6G72

Mouse mitochondrial complex I in the deactive state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Cryo-EM structures of complex I from mouse heart mitochondria in two biochemically defined states.

Agip, A.A.Blaza, J.N.Bridges, H.R.Viscomi, C.Rawson, S.Muench, S.P.Hirst, J.

(2018) Nat Struct Mol Biol 25: 548-556

  • DOI: 10.1038/s41594-018-0073-1
  • Primary Citation of Related Structures:  
    6G2J, 6G72

  • PubMed Abstract: 
  • Complex I (NADH:ubiquinone oxidoreductase) uses the reducing potential of NADH to drive protons across the energy-transducing inner membrane and power oxidative phosphorylation in mammalian mitochondria. Recent cryo-EM analyses have produced near-complete models of all 45 subunits in the bovine, ovine and porcine complexes and have identified two states relevant to complex I in ischemia-reperfusion injury ...

    Complex I (NADH:ubiquinone oxidoreductase) uses the reducing potential of NADH to drive protons across the energy-transducing inner membrane and power oxidative phosphorylation in mammalian mitochondria. Recent cryo-EM analyses have produced near-complete models of all 45 subunits in the bovine, ovine and porcine complexes and have identified two states relevant to complex I in ischemia-reperfusion injury. Here, we describe the 3.3-Å structure of complex I from mouse heart mitochondria, a biomedically relevant model system, in the 'active' state. We reveal a nucleotide bound in subunit NDUFA10, a nucleoside kinase homolog, and define mechanistically critical elements in the mammalian enzyme. By comparisons with a 3.9-Å structure of the 'deactive' state and with known bacterial structures, we identify differences in helical geometry in the membrane domain that occur upon activation or that alter the positions of catalytically important charged residues. Our results demonstrate the capability of cryo-EM analyses to challenge and develop mechanistic models for mammalian complex I.


    Organizational Affiliation

    The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK. jh@mrc-mbu.cam.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3A115Mus musculusMutation(s): 0 
Gene Names: Mtnd3mt-Nd3Nd3
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialB224Mus musculusMutation(s): 0 
Gene Names: Ndufs7
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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IMPC:  MGI:1922656
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrialC263Mus musculusMutation(s): 0 
Gene Names: Ndufs3
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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IMPC:  MGI:1915599
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialD463Mus musculusMutation(s): 0 
Gene Names: Ndufs2
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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IMPC:  MGI:2385112
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialE248Mus musculusMutation(s): 0 
Gene Names: Ndufv2
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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IMPC:  MGI:1920150
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialF464Mus musculusMutation(s): 0 
Gene Names: Ndufv1
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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IMPC:  MGI:107851
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialG727Mus musculusMutation(s): 0 
Gene Names: Ndufs1
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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IMPC:  MGI:2443241
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1H318Mus musculusMutation(s): 0 
Gene Names: Mtnd1mt-Nd1Nd1
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 9
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrialI212Mus musculusMutation(s): 0 
Gene Names: Ndufs8
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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IMPC:  MGI:2385079
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Entity ID: 10
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NADH-ubiquinone oxidoreductase chain 6J172Mus musculusMutation(s): 0 
Gene Names: Mtnd6mt-Nd6Nd6
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LK98Mus musculusMutation(s): 0 
Gene Names: Mtnd4lmt-Nd4lNd4l
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 12
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NADH-ubiquinone oxidoreductase chain 5L607Mus musculusMutation(s): 0 
Gene Names: Mtnd5mt-Nd5Nd5
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 13
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NADH-ubiquinone oxidoreductase chain 4M459Mus musculusMutation(s): 0 
Gene Names: Mtnd4mt-Nd4Nd4
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 14
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NADH-ubiquinone oxidoreductase chain 2N345Mus musculusMutation(s): 0 
Gene Names: Mtnd2mt-Nd2Nd2
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 15
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialO355Mus musculusMutation(s): 0 
Gene Names: Ndufa10
Membrane Entity: Yes 
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IMPC:  MGI:1914523
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Entity ID: 16
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrialP377Mus musculusMutation(s): 0 
Gene Names: Ndufa9
Membrane Entity: Yes 
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IMPC:  MGI:1913358
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Entity ID: 17
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialQ175Mus musculusMutation(s): 0 
Gene Names: Ndufs4
Membrane Entity: Yes 
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Entity ID: 18
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialR116Mus musculusMutation(s): 0 
Gene Names: Ndufs6Ip13
Membrane Entity: Yes 
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Entity ID: 19
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2S99Mus musculusMutation(s): 0 
Gene Names: Ndufa2
Membrane Entity: Yes 
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Entity ID: 20
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Acyl carrier protein, mitochondrialT, U156Mus musculusMutation(s): 0 
Gene Names: Ndufab1
Membrane Entity: Yes 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5V116Mus musculusMutation(s): 0 
Gene Names: Ndufa5
Membrane Entity: Yes 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6W131Mus musculusMutation(s): 0 
Gene Names: Ndufa6
Membrane Entity: Yes 
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IMPC:  MGI:1914380
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8X172Mus musculusMutation(s): 0 
Gene Names: Ndufa8
Membrane Entity: Yes 
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IMPC:  MGI:1915625
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11Y143Mus musculusMutation(s): 0 
Gene Names: Ndufa11
Membrane Entity: Yes 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13Z144Mus musculusMutation(s): 0 
Gene Names: Ndufa13Grim19
Membrane Entity: Yes 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1AA [auth a]70Mus musculusMutation(s): 0 
Gene Names: Ndufa1
Membrane Entity: Yes 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3BA [auth b]84Mus musculusMutation(s): 0 
Gene Names: Ndufa3
Membrane Entity: Yes 
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Entity ID: 28
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NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialCA [auth c]76Mus musculusMutation(s): 0 
Gene Names: Ndufc1
Membrane Entity: Yes 
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Entity ID: 29
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NADH dehydrogenase [ubiquinone] 1 subunit C2DA [auth d]120Mus musculusMutation(s): 0 
Gene Names: Ndufc2
Membrane Entity: Yes 
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IMPC:  MGI:1344370
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Entity ID: 30
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 5EA [auth e]106Mus musculusMutation(s): 0 
Gene Names: Ndufs5
Membrane Entity: Yes 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1FA [auth f]57Mus musculusMutation(s): 0 
Gene Names: Ndufb1
Membrane Entity: Yes 
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Entity ID: 32
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialGA [auth g]151Mus musculusMutation(s): 0 
Gene Names: Ndufb11Np15
Membrane Entity: Yes 
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Entity ID: 33
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialHA [auth h]189Mus musculusMutation(s): 0 
Gene Names: Ndufb5
Membrane Entity: Yes 
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Entity ID: 34
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6IA [auth i]128Mus musculusMutation(s): 0 
Gene Names: Ndufb6Gm137
Membrane Entity: Yes 
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Entity ID: 35
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrialJA [auth j]105Mus musculusMutation(s): 0 
Gene Names: Ndufb2
Membrane Entity: Yes 
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Entity ID: 36
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3KA [auth k]104Mus musculusMutation(s): 0 
Gene Names: Ndufb3
Membrane Entity: Yes 
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Entity ID: 37
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialLA [auth l]186Mus musculusMutation(s): 0 
Gene Names: Ndufb8
Membrane Entity: Yes 
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IMPC:  MGI:1914514
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Entity ID: 38
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4MA [auth m]129Mus musculusMutation(s): 0 
Gene Names: Ndufb4
Membrane Entity: Yes 
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Entity ID: 39
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9NA [auth n]179Mus musculusMutation(s): 0 
Gene Names: Ndufb9
Membrane Entity: Yes 
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IMPC:  MGI:1913468
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Entity ID: 40
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7OA [auth o]137Mus musculusMutation(s): 0 
Gene Names: Ndufb7
Membrane Entity: Yes 
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Entity ID: 41
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10PA [auth p]176Mus musculusMutation(s): 0 
Gene Names: Ndufb10
Membrane Entity: Yes 
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Entity ID: 42
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12QA [auth q]145Mus musculusMutation(s): 0 
Gene Names: Ndufa12
Membrane Entity: Yes 
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Entity ID: 43
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7RA [auth r]113Mus musculusMutation(s): 0 
Gene Names: Ndufa7
Membrane Entity: Yes 
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Entity ID: 44
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NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrialSA [auth s]104Mus musculusMutation(s): 0 
Gene Names: Ndufv3
Membrane Entity: Yes 
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Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP (Subject of Investigation/LOI)
Query on NDP

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DB [auth P]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
EHZ (Subject of Investigation/LOI)
Query on EHZ

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FB [auth T], GB [auth U]~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate
C25 H49 N2 O9 P S
JYSKQPQRUCZFIQ-REWPJTCUSA-N
 Ligand Interaction
FMN (Subject of Investigation/LOI)
Query on FMN

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

Download Ideal Coordinates CCD File 
CB [auth O]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
AB [auth I], BB [auth I], TA [auth B], WA [auth F], XA [auth G], YA [auth G]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
UA [auth E], ZA [auth G]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
EB [auth R]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
AL-PEPTIDE LINKINGC6 H11 N O3 SMET
2MR
Query on 2MR
DL-PEPTIDE LINKINGC8 H18 N4 O2ARG
AYA
Query on AYA
BA [auth b]L-PEPTIDE LINKINGC5 H9 N O3ALA
SAC
Query on SAC
IA [auth i]L-PEPTIDE LINKINGC5 H9 N O4SER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105663141
Medical Research Council (United Kingdom)United KingdomMC_UU_00015/2
Medical Research Council (United Kingdom)United KingdomMC_UU_00015/5

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-07-04
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-01
    Changes: Data collection, Database references
  • Version 1.3: 2018-10-03
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2019-12-11
    Changes: Other