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)
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)
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)
O [auth e]Ndufs5e8befe1 A: alpha bundlesX: cytochrome bc1 complex 11 kDa protein-likeH: CHCH domain (From Topology)T: CHCH domainF: Ndufs5ECOD (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)
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)
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)
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)
H [auth O]Fer2e8befO1 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Ubiquitin-likeF: Fer2ECOD (1.6)
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)

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
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
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
B [auth H]PF00146NADH dehydrogenase (NADHdh)NADH dehydrogenase- Family
C [auth J]PF00499NADH-ubiquinone/plastoquinone oxidoreductase chain 6 (Oxidored_q3)NADH-ubiquinone/plastoquinone oxidoreductase chain 6- Family
D [auth K]PF00420NADH-ubiquinone/plastoquinone oxidoreductase chain 4L (Oxidored_q2)NADH-ubiquinone/plastoquinone oxidoreductase chain 4L- Family
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 ...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 ...Domain
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 ...Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

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

InterPro: Protein Family Classification InterPro Database Homepage

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

Protein Modification Annotation

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