]IPR018086NADH:ubiquinone oxidoreductase, subunit 1, conserved siteConserved Site
EA [auth h]IPR007763NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12Family
DA [auth g]IPR039961NADH-ubiquinone oxidoreductase 9.5kDa subunitFamily
IPR022885NAD(P)H-quinone oxidoreductase subunit D/HFamily
IPR014029NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved siteConserved Site
IPR029014[NiFe]-hydrogenase, large subunitHomologous Superfamily
IPR001135NADH-quinone oxidoreductase, subunit DDomain
CA [auth f]IPR007741Ribosomal protein/NADH dehydrogenase domainDomain
CA [auth f]IPR036249Thioredoxin-like superfamilyHomologous Superfamily
CA [auth f]IPR016464NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2Family
AA [auth d]IPR019377NADH-ubiquinone oxidoreductase, subunit 10Family
AA [auth d]IPR039993NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10Family
Z [auth c]IPR012576NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3Family
V [auth Y]IPR038532NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamilyHomologous Superfamily
V [auth Y]IPR006885NADH dehydrogenase ubiquinone Fe-S protein 4 mitochondrial-likeFamily
U [auth X]IPR019721NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminalDomain
U [auth X]IPR053229NADH-ubiquinone oxidoreductase subunitFamily
U [auth X]IPR024549NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungiDomain
T [auth W]IPR009346GRIM-19Family
IPR019575NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domainDomain
IPR054765SLBB domainDomain
IPR011537NADH ubiquinone oxidoreductase, F subunitFamily
IPR001949NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved siteConserved Site
IPR037225NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamilyHomologous Superfamily
IPR037207NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamilyHomologous Superfamily
IPR011538NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domainDomain
IPR050837Complex I 51 kDa subunitFamily
S [auth U]IPR010625CHCHDomain
S [auth U]IPR016680NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8Family
Q [auth R]IPR033034NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9Family
Q [auth R]IPR045292NDUFB9, LYR domainDomain
P [auth Q]IPR006162Phosphopantetheine attachment sitePTM
P [auth Q]IPR009081Phosphopantetheine binding ACP domainDomain
P [auth Q]IPR036736ACP-like superfamilyHomologous Superfamily
P [auth Q]IPR003231Acyl carrier proteinFamily
O [auth P]IPR016488NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6Family
O [auth P]IPR008011Complex 1 LYR protein domainDomain
O [auth P]IPR045299NDUFA6, LYR domainDomain
N [auth O]IPR006162Phosphopantetheine attachment sitePTM
N [auth O]IPR009081Phosphopantetheine binding ACP domainDomain
N [auth O]IPR036736ACP-like superfamilyHomologous Superfamily
N [auth O]IPR003231Acyl carrier proteinFamily
IPR019401Zinc finger, CHCC-typeDomain
IPR001133NADH-ubiquinone oxidoreductase chain 4L/KFamily
IPR039428NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-likeFamily
IPR006138NADH-ubiquinone oxidoreductase, 20 Kd subunitFamily
IPR006137NADH:ubiquinone oxidoreductase-like, 20kDa subunitDomain
IPR039205NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11Family
IPR006963Molybdopterin oxidoreductase, 4Fe-4S domainDomain
IPR015405NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial-likeDomain
IPR006656Molybdopterin oxidoreductaseDomain
IPR0360102Fe-2S ferredoxin-like superfamilyHomologous Superfamily
IPR0010412Fe-2S ferredoxin-type iron-sulfur binding domainDomain
IPR000283NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved siteConserved Site
IPR054351NADH-ubiquinone oxidoreductase, ferredoxin-like domainDomain
IPR010228NADH:ubiquinone oxidoreductase, subunit GFamily
IPR019574NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur bindingDomain