7P69

Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 6, Resting state


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


Literature

A universal coupling mechanism of respiratory complex I.

Kravchuk, V.Petrova, O.Kampjut, D.Wojciechowska-Bason, A.Breese, Z.Sazanov, L.

(2022) Nature 

  • DOI: 10.1038/s41586-022-05199-7
  • Primary Citation of Related Structures:  
    7P61, 7P62, 7P63, 7P64, 7P69, 7P7C, 7P7E, 7P7J, 7P7K, 7P7L, 7P7M, 7Z7R, 7Z7S, 7Z7T, 7Z7V, 7Z80, 7Z83, 7Z84, 7ZC5, 7ZCI, 7ZD6, 7ZDH, 7ZDJ, 7ZDM, 7ZDP, 7ZEB

  • PubMed Abstract: 
  • Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria 1 . Complex I couples the transfer of two electrons from NADH to quinone and the translocation of four protons across the membrane 2 , but the coupling mechanism remains contentious ...

    Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria 1 . Complex I couples the transfer of two electrons from NADH to quinone and the translocation of four protons across the membrane 2 , but the coupling mechanism remains contentious. Here we present cryo-electron microscopy structures of Escherichia coli complex I (EcCI) in different redox states, including catalytic turnover. EcCI exists mostly in the open state, in which the quinone cavity is exposed to the cytosol, allowing access for water molecules, which enable quinone movements. Unlike the mammalian paralogues 3 , EcCI can convert to the closed state only during turnover, showing that closed and open states are genuine turnover intermediates. The open-to-closed transition results in the tightly engulfed quinone cavity being connected to the central axis of the membrane arm, a source of substrate protons. Consistently, the proportion of the closed state increases with increasing pH. We propose a detailed but straightforward and robust mechanism comprising a 'domino effect' series of proton transfers and electrostatic interactions: the forward wave ('dominoes stacking') primes the pump, and the reverse wave ('dominoes falling') results in the ejection of all pumped protons from the distal subunit NuoL. This mechanism explains why protons exit exclusively from the NuoL subunit and is supported by our mutagenesis data. We contend that this is a universal coupling mechanism of complex I and related enzymes.


    Organizational Affiliation

    Institute of Science and Technology Austria, Klosterneuburg, Austria. sazanov@ist.ac.at.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit FA [auth F]442Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: ECBD_1377
EC: 7.1.1
UniProt
Find proteins for A0A140N9Z7 (Escherichia coli (strain B / BL21-DE3))
Explore A0A140N9Z7 
Go to UniProtKB:  A0A140N9Z7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140N9Z7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase I subunit EB [auth E]156Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: ECBD_1376
UniProt
Find proteins for A0A140N9K4 (Escherichia coli (strain B / BL21-DE3))
Explore A0A140N9K4 
Go to UniProtKB:  A0A140N9K4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140N9K4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductaseC [auth G]905Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: ECBD_1378
EC: 7.1.1
UniProt
Find proteins for A0A140N9P3 (Escherichia coli (strain B / BL21-DE3))
Explore A0A140N9P3 
Go to UniProtKB:  A0A140N9P3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140N9P3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit C/DD [auth C]600Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: nuoCnuoCDnuoDECBD_1375
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A0A140N745 (Escherichia coli (strain B / BL21-DE3))
Explore A0A140N745 
Go to UniProtKB:  A0A140N745
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140N745
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit BE [auth B]220Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: nuoBECBD_1374
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A0A140N560 (Escherichia coli (strain B / BL21-DE3))
Explore A0A140N560 
Go to UniProtKB:  A0A140N560
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140N560
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit IF [auth I]145Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: nuoIECBD_1380
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A0A140N885 (Escherichia coli (strain B / BL21-DE3))
Explore A0A140N885 
Go to UniProtKB:  A0A140N885
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140N885
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit HG [auth H]325Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: nuoHECBD_1379
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A0A140N5X6 (Escherichia coli (strain B / BL21-DE3))
Explore A0A140N5X6 
Go to UniProtKB:  A0A140N5X6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140N5X6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit AH [auth A]147Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: nuoAECBD_1373
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A0A140N7N4 (Escherichia coli (strain B / BL21-DE3))
Explore A0A140N7N4 
Go to UniProtKB:  A0A140N7N4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140N7N4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proton-translocating NADH-quinone oxidoreductase, chain LI [auth L]613Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: ECBD_1383
Membrane Entity: Yes 
UniProt
Find proteins for A0A140N7P6 (Escherichia coli (strain B / BL21-DE3))
Explore A0A140N7P6 
Go to UniProtKB:  A0A140N7P6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140N7P6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase I subunit MJ [auth M]504Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: ECBD_1384
Membrane Entity: Yes 
UniProt
Find proteins for A0A140N571 (Escherichia coli (strain B / BL21-DE3))
Explore A0A140N571 
Go to UniProtKB:  A0A140N571
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140N571
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit NK [auth N]485Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: nuoNECBD_1385
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A0A140N755 (Escherichia coli (strain B / BL21-DE3))
Explore A0A140N755 
Go to UniProtKB:  A0A140N755
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140N755
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit KL [auth K]100Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: nuoKB21_02164ECBD_1382ECD_02204
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for C5W716 (Escherichia coli (strain B / BL21-DE3))
Explore C5W716 
Go to UniProtKB:  C5W716
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC5W716
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit JM [auth J]162Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: ECBD_1381
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A0A140N7W8 (Escherichia coli (strain B / BL21-DE3))
Explore A0A140N7W8 
Go to UniProtKB:  A0A140N7W8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140N7W8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3PE
Query on 3PE

Download Ideal Coordinates CCD File 
AA [auth H],
CA [auth A],
DA [auth A],
EA [auth L],
FA [auth L],
AA [auth H],
CA [auth A],
DA [auth A],
EA [auth L],
FA [auth L],
HA [auth L],
IA [auth L],
JA [auth L],
LA [auth L],
MA [auth M],
NA [auth M],
PA [auth N]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
NAI
Query on NAI

Download Ideal Coordinates CCD File 
P [auth F]1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
FMN
Query on FMN

Download Ideal Coordinates CCD File 
O [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
N [auth F],
R [auth G],
S [auth G],
T [auth G],
W [auth B],
N [auth F],
R [auth G],
S [auth G],
T [auth G],
W [auth B],
X [auth I],
Y [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
LFA
Query on LFA

Download Ideal Coordinates CCD File 
BA [auth A],
GA [auth L],
KA [auth L],
OA [auth N],
QA [auth N],
BA [auth A],
GA [auth L],
KA [auth L],
OA [auth N],
QA [auth N],
Z [auth H]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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

Download Ideal Coordinates CCD File 
V [auth G]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedAustria25541

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2022-09-28
    Changes: Database references