6G72

Mouse mitochondrial complex I in the deactive state

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 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:  

  • 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-com ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 3
A
115Mus musculusMutation(s): 0 
Gene Names: Mtnd3 (mt-Nd3, Nd3)
EC: 7.1.1.2
Find proteins for P03899 (Mus musculus)
Go to UniProtKB:  P03899
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
B
224Mus musculusMutation(s): 0 
Gene Names: Ndufs7
EC: 1.6.99.3, 7.1.1.2
Find proteins for Q9DC70 (Mus musculus)
Go to UniProtKB:  Q9DC70
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
C
263Mus musculusMutation(s): 0 
Gene Names: Ndufs3
EC: 1.6.99.3, 7.1.1.2
Find proteins for Q9DCT2 (Mus musculus)
Go to UniProtKB:  Q9DCT2
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
D
463Mus musculusMutation(s): 0 
Gene Names: Ndufs2
EC: 1.6.99.3, 7.1.1.2
Find proteins for Q91WD5 (Mus musculus)
Go to UniProtKB:  Q91WD5
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
E
248Mus musculusMutation(s): 0 
Gene Names: Ndufv2
EC: 1.6.99.3, 7.1.1.2
Find proteins for Q9D6J6 (Mus musculus)
Go to UniProtKB:  Q9D6J6
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
F
464Mus musculusMutation(s): 0 
Gene Names: Ndufv1
EC: 1.6.99.3, 7.1.1.2
Find proteins for Q91YT0 (Mus musculus)
Go to UniProtKB:  Q91YT0
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
G
727Mus musculusMutation(s): 0 
Gene Names: Ndufs1
EC: 1.6.99.3, 7.1.1.2
Find proteins for Q91VD9 (Mus musculus)
Go to UniProtKB:  Q91VD9
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 1
H
318Mus musculusMutation(s): 0 
Gene Names: Mtnd1 (mt-Nd1, Nd1)
EC: 7.1.1.2
Find proteins for P03888 (Mus musculus)
Go to UniProtKB:  P03888
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
I
212Mus musculusMutation(s): 0 
Gene Names: Ndufs8
EC: 1.6.99.3, 7.1.1.2
Find proteins for Q8K3J1 (Mus musculus)
Go to UniProtKB:  Q8K3J1
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 6
J
172Mus musculusMutation(s): 0 
Gene Names: Mtnd6 (mt-Nd6, Nd6)
EC: 7.1.1.2
Find proteins for P03925 (Mus musculus)
Go to UniProtKB:  P03925
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 4L
K
98Mus musculusMutation(s): 0 
Gene Names: Mtnd4l (mt-Nd4l, Nd4l)
EC: 7.1.1.2
Find proteins for P03903 (Mus musculus)
Go to UniProtKB:  P03903
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 5
L
607Mus musculusMutation(s): 0 
Gene Names: Mtnd5 (mt-Nd5, Nd5)
EC: 7.1.1.2
Find proteins for P03921 (Mus musculus)
Go to UniProtKB:  P03921
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 4
M
459Mus musculusMutation(s): 0 
Gene Names: Mtnd4 (mt-Nd4, Nd4)
EC: 7.1.1.2
Find proteins for P03911 (Mus musculus)
Go to UniProtKB:  P03911
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 2
N
345Mus musculusMutation(s): 0 
Gene Names: Mtnd2 (mt-Nd2, Nd2)
EC: 7.1.1.2
Find proteins for P03893 (Mus musculus)
Go to UniProtKB:  P03893
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
O
355Mus musculusMutation(s): 0 
Gene Names: Ndufa10
Find proteins for Q99LC3 (Mus musculus)
Go to UniProtKB:  Q99LC3
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
P
377Mus musculusMutation(s): 0 
Gene Names: Ndufa9
Find proteins for Q9DC69 (Mus musculus)
Go to UniProtKB:  Q9DC69
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
Q
175Mus musculusMutation(s): 0 
Gene Names: Ndufs4
Find proteins for Q9CXZ1 (Mus musculus)
Go to UniProtKB:  Q9CXZ1
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
R
116Mus musculusMutation(s): 0 
Gene Names: Ndufs6 (Ip13)
Find proteins for P52503 (Mus musculus)
Go to UniProtKB:  P52503
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
S
99Mus musculusMutation(s): 0 
Gene Names: Ndufa2
Find proteins for Q9CQ75 (Mus musculus)
Go to UniProtKB:  Q9CQ75
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Acyl carrier protein, mitochondrial
T, U
156Mus musculusMutation(s): 0 
Gene Names: Ndufab1
Find proteins for Q9CR21 (Mus musculus)
Go to UniProtKB:  Q9CR21
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
V
116Mus musculusMutation(s): 0 
Gene Names: Ndufa5
Find proteins for Q9CPP6 (Mus musculus)
Go to UniProtKB:  Q9CPP6
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
W
131Mus musculusMutation(s): 0 
Gene Names: Ndufa6
Find proteins for Q9CQZ5 (Mus musculus)
Go to UniProtKB:  Q9CQZ5
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
X
172Mus musculusMutation(s): 0 
Gene Names: Ndufa8
Find proteins for Q9DCJ5 (Mus musculus)
Go to UniProtKB:  Q9DCJ5
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
Y
143Mus musculusMutation(s): 0 
Gene Names: Ndufa11
Find proteins for G5E814 (Mus musculus)
Go to UniProtKB:  G5E814
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
Z
144Mus musculusMutation(s): 0 
Gene Names: Ndufa13 (Grim19)
Find proteins for Q9ERS2 (Mus musculus)
Go to UniProtKB:  Q9ERS2
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
a
70Mus musculusMutation(s): 0 
Gene Names: Ndufa1
Find proteins for O35683 (Mus musculus)
Go to UniProtKB:  O35683
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
b
84Mus musculusMutation(s): 0 
Gene Names: Ndufa3
Find proteins for Q9CQ91 (Mus musculus)
Go to UniProtKB:  Q9CQ91
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
c
76Mus musculusMutation(s): 0 
Gene Names: Ndufc1
Find proteins for Q9CQY9 (Mus musculus)
Go to UniProtKB:  Q9CQY9
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 subunit C2
d
120Mus musculusMutation(s): 0 
Gene Names: Ndufc2
Find proteins for Q9CQ54 (Mus musculus)
Go to UniProtKB:  Q9CQ54
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
e
106Mus musculusMutation(s): 0 
Gene Names: Ndufs5
Find proteins for Q99LY9 (Mus musculus)
Go to UniProtKB:  Q99LY9
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
f
57Mus musculusMutation(s): 0 
Gene Names: Ndufb1
Find proteins for P0DN34 (Mus musculus)
Go to UniProtKB:  P0DN34
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
g
151Mus musculusMutation(s): 0 
Gene Names: Ndufb11 (Np15)
Find proteins for O09111 (Mus musculus)
Go to UniProtKB:  O09111
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
h
189Mus musculusMutation(s): 0 
Gene Names: Ndufb5
Find proteins for Q9CQH3 (Mus musculus)
Go to UniProtKB:  Q9CQH3
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
i
128Mus musculusMutation(s): 0 
Gene Names: Ndufb6 (Gm137)
Find proteins for Q3UIU2 (Mus musculus)
Go to UniProtKB:  Q3UIU2
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial
j
105Mus musculusMutation(s): 0 
Gene Names: Ndufb2
Find proteins for Q9CPU2 (Mus musculus)
Go to UniProtKB:  Q9CPU2
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
k
104Mus musculusMutation(s): 0 
Gene Names: Ndufb3
Find proteins for Q9CQZ6 (Mus musculus)
Go to UniProtKB:  Q9CQZ6
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
l
186Mus musculusMutation(s): 0 
Gene Names: Ndufb8
Find proteins for Q9D6J5 (Mus musculus)
Go to UniProtKB:  Q9D6J5
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
m
129Mus musculusMutation(s): 0 
Gene Names: Ndufb4
Find proteins for Q9CQC7 (Mus musculus)
Go to UniProtKB:  Q9CQC7
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
n
179Mus musculusMutation(s): 0 
Gene Names: Ndufb9
Find proteins for Q9CQJ8 (Mus musculus)
Go to UniProtKB:  Q9CQJ8
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
o
137Mus musculusMutation(s): 0 
Gene Names: Ndufb7
Find proteins for Q9CR61 (Mus musculus)
Go to UniProtKB:  Q9CR61
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
p
176Mus musculusMutation(s): 0 
Gene Names: Ndufb10
Find proteins for Q9DCS9 (Mus musculus)
Go to UniProtKB:  Q9DCS9
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
q
145Mus musculusMutation(s): 0 
Gene Names: Ndufa12
Find proteins for Q7TMF3 (Mus musculus)
Go to UniProtKB:  Q7TMF3
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
r
113Mus musculusMutation(s): 0 
Gene Names: Ndufa7
Find proteins for Q9Z1P6 (Mus musculus)
Go to UniProtKB:  Q9Z1P6
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
s
104Mus musculusMutation(s): 0 
Gene Names: Ndufv3
Find proteins for Q8BK30 (Mus musculus)
Go to UniProtKB:  Q8BK30
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4
Download SDF File 
Download CCD File 
B, F, G, I
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN
Download SDF File 
Download CCD File 
R
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FMN
Query on FMN
Download SDF File 
Download CCD File 
F
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
ADP
Query on ADP
Download SDF File 
Download CCD File 
O
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
EHZ
Query on EHZ
Download SDF File 
Download CCD File 
T, 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
FES
Query on FES
Download SDF File 
Download CCD File 
E, G
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
NDP
Query on NDP
Download SDF File 
Download CCD File 
P
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
AME
Query on AME
q
NON-POLYMERC7 H13 N O3 S

--

AYA
Query on AYA
b, r
L-PEPTIDE LINKINGC5 H9 N O3ALA
FME
Query on FME
A, H, J, K, L, M, N
L-PEPTIDE LINKINGC6 H11 N O3 SMET
SAC
Query on SAC
i
L-PEPTIDE LINKINGC5 H9 N O4SER
2MR
Query on 2MR
D
L-PEPTIDE LINKINGC8 H18 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

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 

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