7ZKP | pdb_00007zkp

Late assembly intermediate of the proximal proton pumping module of complex I with assembly factors NDUFAF1 and CIA84


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
I [auth 6]SCOP2B SuperfamilyNADH-quinone oxidoreductase, subunit 11-like 8053517 3002200 SCOP2B (2022-06-29)
H [auth 3]SCOP2B SuperfamilyNADH-quinone oxidoreductase, subunit 11-like 8106708 3002200 SCOP2B (2022-06-29)
F [auth 1]SCOP2B SuperfamilyAntiporter subunits half-channel-like 8067553 3002280 SCOP2B (2022-06-29)
B [auth L]SCOP2B SuperfamilyNADH-quinone oxidoreductase, subunit 11-like 8053510 3002200 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
G [auth 2]Proton_antipo_Me7zkp21 A: alpha complex topologyX: Sodium/proton antiporter subunits-like (From Homology)H: Sodium/proton antiporter subunits-likeT: NADH-quinone oxidoreductase subunit L (NuoL)-relatedF: Proton_antipo_MECOD (1.6)
F [auth 1]NADHdhe7zkp11 A: alpha complex topologyX: Sodium/proton antiporter subunits-like (From Homology)H: Sodium/proton antiporter subunits-likeT: NADH-quinone oxidoreductase subunit 8 (Nqo8)-relatedF: NADHdhECOD (1.6)
D [auth W]GRIM-19e7zkpW1 A: extended segmentsX: Mitochondrial complex I, B16.6 subunit (From Topology)H: Mitochondrial complex I, B16.6 subunit (From Topology)T: Mitochondrial complex I, B16.6 subunitF: GRIM-19ECOD (1.6)
C [auth U]CHCHe7zkpU1 A: few secondary structure elementsX: p8-MTCP1-related (From Topology)H: p8-MTCP1-related (From Topology)T: p8-MTCP1-relatedF: CHCHECOD (1.6)
B [auth L]Oxidored_q2e7zkpL1 A: alpha complex topologyX: NADH-quinone oxidoreductase subunit K (From Topology)H: NADH-quinone oxidoreductase subunit K (From Topology)T: NADH-quinone oxidoreductase subunit KF: Oxidored_q2ECOD (1.6)
N [auth A]F_UNCLASSIFIEDe7zkpA1 A: beta sandwichesX: jelly-rollH: Concanavalin A-likeT: Galactose-binding domain-likeF: F_UNCLASSIFIEDECOD (1.6)
L [auth 9]Ndufs5e7zkp91 A: alpha bundlesX: cytochrome bc1 complex 11 kDa protein-likeH: CHCH domain (From Topology)T: CHCH domainF: Ndufs5ECOD (1.6)
A [auth D]MWFEe7zkpD1 A: extended segmentsX: Mitochondrial complex I, MWFE subunit (From Topology)H: Mitochondrial complex I, MWFE subunit (From Topology)T: Mitochondrial complex I, MWFE subunitF: MWFEECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
H [auth 3]1.20.58.1610 Mainly Alpha Up-down Bundle Methane Monooxygenase Hydroxylase Chain G, domain 1CATH (utative)
N [auth A]2.60.120.430 Mainly Beta Sandwich Jelly Rolls Galactose-binding lectinCATH (utative)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
I [auth 6]PF00499NADH-ubiquinone/plastoquinone oxidoreductase chain 6 (Oxidored_q3)NADH-ubiquinone/plastoquinone oxidoreductase chain 6- Family
H [auth 3]PF00507NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 (Oxidored_q4)NADH-ubiquinone/plastoquinone oxidoreductase, chain 3- Family
G [auth 2]PF00361NADH:quinone oxidoreductase/Mrp antiporter, TM (Proton_antipo_M)NADH:quinone oxidoreductase/Mrp antiporter, TMThis entry includes membrane transporters and represents some 7 of potentially 14-16 TM regions. In many instances, its members forms part of complex I that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associa ...This entry includes membrane transporters and represents some 7 of potentially 14-16 TM regions. In many instances, its members forms part of complex I that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane, and in this context is a combination predominantly of subunits 2, 4, 5, 14, L, M and N [1]. In many bacterial species these proteins are probable stand-alone transporters not coupled with oxidoreduction [2].
Domain
F [auth 1]PF00146NADH dehydrogenase (NADHdh)NADH dehydrogenase- Family
E [auth X]PF12853C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit (NADH_u_ox_C)C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunitThis family is the C-terminal domain of NADH-ubiquinone oxidoreductase 21 kDa subunits from fungi. Domain
E [auth X]PF10785NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit (NADH-u_ox-rdase)NADH-ubiquinone oxidoreductase complex I, 21 kDa subunitThis family is the N-terminal domain of NADH-ubiquinone oxidoreductase 21 kDa subunits from fungi, lower metazoa and plants. Domain
C [auth U]PF06747CHCH domain (CHCH)CHCH domainwe 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 ...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 extended) and C (C-terminal extended) subgroups. All three sub-groups of proteins have in common that they contain a predicted conserved [coiled coil 1]-[helix 1]-[coiled coil 2]-[helix 2] domain (CHCH domain). Within each helix of the CHCH domain, there are two cysteines present in a C-X9-C motif. The N-group contains an additional double helix domain, and each helix contains the C-X9-C motif. This family contains a number of characterised proteins: Cox19 protein - a nuclear gene of Saccharomyces cerevisiae, codes for an 11-kDa protein (Cox19p) required for expression of cytochrome oxidase. Because cox19 mutants are able to synthesise the mitochondrial and nuclear gene products of cytochrome oxidase, Cox19p probably functions post-translationally during assembly of the enzyme. Cox19p is present in the cytoplasm and mitochondria, where it exists as a soluble intermembrane protein. This dual location is similar to what was previously reported for Cox17p, a low molecular weight copper protein thought to be required for maturation of the CuA centre of subunit 2 of cytochrome oxidase. Cox19p have four conserved potential metal ligands, these are three cysteines and one histidine. Mrp10 - belongs to the class of yeast mitochondrial ribosomal proteins that are essential for translation [2]. Eukaryotic NADH-ubiquinone oxidoreductase 19 kDa (NDUFA8) subunit [3]. The CHCH domain was previously called DUF657 [4].
Domain
B [auth L]PF00420NADH-ubiquinone/plastoquinone oxidoreductase chain 4L (Oxidored_q2)NADH-ubiquinone/plastoquinone oxidoreductase chain 4L- Family
N [auth A]PF08547Complex I intermediate-associated protein 30 (CIA30) (CIA30)Complex I intermediate-associated protein 30 (CIA30)- Family
L [auth 9]PF10200NADH:ubiquinone oxidoreductase, NDUFS5-15kDa (Ndufs5)NADH:ubiquinone oxidoreductase, NDUFS5-15kDa- Family
A [auth D]PF15879NADH-ubiquinone oxidoreductase MWFE subunit (MWFE)NADH-ubiquinone oxidoreductase MWFE subunit- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
I [auth 6]NADH-ubiquinone oxidoreductase chain 6 -
H [auth 3]NADH-ubiquinone oxidoreductase chain 3 -
G [auth 2]NADH dehydrogenase subunit 2 -
F [auth 1]NADH-ubiquinone oxidoreductase chain 1
E [auth X]NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit-domain-containing protein- -
D [auth W]Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)- -
C [auth U]Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)-
B [auth L]NADH-ubiquinone oxidoreductase chain 4L
N [auth A]CIA30 domain-containing protein
M [auth C]assembly factor CIA84
L [auth 9]Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)-
K [auth b]Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)- - -
J [auth g]subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)- -
A [auth D]Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)- -

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
I [auth 6]IPR042106NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJHomologous Superfamily
I [auth 6]IPR001457NADH:ubiquinone/plastoquinone oxidoreductase, chain 6Family
H [auth 3]IPR000440NADH:ubiquinone/plastoquinone oxidoreductase, chain 3Family
H [auth 3]IPR038430NADH:ubiquinone oxidoreductase, subunit 3 superfamilyHomologous Superfamily
G [auth 2]IPR001750NADH:quinone oxidoreductase/Mrp antiporter, transmembrane domainDomain
F [auth 1]IPR001694NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit HFamily
F [auth 1]IPR018086NADH:ubiquinone oxidoreductase, subunit 1, conserved siteConserved Site
E [auth X]IPR019721NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminalDomain
E [auth X]IPR053229NADH-ubiquinone oxidoreductase subunitFamily
E [auth X]IPR024549NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungiDomain
D [auth W]IPR009346GRIM-19Family
C [auth U]IPR010625CHCHDomain
C [auth U]IPR016680NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8Family
B [auth L]IPR001133NADH-ubiquinone oxidoreductase chain 4L/KFamily
B [auth L]IPR039428NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-likeFamily
N [auth A]IPR039131Complex I intermediate-associated protein 30, mitochondrialFamily
N [auth A]IPR013857NADH:ubiquinone oxidoreductase intermediate-associated protein 30Domain
N [auth A]IPR008979Galactose-binding-like domain superfamilyHomologous Superfamily
L [auth 9]IPR019342NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5Family
J [auth g]IPR039961NADH-ubiquinone oxidoreductase 9.5kDa subunitFamily
A [auth D]IPR017384NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1Family

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
I [auth 6]FME Parent Component: MET

RESIDAA0021 , AA0566

PSI-MOD :  N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891
H [auth 3]FME Parent Component: MET

RESIDAA0021 , AA0566 , AA0021 , AA0566

PSI-MOD :  N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891 , N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891
G [auth 2]FME Parent Component: MET

RESIDAA0021 , AA0566 , AA0021 , AA0566 , AA0021 , AA0566

PSI-MOD :  N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891 , N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891 , N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891
F [auth 1]FME Parent Component: MET

RESIDAA0021 , AA0566 , AA0021 , AA0566 , AA0021 , AA0566 , AA0021 , AA0566

PSI-MOD :  N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891 , N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891 , N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891 , N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891
B [auth L]FME Parent Component: MET

RESIDAA0021 , AA0566 , AA0021 , AA0566 , AA0021 , AA0566 , AA0021 , AA0566 , AA0021 , AA0566

PSI-MOD :  N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891 , N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891 , N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891 , N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891 , N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891