7W4F

Active state CI from Q1-NADH dataset, Subclass 4

  • Classification: ELECTRON TRANSPORT
  • Organism(s): Sus scrofa
  • Mutation(s): No 
  • Membrane Protein: Yes  PDBTM

  • Deposited: 2021-11-27 Released: 2023-01-25 
  • Deposition Author(s): Gu, J., Yang, M.
  • Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The coupling mechanism of mammalian mitochondrial complex I.

Gu, J.Liu, T.Guo, R.Zhang, L.Yang, M.

(2022) Nat Struct Mol Biol 29: 172-182

  • DOI: https://doi.org/10.1038/s41594-022-00722-w
  • Primary Citation of Related Structures:  
    7V2C, 7V2D, 7V2E, 7V2F, 7V2H, 7V2K, 7V2R, 7V30, 7V31, 7V32, 7V33, 7V3M, 7VB7, 7VBL, 7VBN, 7VBP, 7VBZ, 7VC0, 7VWJ, 7VWL, 7VXP, 7VXS, 7VXU, 7VY1, 7VY8, 7VY9, 7VYA, 7VYE, 7VYF, 7VYG, 7VYH, 7VYI, 7VYN, 7VYS, 7VZ1, 7VZ8, 7VZV, 7VZW, 7W00, 7W0H, 7W0R, 7W0Y, 7W1O, 7W1P, 7W1T, 7W1U, 7W1V, 7W1Z, 7W20, 7W2K

  • PubMed Abstract: 

    Mammalian respiratory complex I (CI) is a 45-subunit, redox-driven proton pump that generates an electrochemical gradient across the mitochondrial inner membrane to power ATP synthesis in mitochondria. In the present study, we report cryo-electron microscopy structures of CI from Sus scrofa in six treatment conditions at a resolution of 2.4-3.5 Å, in which CI structures of each condition can be classified into two biochemical classes (active or deactive), with a notably higher proportion of active CI particles. These structures illuminate how hydrophobic ubiquinone-10 (Q10) with its long isoprenoid tail is bound and reduced in a narrow Q chamber comprising four different Q10-binding sites. Structural comparisons of active CI structures from our decylubiquinone-NADH and rotenone-NADH datasets reveal that Q10 reduction at site 1 is not coupled to proton pumping in the membrane arm, which might instead be coupled to Q10 oxidation at site 2. Our data overturn the widely accepted previous proposal about the coupling mechanism of CI.


  • Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial433Sus scrofaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for A0A4X1SZP7 (Sus scrofa)
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UniProt GroupA0A4X1SZP7
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial176Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287BDC0 (Sus scrofa)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial156Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1TL60 (Sus scrofa)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6D [auth E]115Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2E [auth F]86Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier proteinF [auth G],
V [auth X]
88Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I subunit B13G [auth H]112Sus scrofaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-B14.5aH [auth I]112Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A8W4F7N8 (Sus scrofa)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase ubiquinone 1 alpha subcomplex subunit 9, mitochondrialI [auth J]342Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-9kDJ [auth K]43Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for I3LRR4 (Sus scrofa)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialK [auth L]125Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for G8IFA6 (Sus scrofa)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialL [auth M]690Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1V1H9 (Sus scrofa)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12M [auth N]144Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialN [auth O]217Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287BG40 (Sus scrofa)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-30kDO [auth P]208Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZNN4 (Sus scrofa)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-49kDP [auth Q]430Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F1S1A8 (Sus scrofa)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1Q [auth S]70Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for K7GR43 (Sus scrofa)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialR [auth T]96Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F1S031 (Sus scrofa)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3S [auth U]83Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A4X1VQ42 (Sus scrofa)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11T [auth V]140Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-B16.6U [auth W]142Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A8D1NRT6 (Sus scrofa)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-AGGGW [auth Y]70Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A5G2QW32 (Sus scrofa)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-B12X [auth Z]84Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A4X1VD84 (Sus scrofa)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-SGDHY [auth a]140Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-B17Z [auth b]126Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A480KM09 (Sus scrofa)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialAA [auth c]156Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10BA [auth d]175Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for A0A8D0R7A9 (Sus scrofa)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialCA [auth e]107Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for A0A8D1EYI7 (Sus scrofa)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialDA [auth f]49Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2EA [auth g]122Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A480JRW3 (Sus scrofa)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5FA [auth h]105Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2GA [auth i]347Sus scrofaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3HA [auth j]115Sus scrofaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LIA [auth k]98Sus scrofaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P56632 (Sus scrofa)
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5JA [auth l]606Sus scrofaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q9TDR1 (Sus scrofa)
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6KA [auth m]175Sus scrofaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for O79882 (Sus scrofa)
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1LA [auth n]56Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D2CGH8 (Sus scrofa)
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4MA [auth o]128Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A4X1T6M0 (Sus scrofa)
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9NA [auth p]178Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for K7GSE5 (Sus scrofa)
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4OA [auth r]459Sus scrofaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for O79881 (Sus scrofa)
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1PA [auth s]318Sus scrofaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for O79874 (Sus scrofa)
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Go to UniProtKB:  O79874
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO79874
Sequence Annotations
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8QA [auth u]171Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SLR1 (Sus scrofa)
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UniProt GroupF1SLR1
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-B18RA [auth v]124Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F1SCH1 (Sus scrofa)
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UniProt GroupF1SCH1
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialSA [auth w]320Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SIS9 (Sus scrofa)
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UniProt GroupF1SIS9
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Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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AC [auth k]
CC [auth l]
DC [auth l]
EB [auth I]
GC [auth o]
AC [auth k],
CC [auth l],
DC [auth l],
EB [auth I],
GC [auth o],
JC [auth s],
LC [auth u],
PB [auth V],
SB [auth a],
WB [auth g]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
UQ (Subject of Investigation/LOI)
Query on UQ

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GB [auth J],
KC [auth s]
Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer
C59 H90 O4
ACTIUHUUMQJHFO-RECDIHICSA-N
PLX (Subject of Investigation/LOI)
Query on PLX

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CB [auth C]
HB [auth J]
TB [auth a]
UB [auth e]
VB [auth g]
CB [auth C],
HB [auth J],
TB [auth a],
UB [auth e],
VB [auth g],
ZB [auth j]
(9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL
C42 H89 N O8 P
YVNJQRQLQPWVSQ-IWSHAHEXSA-O
NDP (Subject of Investigation/LOI)
Query on NDP

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FB [auth J]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
PEE (Subject of Investigation/LOI)
Query on PEE

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BB [auth C]
BC [auth l]
EC [auth l]
FC [auth l]
HC [auth r]
BB [auth C],
BC [auth l],
EC [auth l],
FC [auth l],
HC [auth r],
IC [auth s],
QB [auth W],
XB [auth i],
YA [auth B],
YB [auth j]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
NAI (Subject of Investigation/LOI)
Query on NAI

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VA [auth A]1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
8Q1 (Subject of Investigation/LOI)
Query on 8Q1

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DB [auth G],
RB [auth X]
S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
C23 H45 N2 O8 P S
MVHUOSAYFQKAMT-NRFANRHFSA-N
FMN (Subject of Investigation/LOI)
Query on FMN

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UA [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

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MC [auth w]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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AB [auth C]
IB [auth M]
JB [auth M]
TA [auth A]
WA [auth B]
AB [auth C],
IB [auth M],
JB [auth M],
TA [auth A],
WA [auth B],
XA [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
UQ1 (Subject of Investigation/LOI)
Query on UQ1

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NB [auth Q],
ZA [auth C]
UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

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KB [auth M],
MB [auth O]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

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OB [auth T]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

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LB [auth M]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
2MR
Query on 2MR
P [auth Q]L-PEPTIDE LINKINGC8 H18 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2017YFA0504600 and 2016YFA0501100
National Natural Science Foundation of China (NSFC)China31625008
National Natural Science Foundation of China (NSFC)China32030056, 21532004 and 31570733 and 31800620

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-06-28
    Changes: Database references