1NEN

Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 inhibitor co-crystallized at the ubiquinone binding site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.271 

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, 1NEK

  • 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Succinate dehydrogenase flavoprotein subunitA588Escherichia coliMutation(s): 0 
Gene Names: SDHA OR B0723 OR Z0877 OR ECS0748
EC: 1.3.99.1 (PDB Primary Data), 1.3.5.1 (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)
Find proteins for P0AC41 (Escherichia coli (strain K12))
Explore P0AC41 
Go to UniProtKB:  P0AC41
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Succinate dehydrogenase iron-sulfur proteinB238Escherichia coliMutation(s): 0 
Gene Names: SDHB OR B0724
EC: 1.3.99.1 (PDB Primary Data), 1.3.5.1 (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)
Find proteins for P07014 (Escherichia coli (strain K12))
Explore P07014 
Go to UniProtKB:  P07014
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Succinate dehydrogenase cytochrome b-556 subunitC129Escherichia coliMutation(s): 0 
Gene Names: SDHC OR CYBA OR B0721 OR Z0875 OR ECS0746
Membrane protein
Mpstruc
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))
Explore P69054 
Go to UniProtKB:  P69054
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Succinate dehydrogenase hydrophobic membrane anchor proteinD115Escherichia coliMutation(s): 0 
Gene Names: SDHD OR B0722
Membrane protein
Mpstruc
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))
Explore P0AC44 
Go to UniProtKB:  P0AC44
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDN
Query on CDN

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

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

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

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

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C
2-[1-METHYLHEXYL]-4,6-DINITROPHENOL
C13 H18 N2 O5
RROCMCBQTUYDSD-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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

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

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A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.271 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.8α = 90
b = 138.8β = 90
c = 521.9γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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