1NEK

Complex II (Succinate Dehydrogenase) From E. Coli with ubiquinone bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Architecture of succinate dehydrogenase and reactive oxygen species generation.

Yankovskaya, V.Horsefield, R.Tornroth, S.Luna-Chavez, C.Miyoshi, H.Leger, C.Byrne, B.Cecchini, G.Iwata, S.

(2003) Science 299: 700-704

  • DOI: 10.1126/science.1079605
  • Primary Citation of Related Structures:  1NEN

  • PubMed Abstract: 
  • The structure of Escherichia coli succinate dehydrogenase (SQR), analogous to the mitochondrial respiratory complex II, has been determined, revealing the electron transport pathway from the electron donor, succinate, to the terminal electron accepto ...

    The structure of Escherichia coli succinate dehydrogenase (SQR), analogous to the mitochondrial respiratory complex II, has been determined, revealing the electron transport pathway from the electron donor, succinate, to the terminal electron acceptor, ubiquinone. It was found that the SQR redox centers are arranged in a manner that aids the prevention of reactive oxygen species (ROS) formation at the flavin adenine dinucleotide. This is likely to be the main reason SQR is expressed during aerobic respiration rather than the related enzyme fumarate reductase, which produces high levels of ROS. Furthermore, symptoms of genetic disorders associated with mitochondrial SQR mutations may be a result of ROS formation resulting from impaired electron transport in the enzyme.


    Organizational Affiliation

    Molecular Biology Division, VA Medical Center, San Francisco, CA 94121, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase flavoprotein subunit
A
588Escherichia coli (strain K12)Gene Names: sdhA
EC: 1.3.5.1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex II
Protein: 
Succinate:quinone oxidoreductase (SQR, Complex II)
Find proteins for P0AC41 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AC41
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase iron-sulfur protein
B
238Escherichia coli (strain K12)Gene Names: sdhB
EC: 1.3.5.1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex II
Protein: 
Succinate:quinone oxidoreductase (SQR, Complex II)
Find proteins for P07014 (Escherichia coli (strain K12))
Go to UniProtKB:  P07014
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase cytochrome b-556 subunit
C
129Escherichia coli (strain K12)Gene Names: sdhC (cybA)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex II
Protein: 
Succinate:quinone oxidoreductase (SQR, Complex II)
Find proteins for P69054 (Escherichia coli (strain K12))
Go to UniProtKB:  P69054
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase hydrophobic membrane anchor protein
D
115Escherichia coli (strain K12)Gene Names: sdhD
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex II
Protein: 
Succinate:quinone oxidoreductase (SQR, Complex II)
Find proteins for P0AC44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AC44
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

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B
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FAD
Query on FAD

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A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
CA
Query on CA

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A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CDN
Query on CDN

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C
CARDIOLIPIN
C58 H120 O17 P2
GKRASOJOCMJQMF-DUXRJKJQSA-N
 Ligand Interaction
FES
Query on FES

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B
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
EPH
Query on EPH

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C
L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
C39 H68 N O8 P
MABRTXOVHMDVAT-AAEGOEIASA-N
 Ligand Interaction
OAA
Query on OAA

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A
OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
C
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
UQ2
Query on UQ2

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D
UBIQUINONE-2
C19 H26 O4
SQQWBSBBCSFQGC-JLHYYAGUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.247 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 138.800α = 90.00
b = 138.800β = 90.00
c = 521.900γ = 120.00
Software Package:
Software NamePurpose
MLPHAREphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-25
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance