7O6Y

Cryo-EM structure of respiratory complex I under turnover


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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

High-resolution structure and dynamics of mitochondrial complex I-Insights into the proton pumping mechanism.

Parey, K.Lasham, J.Mills, D.J.Djurabekova, A.Haapanen, O.Yoga, E.G.Xie, H.Kuhlbrandt, W.Sharma, V.Vonck, J.Zickermann, V.

(2021) Sci Adv 7: eabj3221-eabj3221

  • DOI: https://doi.org/10.1126/sciadv.abj3221
  • Primary Citation of Related Structures:  
    7O6Y, 7O71

  • PubMed Abstract: 

    Mitochondrial NADH:ubiquinone oxidoreductase (complex I) is a 1-MDa membrane protein complex with a central role in energy metabolism. Redox-driven proton translocation by complex I contributes substantially to the proton motive force that drives ATP synthase. Several structures of complex I from bacteria and mitochondria have been determined, but its catalytic mechanism has remained controversial. We here present the cryo-EM structure of complex I from Yarrowia lipolytica at 2.1-Å resolution, which reveals the positions of more than 1600 protein-bound water molecules, of which ~100 are located in putative proton translocation pathways. Another structure of the same complex under steady-state activity conditions at 3.4-Å resolution indicates conformational transitions that we associate with proton injection into the central hydrophilic axis. By combining high-resolution structural data with site-directed mutagenesis and large-scale molecular dynamic simulations, we define details of the proton translocation pathways and offer insights into the redox-coupled proton pumping mechanism of complex I.


  • Organizational Affiliation

    Department of Physics, University of Helsinki, 00014 Helsinki, Finland.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)728Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial488Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NUCM protein466Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I)D [auth G]281Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)E [auth H]243Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)F [auth I]229Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)G [auth K]210Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LH [auth L]89Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)I [auth S]249Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)J [auth j]93Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1K [auth 1]341Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 2L [auth 2]469Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3M [auth 3]128Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I)N [auth 4]486Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I)O [auth 5]655Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6P [auth 6]185Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)Q [auth g]78Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)R [auth D]87Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I)S [auth E]375Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)T [auth F]144Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)U [auth J]198Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I)V [auth M]136Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I)W [auth O]109Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)X [auth P]124Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I)Y [auth Q]132Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)Z [auth R]109Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)AA [auth U]172Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)BA [auth W]123Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)CA [auth X]169Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)DA [auth Y]161Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)EA [auth Z]182Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)FA [auth a]149Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)GA [auth b]74Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)HA [auth c]60Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)IA [auth d]92Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)JA [auth e]67Yarrowia lipolyticaMutation(s): 0 
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Find proteins for A0A1D8NFX6 (Yarrowia lipolytica)
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)KA [auth f]87Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)LA [auth h]138Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q6CG53 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Go to UniProtKB:  Q6CG53
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UniProt GroupQ6CG53
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)MA [auth i]90Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1H6Q311 (Yarrowia lipolytica)
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Go to UniProtKB:  A0A1H6Q311
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UniProt GroupA0A1H6Q311
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I)NA [auth n]139Yarrowia lipolyticaMutation(s): 0 
UniProt
Find proteins for Q6C1R9 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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UniProt GroupQ6C1R9
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)OA [auth 8]99Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B5FVG1 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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UniProt GroupB5FVG1
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)PA [auth 9]89Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B5RSL7 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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UniProt GroupB5RSL7
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Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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FC [auth W]
GC [auth X]
HC [auth Z]
MC [auth n]
UB [auth g]
FC [auth W],
GC [auth X],
HC [auth Z],
MC [auth n],
UB [auth g],
YB [auth E]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
LMN
Query on LMN

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AC [auth J],
IC [auth a]
Lauryl Maltose Neopentyl Glycol
C47 H88 O22
MADJBYLAYPCCOO-XYPZXBMFSA-N
T7X
Query on T7X

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IB [auth 2],
JC [auth b],
KB [auth 3]
Phosphatidylinositol
C47 H83 O13 P
KRTOMQDUKGRFDJ-TWUHCGEESA-N
UQ9
Query on UQ9

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WA [auth C]Ubiquinone-9
C54 H82 O4
UUGXJSBPSRROMU-YJKFELPISA-N
CPL
Query on CPL

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HB [auth 2]1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C42 H80 N O8 P
JLPULHDHAOZNQI-ZTIMHPMXSA-N
3PE
Query on 3PE

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EB [auth 1]
FB [auth 1]
JB [auth 2]
KC [auth b]
LB [auth 4]
EB [auth 1],
FB [auth 1],
JB [auth 2],
KC [auth b],
LB [auth 4],
MB [auth 4],
NB [auth 4],
PB [auth 5],
QB [auth 5],
RB [auth 5],
SB [auth 6],
TB [auth 6],
VB [auth g],
XB [auth E],
YA [auth I],
ZB [auth J]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP
Query on NDP

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WB [auth E]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
NAI
Query on NAI

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VA [auth B]1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
PLC
Query on PLC

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CB [auth K]
DB [auth 1]
EC [auth W]
GB [auth 1]
LC [auth i]
CB [auth K],
DB [auth 1],
EC [auth W],
GB [auth 1],
LC [auth i],
OB [auth 4]
DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
ZMP
Query on ZMP

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CC [auth O],
DC [auth R]
S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
C25 H49 N2 O8 P S
HDTINWYIVVMRIN-HSZRJFAPSA-N
FMN
Query on FMN

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UA [auth B]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

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AB [auth I]
BB [auth K]
QA [auth A]
RA [auth A]
TA [auth B]
AB [auth I],
BB [auth K],
QA [auth A],
RA [auth A],
TA [auth B],
ZA [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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SA [auth A],
XA [auth H]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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BC [auth M]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
2MR
Query on 2MR
C
L-PEPTIDE LINKINGC8 H18 N4 O2ARG
FME
Query on FME
H [auth L]L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyZI 552/4-2

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-10
    Type: Initial release
  • Version 1.1: 2021-12-01
    Changes: Database references