3M9S | pdb_00003m9s

Crystal structure of respiratory complex I from Thermus thermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Work: 
    0.394 (DCC) 

Starting Models: experimental
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This is version 1.3 of the entry. See complete history

Literature

The architecture of respiratory complex I

Efremov, R.G.Baradaran, R.Sazanov, L.A.

(2010) Nature 465: 441-445

  • DOI: https://doi.org/10.1038/nature09066
  • Primary Citation Related Structures: 
    3M9C, 3M9S

  • PubMed Abstract: 

    Complex I is the first enzyme of the respiratory chain and has a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation by an unknown mechanism. Dysfunction of complex I has been implicated in many human neurodegenerative diseases. We have determined the structure of its hydrophilic domain previously. Here, we report the alpha-helical structure of the membrane domain of complex I from Escherichia coli at 3.9 A resolution. The antiporter-like subunits NuoL/M/N each contain 14 conserved transmembrane (TM) helices. Two of them are discontinuous, as in some transporters. Unexpectedly, subunit NuoL also contains a 110-A long amphipathic alpha-helix, spanning almost the entire length of the domain. Furthermore, we have determined the structure of the entire complex I from Thermus thermophilus at 4.5 A resolution. The L-shaped assembly consists of the alpha-helical model for the membrane domain, with 63 TM helices, and the known structure of the hydrophilic domain. The architecture of the complex provides strong clues about the coupling mechanism: the conformational changes at the interface of the two main domains may drive the long amphipathic alpha-helix of NuoL in a piston-like motion, tilting nearby discontinuous TM helices, resulting in proton translocation.


  • Organizational Affiliation
    • Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK.

Macromolecule Content 

  • Total Structure Weight: 857.55 kDa 
  • Atom Count: 47,664 
  • Modeled Residue Count: 8,122 
  • Deposited Residue Count: 8,410 
  • Unique protein chains: 13

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 1A [auth 1],
N [auth A]
438Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q56222 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity Groups
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UniProt GroupQ56222
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 2B [auth 2],
O [auth B]
181Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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UniProt GroupQ56221
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 3C [auth 3],
P [auth C]
783Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q56223 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ56223
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 4D [auth 4],
Q [auth D]
409Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit CE [auth 5],
R [auth E]
207Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit BF [auth 6],
S [auth F]
181Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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UniProt GroupQ56218
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit IG [auth 9],
T [auth G]
182Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q56224 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ56224
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 15H [auth 7],
U [auth J]
129Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q5SKZ7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ5SKZ7
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 12I [auth L],
V [auth O]
469Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 13J [auth M],
W [auth P]
392Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 14K [auth N],
X [auth Q]
379Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunits 7, 10 and 11L [auth R],
Y [auth S]
274Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 8M [auth H],
Z [auth T]
181Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN

Query on FMN



Download:Ideal Coordinates CCD File
BA [auth 1],
LA [auth A]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
AA [auth 1]
DA [auth 3]
EA [auth 3]
FA [auth 3]
HA [auth 6]
AA [auth 1],
DA [auth 3],
EA [auth 3],
FA [auth 3],
HA [auth 6],
IA [auth 9],
JA [auth 9],
KA [auth A],
NA [auth C],
OA [auth C],
PA [auth C],
RA [auth F],
SA [auth G],
TA [auth G]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES

Query on FES



Download:Ideal Coordinates CCD File
CA [auth 2],
GA [auth 3],
MA [auth B],
QA [auth C]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Work:  0.394 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.39α = 90
b = 336.09β = 100.59
c = 262.24γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-27
    Changes: Structure summary