6Q8W

Respiratory complex I from Thermus thermophilus with bound Aureothin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Key role of quinone in the mechanism of respiratory complex I.

Gutierrez-Fernandez, J.Kaszuba, K.Minhas, G.S.Baradaran, R.Tambalo, M.Gallagher, D.T.Sazanov, L.A.

(2020) Nat Commun 11: 4135-4135

  • DOI: 10.1038/s41467-020-17957-0
  • Primary Citation of Related Structures:  
    6I0D, 6I1P, 6Q8O, 6Q8W, 6Q8X, 6Y11, 6ZIY, 6ZJL, 6ZJN, 6ZJY

  • PubMed Abstract: 
  • Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T ...

    Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I.


    Organizational Affiliation

    Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria. sazanov@ist.ac.at.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 1A [auth 1],
Q [auth B]
438Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo1TTHA0089
EC: 1.6.5.11 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 2B [auth 2],
R [auth C]
181Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo2TTHA0088
EC: 1.6.5.11 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 3C [auth 3],
S [auth D]
783Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo3TTHA0090
EC: 1.6.5.11 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 4D [auth 4],
T [auth E]
409Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo4TTHA0087
EC: 1.6.5.11 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 5E [auth 5],
U [auth F]
207Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo5TTHA0086
EC: 1.6.5.11 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 6F [auth 6],
V [auth G]
181Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo6TTHA0085
EC: 1.6.5.11 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 9G [auth 9],
W [auth O]
182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo9TTHA0092
EC: 1.6.5.11 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 15H [auth 7],
X [auth I]
129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo15TTHA0496
EC: 1.6.5.11 (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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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinI [auth W],
Y [auth X]
131Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA1528
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 7J [auth A],
Z [auth P]
119Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo7TTHA0084
EC: 1.6.5.11 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 10K [auth J],
AA [auth R]
176Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo10TTHA0093
EC: 1.6.5.11 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 11L [auth K],
BA [auth S]
95Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo11TTHA0094
EC: 1.6.5.11 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 12M [auth L],
CA [auth T]
606Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo12TTHA0095
EC: 1.6.5.11 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 13N [auth M],
DA [auth U]
469Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo13TTHA0096
EC: 1.6.5.11 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 14O [auth N],
EA [auth V]
427Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo14TTHA0097
EC: 1.6.5.11 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 8P [auth H],
FA [auth Q]
365Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo8TTHA0091
EC: 1.6.5.11 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q60019 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
HA [auth 1],
SA [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
HQW (Subject of Investigation/LOI)
Query on HQW

Download Ideal Coordinates CCD File 
NA [auth 4],
YA [auth E]
Aureothin
C22 H23 N O6
GQKXCBCSVYJUMI-WACKOAQBSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
AB [auth O],
BB [auth O],
GA [auth 1],
JA [auth 3],
KA [auth 3],
AB [auth O],
BB [auth O],
GA [auth 1],
JA [auth 3],
KA [auth 3],
LA [auth 3],
OA [auth 6],
PA [auth 9],
QA [auth 9],
RA [auth B],
UA [auth D],
VA [auth D],
WA [auth D],
ZA [auth G]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

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IA [auth 2],
MA [auth 3],
TA [auth C],
XA [auth D]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.98α = 90
b = 340.5β = 100.44
c = 264.27γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105674180

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release