2FBW

Avian respiratory complex II with carboxin bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 5965-5972

  • DOI: 10.1074/jbc.M511270200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • We report three new structures of mitochondrial respiratory Complex II (succinate ubiquinone oxidoreductase, E.C. 1.3.5.1) at up to 2.1 A resolution, with various inhibitors. The structures define the conformation of the bound inhibitors and suggest ...

    We report three new structures of mitochondrial respiratory Complex II (succinate ubiquinone oxidoreductase, E.C. 1.3.5.1) at up to 2.1 A resolution, with various inhibitors. The structures define the conformation of the bound inhibitors and suggest the residues involved in substrate binding and catalysis at the dicarboxylate site. In particular they support the role of Arg(297) as a general base catalyst accepting a proton in the dehydrogenation of succinate. The dicarboxylate ligand in oxaloacetate-containing crystals appears to be the same as that reported for Shewanella flavocytochrome c treated with fumarate. The plant and fungal toxin 3-nitropropionic acid, an irreversible inactivator of succinate dehydrogenase, forms a covalent adduct with the side chain of Arg(297). The modification eliminates a trypsin cleavage site in the flavoprotein, and tandem mass spectroscopic analysis of the new fragment shows the mass of Arg(297) to be increased by 83 Da and to have the potential of losing 44 Da, consistent with decarboxylation, during fragmentation.


    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 D Biol Crystallogr 61: 380
    • 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

    Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

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 UniProtKB:  Q9YHT2

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase cytochrome B, large subunit
C, P
141Gallus gallusMutation(s): 0 
EC: 1.3.5.1
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase cytochrome B, small subunit
D, Q
103Gallus gallusMutation(s): 0 
Gene Names: SDHDRCJMB04_23p7
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 Q5ZIS0 (Gallus gallus)
Go to UniProtKB:  Q5ZIS0

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 UniProtKB:  Q9YHT1
Small Molecules
Ligands 13 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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

Download CCD File 
D, Q
1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H83 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-O
 Ligand Interaction
HEM
Query on HEM

Download CCD File 
C, P
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
SF4
Query on SF4

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

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

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

Download CCD File 
C, P
2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE
C12 H13 N O2 S
GYSSRZJIHXQEHQ-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

Download CCD File 
B, O
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
TEO
Query on TEO

Download CCD File 
A, N
MALATE LIKE INTERMEDIATE
C4 H4 O5
QFBHYOKSQPPXHZ-UWTATZPHSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
B, C, O, P
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
AZI
Query on AZI

Download CCD File 
A
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A, B, N, O
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
UNL
Query on UNL

Download CCD File 
A, B, C, D, N, O, P, Q
Unknown ligand
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.7α = 90
b = 200.753β = 90.06
c = 67.631γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-12-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2014-10-29
    Changes: Non-polymer description