2H88

Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystallographic studies of the binding of ligands to the dicarboxylate site of Complex II, and the identity of the ligand in the

Huang, L.S.Shen, J.T.Wang, A.C.Berry, E.A.

(--) Biochim.Biophys.Acta 1757: 1073-1083

  • DOI: 10.1016/j.bbabio.2006.06.015
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mitochondrial Complex II (succinate:ubiquinone oxidoreductase) is purified in a partially inactivated state, which can be activated by removal of tightly bound oxaloacetate (E.B. Kearney, et al., Biochem. Biophys. Res. Commun. 49 1115-1121). We cryst ...

    Mitochondrial Complex II (succinate:ubiquinone oxidoreductase) is purified in a partially inactivated state, which can be activated by removal of tightly bound oxaloacetate (E.B. Kearney, et al., Biochem. Biophys. Res. Commun. 49 1115-1121). We crystallized Complex II in the presence of oxaloacetate or with the endogenous inhibitor bound. The structure showed a ligand essentially identical to the "malate-like intermediate" found in Shewanella Flavocytochrome c crystallized with fumarate (P. Taylor, et al., Nat. Struct. Biol. 6 1108-1112) Crystallization of Complex II in the presence of excess fumarate also gave the malate-like intermediate or a mixture of that and fumarate at the active site. In order to more conveniently monitor the occupation state of the dicarboxylate site, we are developing a library of UV/Vis spectral effects induced by binding different ligands to the site. Treatment with fumarate results in rapid development of the fumarate difference spectrum and then a very slow conversion into a species spectrally similar to the OAA-liganded complex. Complex II is known to be capable of oxidizing malate to the enol form of oxaloacetate (Y.O. Belikova, et al., Biochim. Biophys. Acta 936 1-9). The observations above suggest it may also be capable of interconverting fumarate and malate. It may be useful for understanding the mechanism and regulation of the enzyme to identify the malate-like intermediate and its pathway of formation from oxaloacetate or fumarate.


    Related Citations: 
    • Crystallization of mitochondrial respiratory complex II from chicken heart: a membrane-protein complex diffracting to 2.0 A
      Huang, L.S.,Borders, T.M.,Shen, J.T.,Wang, C.J.,Berry, E.A.
      (2005) Acta Crystallogr.,Sect.D 61: 380
    • 3-nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme.
      Huang, L.S.,Sun, G.,Cobessi, D.,Wang, A.C.,Shen, J.T.,Tung, E.Y.,Anderson, V.E.,Berry, E.A.
      (2006) J.Biol.Chem. 281: 5965
    • 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


    Organizational Affiliation

    Physical Biosciences Division, Lawrence Berkeley National Lab., MS 64-0121, 1 Cyclotron Road, Berkeley CA 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
A, N
621Gallus gallusMutation(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; chicken heart) w. carboxin inhibitor
Find proteins for Q9YHT1 (Gallus gallus)
Go to Gene View: SDHA
Go to UniProtKB:  Q9YHT1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase Ip subunit
B, O
252Gallus gallusMutation(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; chicken heart) w. carboxin inhibitor
Find proteins for Q9YHT2 (Gallus gallus)
Go to Gene View: SDHB
Go to UniProtKB:  Q9YHT2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT
C, P
140Gallus gallusMutation(s): 0 
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; chicken heart) w. carboxin inhibitor
Find proteins for D0VWW3 (Gallus gallus)
Go to UniProtKB:  D0VWW3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase cytochrome B, small subunit
D, Q
103Gallus gallusMutation(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; chicken heart) w. carboxin inhibitor
Find proteins for Q5ZIS0 (Gallus gallus)
Go to Gene View: SDHD
Go to UniProtKB:  Q5ZIS0
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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A, B, N, O
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SF4
Query on SF4

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Download CCD File 
B, O
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

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Download CCD File 
B, O
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FAD
Query on FAD

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

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B, O
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BHG
Query on BHG

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Download CCD File 
C, P
2-HEXYLOXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL
C12 H24 O6
JVAZJLFFSJARQM-YBXAARCKSA-N
 Ligand Interaction
AZI
Query on AZI

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A, N
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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

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

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Download CCD File 
A, N
MALATE LIKE INTERMEDIATE
C4 H4 O5
QFBHYOKSQPPXHZ-UWTATZPHSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 119.972α = 90.00
b = 199.391β = 90.35
c = 68.063γ = 90.00
Software Package:
Software NamePurpose
BOSdata collection
SCALEPACKdata scaling
CNSphasing
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description