1ZOY

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

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 

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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: https://doi.org/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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FAD-binding protein622Sus scrofaMutation(s): 0 
Gene Names: SDHA
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for Q0QF01 (Sus scrofa)
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Go to UniProtKB:  Q0QF01
Entity Groups  
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UniProt GroupQ0QF01
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Iron-sulfur protein252Sus scrofaMutation(s): 0 
Gene Names: SDHB
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for Q007T0 (Sus scrofa)
Explore Q007T0 
Go to UniProtKB:  Q007T0
Entity Groups  
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UniProt GroupQ007T0
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Large cytochrome binding protein140Sus scrofaMutation(s): 0 
Gene Names: SDHC
Membrane Entity: Yes 
UniProt
Find proteins for D0VWV4 (Sus scrofa)
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Go to UniProtKB:  D0VWV4
Entity Groups  
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UniProt GroupD0VWV4
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Small cytochrome binding protein103Sus scrofaMutation(s): 0 
Gene Names: SDHD
Membrane Entity: Yes 
UniProt
Find proteins for A5GZW8 (Sus scrofa)
Explore A5GZW8 
Go to UniProtKB:  A5GZW8
Entity Groups  
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UniProt GroupA5GZW8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
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E [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
EPH
Query on EPH
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K [auth D],
L [auth D]		L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
C39 H68 N O8 P
MABRTXOVHMDVAT-AAEGOEIASA-N		 Ligand Interaction
HEM
Query on HEM
Download Ideal Coordinates CCD File 
J [auth C]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
SF4
Query on SF4
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G [auth B]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
F3S
Query on F3S
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H [auth B]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW		 Ligand Interaction
UQ1
Query on UQ1
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I [auth B]UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N		 Ligand Interaction
FES
Query on FES
Download Ideal Coordinates CCD File 
F [auth B]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N		 Ligand Interaction
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 = 70.238α = 90
b = 83.557β = 90
c = 293.896γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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