1ZOY

Crystal Structure of Mitochondrial Respiratory Complex II from porcine heart at 2.4 Angstroms

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history. 

Literature

Crystal Structure of Mitochondrial Respiratory Membrane Protein Complex II

Sun, F., Huo, X., Zhai, Y., Wang, A., Xu, J., Su, D., Bartlam, M., Rao, Z.

(2005) Cell 121: 1043-1057

  • DOI: 10.1016/j.cell.2005.05.025
  • Primary Citation of Related Structures:  
  • Also Cited By: 6MYU, 6MYT, 6MYS, 6MYR, 6MYQ, 6MYP, 6MYO

  • PubMed Abstract: 

    • The mitochondrial respiratory Complex II or succinate:ubiquinone oxidoreductase (SQR) is an integral membrane protein complex in both the tricarboxylic acid cycle and aerobic respiration. Here we report the first crystal structure of Complex II from ...

    The mitochondrial respiratory Complex II or succinate:ubiquinone oxidoreductase (SQR) is an integral membrane protein complex in both the tricarboxylic acid cycle and aerobic respiration. Here we report the first crystal structure of Complex II from porcine heart at 2.4 A resolution and its complex structure with inhibitors 3-nitropropionate and 2-thenoyltrifluoroacetone (TTFA) at 3.5 A resolution. Complex II is comprised of two hydrophilic proteins, flavoprotein (Fp) and iron-sulfur protein (Ip), and two transmembrane proteins (CybL and CybS), as well as prosthetic groups required for electron transfer from succinate to ubiquinone. The structure correlates the protein environments around prosthetic groups with their unique midpoint redox potentials. Two ubiquinone binding sites are discussed and elucidated by TTFA binding. The Complex II structure provides a bona fide model for study of the mitochondrial respiratory system and human mitochondrial diseases related to mutations in this complex.

    Organizational Affiliation: 

    Tsinghua-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FAD-binding protein
A
622Sus scrofaMutation(s): 0 
Gene Names: SDHA
EC: 1.3.5.1
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex II		Protein: 
Succinate:ubiquinone oxidoreductase (SQR, Complex II; pig heart)
Find proteins for Q0QF01 (Sus scrofa)
Go to Gene View: SDHA
Go to UniProtKB:  Q0QF01
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Iron-sulfur protein
B
252Sus scrofaMutation(s): 0 
Gene Names: SDHB
EC: 1.3.5.1
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex II		Protein: 
Succinate:ubiquinone oxidoreductase (SQR, Complex II; pig heart)
Find proteins for Q007T0 (Sus scrofa)
Go to Gene View: SDHB
Go to UniProtKB:  Q007T0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Large cytochrome binding protein
C
140Sus scrofaMutation(s): 0 
Gene Names: SDHC
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex II		Protein: 
Succinate:ubiquinone oxidoreductase (SQR, Complex II; pig heart)
Find proteins for D0VWV4 (Sus scrofa)
Go to Gene View: SDHC
Go to UniProtKB:  D0VWV4
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Small cytochrome binding protein
D
103Sus scrofaMutation(s): 0 
Gene Names: SDHD
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex II		Protein: 
Succinate:ubiquinone oxidoreductase (SQR, Complex II; pig heart)
Find proteins for A5GZW8 (Sus scrofa)
Go to Gene View: SDHD
Go to UniProtKB:  A5GZW8
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4
Download SDF File 
Download CCD File 
B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S
Download SDF File 
Download CCD File 
B
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
UQ1
Query on UQ1
Download SDF File 
Download CCD File 
B
UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD
Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
FES
Query on FES
Download SDF File 
Download CCD File 
B
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
EPH
Query on EPH
Download SDF File 
Download CCD File 
D
L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
C39 H68 N O8 P
MABRTXOVHMDVAT-AAEGOEIASA-N
 Ligand Interaction
HEM
Query on HEM
Download SDF File 
Download CCD File 
C
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.238α = 90.00
b = 83.557β = 90.00
c = 293.896γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
CNSphasing
CNSrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-07-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 2.0: 2019-09-04
    Type: Advisory, Atomic model, Data collection, Derived calculations