8BEF | pdb_00008bef

Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI membrane core)


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
D [auth K]SCOP2B SuperfamilyNADH-quinone oxidoreductase, subunit 11-like 8101595 3002200 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
I [auth X]F_UNCLASSIFIEDe8befX1 A: few secondary structure elementsX: p8-MTCP1-related (From Topology)H: p8-MTCP1-related (From Topology)T: p8-MTCP1-relatedF: F_UNCLASSIFIEDECOD (1.6)
I [auth X]CHCHe8befX2 A: few secondary structure elementsX: p8-MTCP1-related (From Topology)H: p8-MTCP1-related (From Topology)T: p8-MTCP1-relatedF: CHCHECOD (1.6)
H [auth O]Fer2e8befO1 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Ubiquitin-likeF: Fer2ECOD (1.6)
G [auth N]Proton_antipo_Me8befN1 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)
D [auth K]Oxidored_q2e8befK1 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)
T [auth x]Hexapep_2_1e8befx1 A: beta duplicates or obligate multimersX: Single-stranded left-handed beta-helixH: Trimeric LpxA-like enzymes (From Topology)T: Trimeric LpxA-like enzymesF: Hexapep_2_1ECOD (1.6)
B [auth H]NADHdhe8befH1 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)
O [auth e]Ndufs5e8befe1 A: alpha bundlesX: cytochrome bc1 complex 11 kDa protein-likeH: CHCH domain (From Topology)T: CHCH domainF: Ndufs5ECOD (1.6)
L [auth a]MWFEe8befa1 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)
K [auth Z]GRIM-19e8befZ1 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)

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
I [auth X]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
G [auth N]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 M]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
D [auth K]PF00420NADH-ubiquinone/plastoquinone oxidoreductase chain 4L (Oxidored_q2)NADH-ubiquinone/plastoquinone oxidoreductase chain 4L- Family
C [auth J]PF00499NADH-ubiquinone/plastoquinone oxidoreductase chain 6 (Oxidored_q3)NADH-ubiquinone/plastoquinone oxidoreductase chain 6- Family
B [auth H]PF00146NADH dehydrogenase (NADHdh)NADH dehydrogenase- Family
J [auth Y]PF00132Bacterial transferase hexapeptide (six repeats) (Hexapep)Bacterial transferase hexapeptide (six repeats)- Repeat
J [auth Y]PF02466Tim17/Tim22/Tim23/Pmp24 family (Tim17)Tim17/Tim22/Tim23/Pmp24 family- Family
PF15879NADH-ubiquinone oxidoreductase MWFE subunit (MWFE)NADH-ubiquinone oxidoreductase MWFE subunit- Family
PF00507NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 (Oxidored_q4)NADH-ubiquinone/plastoquinone oxidoreductase, chain 3- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
I [auth X]NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B-
H [auth O]AT3G07480.1
G [auth N]NADH-ubiquinone oxidoreductase chain 2
F [auth M]NADH-ubiquinone oxidoreductase chain 4
E [auth L]NADH-ubiquinone oxidoreductase chain 5
D [auth K]NADH-ubiquinone oxidoreductase chain 4L
C [auth J]NADH-ubiquinone oxidoreductase chain 6 -
V [auth z]Gamma carbonic anhydrase 1, mitochondrial
U [auth y]Gamma carbonic anhydrase 2, mitochondrial
T [auth x]Gamma carbonic anhydrase-like 2, mitochondrial
B [auth H]NADH-ubiquinone oxidoreductase chain 1
S [auth v]Uncharacterized protein At2g27730, mitochondrial
R [auth u]Uncharacterized protein At1g67785- -
Q [auth i]P1-
P [auth f]At4g16450-
O [auth e]NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B- -
N [auth d]Excitatory amino acid transporter- -
M [auth b]At2g46540/F11C10.23- -
L [auth a]NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1- -
K [auth Z]NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A-
J [auth Y]Outer envelope pore protein 16-3, chloroplastic/mitochondrial
NADH-ubiquinone oxidoreductase chain 3 -

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
I [auth X]IPR010625CHCHDomain
I [auth X]IPR016680NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8Family
H [auth O]IPR001055Adrenodoxin-likeFamily
H [auth O]IPR0360102Fe-2S ferredoxin-like superfamilyHomologous Superfamily
H [auth O]IPR012675Beta-grasp domain superfamilyHomologous Superfamily
G [auth N]IPR010096NAD(P)H-quinone oxidoreductase, subunit N/subunit 2Family
G [auth N]IPR001750NADH:quinone oxidoreductase/Mrp antiporter, transmembrane domainDomain
F [auth M]IPR003918NADH:ubiquinone oxidoreductaseFamily
F [auth M]IPR010227NADH-quinone oxidoreductase, chain M/4Family
F [auth M]IPR001750NADH:quinone oxidoreductase/Mrp antiporter, transmembrane domainDomain
E [auth L]IPR003945NADH-quinone oxidoreductase, chain 5-likeFamily
E [auth L]IPR010934NADH dehydrogenase subunit 5, C-terminalDomain
E [auth L]IPR001516NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminalDomain
E [auth L]IPR001750NADH:quinone oxidoreductase/Mrp antiporter, transmembrane domainDomain
E [auth L]IPR018393NADH-plastoquinone oxidoreductase, chain 5 subgroupFamily
D [auth K]IPR001133NADH-ubiquinone oxidoreductase chain 4L/KFamily
D [auth K]IPR039428NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-likeFamily
C [auth J]IPR042106NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJHomologous Superfamily
C [auth J]IPR001457NADH:ubiquinone/plastoquinone oxidoreductase, chain 6Family
V [auth z]IPR047324Gamma carbonic anhydrase-likeFamily
V [auth z]IPR011004Trimeric LpxA-like superfamilyHomologous Superfamily
V [auth z]IPR050484Transferase Hexapeptide/Carbonic AnhydraseFamily
U [auth y]IPR047324Gamma carbonic anhydrase-likeFamily
U [auth y]IPR001451Hexapeptide repeatRepeat
U [auth y]IPR011004Trimeric LpxA-like superfamilyHomologous Superfamily
U [auth y]IPR050484Transferase Hexapeptide/Carbonic AnhydraseFamily
T [auth x]IPR047324Gamma carbonic anhydrase-likeFamily
T [auth x]IPR011004Trimeric LpxA-like superfamilyHomologous Superfamily
T [auth x]IPR050484Transferase Hexapeptide/Carbonic AnhydraseFamily
B [auth H]IPR001694NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit HFamily
B [auth H]IPR018086NADH:ubiquinone oxidoreductase, subunit 1, conserved siteConserved Site
S [auth v]IPR045284At2g27730-likeFamily
Q [auth i]IPR035204NADH-ubiquinone oxidoreductase 11kDa subunitFamily
P [auth f]IPR019721NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminalDomain
P [auth f]IPR053229NADH-ubiquinone oxidoreductase subunitFamily
O [auth e]IPR019342NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5Family
L [auth a]IPR017384NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1Family
K [auth Z]IPR009346GRIM-19Family
J [auth Y]IPR039175Mitochondrial import inner membrane translocase subunit TIM22Family
IPR023043NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastidFamily
IPR000440NADH:ubiquinone/plastoquinone oxidoreductase, chain 3Family
IPR038430NADH:ubiquinone oxidoreductase, subunit 3 superfamilyHomologous Superfamily

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
D [auth K]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
P [auth f]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
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