Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 127.24 kDa 
• Atom Count: 9024 
• Modelled Residue Count: 1092 
• Deposited Residue Count: 1117 
• Unique protein chains: 4

1ZOY

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

• DOI: 10.2210/pdb1ZOY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2005-05-15 Released: 2005-07-12 
• Deposition Author(s): Sun, F., Huo, X., Zhai, Y., Wang, A., Xu, J., Su, D., Bartlam, M., Rao, Z.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.259 
• R-Value Work: 0.213 
• R-Value Observed: 0.232 

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

• PubMed: 15989954 
• DOI: 10.1016/j.cell.2005.05.025
• Primary Citation of Related Structures:  
  1ZOY, 1ZP0


• 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 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAD-binding protein	A	622	Sus scrofa	Mutation(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) Explore Q0QF01  Go to UniProtKB:  Q0QF01

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron-sulfur protein	B	252	Sus scrofa	Mutation(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) Explore Q007T0  Go to UniProtKB:  Q007T0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Large cytochrome binding protein	C	140	Sus scrofa	Mutation(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) Explore D0VWV4  Go to UniProtKB:  D0VWV4

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Small cytochrome binding protein	D	103	Sus scrofa	Mutation(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) Explore A5GZW8  Go to UniProtKB:  A5GZW8

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
EPH	K [auth D], L [auth D]	L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE C39 H68 N O8 P MABRTXOVHMDVAT-AAEGOEIASA-N
HEM	J [auth C]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SF4	G [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
F3S	H [auth B]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-MZMDZPPWAW
UQ1	I [auth B]	UBIQUINONE-1 C14 H18 O4 SOECUQMRSRVZQQ-UHFFFAOYSA-N
FES	F [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.259 
• R-Value Work: 0.213 
• R-Value Observed: 0.232 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.238	α = 90
b = 83.557	β = 90
c = 293.896	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-05-15 
• Released Date: 2005-07-12 
Deposition Author(s): Sun, F., Huo, X., Zhai, Y., Wang, A., Xu, J., Su, D., Bartlam, M., Rao, Z.

Revision History  

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