6ZTQ

Cryo-EM structure of respiratory complex I from Mus musculus inhibited by piericidin A at 3.0 A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 8OLT


Literature

Structure of inhibitor-bound mammalian complex I.

Bridges, H.R.Fedor, J.G.Blaza, J.N.Di Luca, A.Jussupow, A.Jarman, O.D.Wright, J.J.Agip, A.A.Gamiz-Hernandez, A.P.Roessler, M.M.Kaila, V.R.I.Hirst, J.

(2020) Nat Commun 11: 5261-5261

  • DOI: https://doi.org/10.1038/s41467-020-18950-3
  • Primary Citation of Related Structures:  
    6ZR2, 6ZTQ

  • PubMed Abstract: 

    Respiratory complex I (NADH:ubiquinone oxidoreductase) captures the free energy from oxidising NADH and reducing ubiquinone to drive protons across the mitochondrial inner membrane and power oxidative phosphorylation. Recent cryo-EM analyses have produced near-complete models of the mammalian complex, but leave the molecular principles of its long-range energy coupling mechanism open to debate. Here, we describe the 3.0-Å resolution cryo-EM structure of complex I from mouse heart mitochondria with a substrate-like inhibitor, piericidin A, bound in the ubiquinone-binding active site. We combine our structural analyses with both functional and computational studies to demonstrate competitive inhibitor binding poses and provide evidence that two inhibitor molecules bind end-to-end in the long substrate binding channel. Our findings reveal information about the mechanisms of inhibition and substrate reduction that are central for understanding the principles of energy transduction in mammalian complex I.


  • Organizational Affiliation

    The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3115Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial224Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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IMPC:  MGI:1922656
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial263Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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IMPC:  MGI:1915599
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial463Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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IMPC:  MGI:2385112
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial248Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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IMPC:  MGI:1920150
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial464Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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IMPC:  MGI:107851
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial727Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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IMPC:  MGI:2443241
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1318Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Find proteins for P03888 (Mus musculus)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial212Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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IMPC:  MGI:2385079
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6172Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Find proteins for P03925 (Mus musculus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4L98Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5607Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4459Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2345Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial355Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1914523
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial377Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1913358
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial175Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9CXZ1 (Mus musculus)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial116Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:107932
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 299Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9CQ75 (Mus musculus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrial
T, U
156Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9CR21 (Mus musculus)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5116Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9CPP6 (Mus musculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6131Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1914380
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8172Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1915625
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
MCG5603143Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1917125
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13144Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1AA [auth a]70Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3BA [auth b]84Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialCA [auth c]76Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2DA [auth d]120Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5EA [auth e]106Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1890889
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1FA [auth f]57Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialGA [auth g]151Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialHA [auth h]189Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1913296
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6IA [auth i]128Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrialJA [auth j]105Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3KA [auth k]104Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialLA [auth l]186Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1914514
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4MA [auth m]129Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9NA [auth n]179Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1913468
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7OA [auth o]137Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10PA [auth p]176Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12QA [auth q]145Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q7TMF3 (Mus musculus)
Explore Q7TMF3 
Go to UniProtKB:  Q7TMF3
Entity Groups  
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UniProt GroupQ7TMF3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7RA [auth r]113Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Z1P6 (Mus musculus)
Explore Q9Z1P6 
Go to UniProtKB:  Q9Z1P6
IMPC:  MGI:1913666
Entity Groups  
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UniProt GroupQ9Z1P6
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  • Reference Sequence
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrialSA [auth s]104Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8BK30 (Mus musculus)
Explore Q8BK30 
Go to UniProtKB:  Q8BK30
IMPC:  MGI:1890894
Entity Groups  
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UniProt GroupQ8BK30
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  • Reference Sequence
Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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BC [auth q]
JB [auth L]
MB [auth N]
NB [auth N]
VB [auth d]
BC [auth q],
JB [auth L],
MB [auth N],
NB [auth N],
VB [auth d],
WB [auth d],
XB [auth h]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PC1
Query on PC1

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HB [auth J],
UA [auth B],
UB [auth Z],
VA [auth B]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE
Query on 3PE

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AC [auth l]
EB [auth H]
IB [auth K]
KB [auth L]
LB [auth M]
AC [auth l],
EB [auth H],
IB [auth K],
KB [auth L],
LB [auth M],
TB [auth Y],
XA [auth D],
YB [auth h],
ZB [auth i]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP
Query on NDP

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PB [auth P]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
EHZ
Query on EHZ

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RB [auth T],
SB [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
ATP
Query on ATP

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OB [auth O]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
FMN
Query on FMN

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

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WA [auth D]Piericidin A
C25 H37 N O4
BBLGCDSLCDDALX-LKGBESRRSA-N
SF4
Query on SF4

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AB [auth F]
BB [auth G]
CB [auth G]
FB [auth I]
GB [auth I]
AB [auth F],
BB [auth G],
CB [auth G],
FB [auth I],
GB [auth I],
TA [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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DB [auth G],
YA [auth E]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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QB [auth R]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  4 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A
L-PEPTIDE LINKINGC6 H11 N O3 SMET
2MR
Query on 2MR
D
L-PEPTIDE LINKINGC8 H18 N4 O2ARG
SAC
Query on SAC
IA [auth i]L-PEPTIDE LINKINGC5 H9 N O4SER
AYA
Query on AYA
RA [auth r]L-PEPTIDE LINKINGC5 H9 N O3ALA
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.16

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_U105663141
Medical Research Council (MRC, United Kingdom)United KingdomMC_UU_00015/2
Wellcome TrustUnited Kingdom108466/Z/15/Z

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release
  • Version 1.1: 2020-10-28
    Changes: Database references