2WDQ

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 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report



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 Biol Chem 284: 29836-29846

  • DOI: 10.1074/jbc.M109.010058
  • Structures With Same Primary Citation

  • 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 ...

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
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 protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex II
Protein: 
Succinate:quinone oxidoreductase (SQR, Complex II) with carboxin in Q-site
Find proteins for P0AC41 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AC41
Protein Feature View
  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
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 protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex II
Protein: 
Succinate:quinone oxidoreductase (SQR, Complex II) with carboxin in Q-site
Find proteins for P07014 (Escherichia coli (strain K12))
Go to UniProtKB:  P07014
Protein Feature View
  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT
C, G, K
129Escherichia coliMutation(s): 0 
EC: 1.3.5.1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex II
Protein: 
Succinate:quinone oxidoreductase (SQR, Complex II) with carboxin in Q-site
Find proteins for P69054 (Escherichia coli (strain K12))
Go to UniProtKB:  P69054
Protein Feature View
  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT
D, H, L
115Escherichia coliMutation(s): 0 
EC: 1.3.5.1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex II
Protein: 
Succinate:quinone oxidoreductase (SQR, Complex II) with carboxin in Q-site
Find proteins for P0AC44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AC44
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download CCD File 
A, E, I
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
HEM
Query on HEM

Download CCD File 
C, G, K
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
SF4
Query on SF4

Download CCD File 
B, F, J
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download CCD File 
B, F, J
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
CBE
Query on CBE

Download CCD File 
C, G, K
2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE
C12 H13 N O2 S
GYSSRZJIHXQEHQ-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

Download CCD File 
B, F, J
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
TEO
Query on TEO

Download CCD File 
A, E, I
MALATE LIKE INTERMEDIATE
C4 H4 O5
QFBHYOKSQPPXHZ-UWTATZPHSA-L
 Ligand Interaction
SO4
Query on SO4

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A, E, I
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, E, I
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • 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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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