2WDQ | pdb_00002wdq

E. coli succinate:quinone oxidoreductase (SQR) with carboxin bound

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.200 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history. 

Literature

Structure of Escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site.

Ruprecht, J., Yankovskaya, V., Maklashina, E., Iwata, S., Cecchini, G.

(2009) J Biological Chem 284: 29836-29846

  • DOI: https://doi.org/10.1074/jbc.M109.010058
  • Primary Citation Related Structures: 
    2WDQ, 2WDR, 2WDV

  • PubMed Abstract: 

    Three new structures of Escherichia coli succinate-quinone oxidoreductase (SQR) have been solved. One with the specific quinone-binding site (Q-site) inhibitor carboxin present has been solved at 2.4 A resolution and reveals how carboxin inhibits the Q-site. The other new structures are with the Q-site inhibitor pentachlorophenol and with an empty Q-site. These structures reveal important details unresolved in earlier structures. Comparison of the new SQR structures shows how subtle rearrangements of the quinone-binding site accommodate the different inhibitors. The position of conserved water molecules near the quinone binding pocket leads to a reassessment of possible water-mediated proton uptake networks that complete reduction of ubiquinone. The dicarboxylate-binding site in the soluble domain of SQR is highly similar to that seen in high resolution structures of avian SQR (PDB 2H88) and soluble flavocytochrome c (PDB 1QJD) showing mechanistically significant structural features conserved across prokaryotic and eukaryotic SQRs.

    • Organizational Affiliation: 
    • Membrane Protein Crystallography Group, Molecular Biosciences Division, Imperial College, London SW72AZ, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 363.61 kDa 
  • Atom Count: 26,034 
  • Modeled Residue Count: 3,156 
  • Deposited Residue Count: 3,210 
  • Unique protein chains: 4

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
A, E, I
588Escherichia coliMutation(s): 0 
EC: 1.3.5.1 (PDB Primary Data), 1.3.99.1 (PDB Primary Data)
Membrane Entity: Yes 
UniProt
Find proteins for P0AC41 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0AC41
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AC41
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT
B, F, J
238Escherichia coliMutation(s): 0 
EC: 1.3.5.1 (PDB Primary Data), 1.3.99.1 (PDB Primary Data)
Membrane Entity: Yes 
UniProt
Find proteins for P07014 (Escherichia coli (strain K12))
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Go to UniProtKB:  P07014
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UniProt GroupP07014
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT
C, G, K
129Escherichia coliMutation(s): 0 
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for P69054 (Escherichia coli (strain K12))
Explore P69054 
Go to UniProtKB:  P69054
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UniProt GroupP69054
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT
D, H, L
115Escherichia coliMutation(s): 0 
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for P0AC44 (Escherichia coli (strain K12))
Explore P0AC44 
Go to UniProtKB:  P0AC44
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UniProt GroupP0AC44
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Reference Sequence

Small Molecules

Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD


Download:Ideal Coordinates CCD File
EA [auth I],
M [auth A],
V [auth E]		FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
HEM

Query on HEM


Download:Ideal Coordinates CCD File
CA [auth G],
LA [auth K],
T [auth C]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SF4

Query on SF4


Download:Ideal Coordinates CCD File
AA [auth F],
JA [auth J],
R [auth B]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S

Query on F3S


Download:Ideal Coordinates CCD File
BA [auth F],
KA [auth J],
S [auth B]		FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
CBE

Query on CBE


Download:Ideal Coordinates CCD File
DA [auth G],
MA [auth K],
U [auth C]		2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE
C12 H13 N O2 S
GYSSRZJIHXQEHQ-UHFFFAOYSA-N
FES

Query on FES


Download:Ideal Coordinates CCD File
IA [auth J],
Q [auth B],
Z [auth F]		FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
TEO

Query on TEO


Download:Ideal Coordinates CCD File
FA [auth I],
N [auth A],
W [auth E]		MALATE LIKE INTERMEDIATE
C4 H4 O5
QFBHYOKSQPPXHZ-UWTATZPHSA-L
SO4

Query on SO4


Download:Ideal Coordinates CCD File
HA [auth I],
P [auth A],
Y [auth E]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
NA

Query on NA


Download:Ideal Coordinates CCD File
GA [auth I],
O [auth A],
X [auth E]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.200 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.4α = 90
b = 178.46β = 90
c = 200.94γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 2.0: 2019-01-30
    Changes: Atomic model, Data collection, Database references, Experimental preparation
  • Version 2.1: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 2.2: 2024-10-23
    Changes: Structure summary