3VR8

Mitochondrial rhodoquinol-fumarate reductase from the parasitic nematode Ascaris suum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of mitochondrial quinol-fumarate reductase from the parasitic nematode Ascaris suum

Shimizu, H.Osanai, A.Sakamoto, K.Inaoka, D.K.Shiba, T.Harada, S.Kita, K.

(2012) J Biochem 151: 589-592

  • DOI: 10.1093/jb/mvs051
  • Primary Citation of Related Structures:  
    3VRB, 3VR8

  • PubMed Abstract: 
  • In the anaerobic respiratory chain of the parasitic nematode Ascaris suum, complex II couples the reduction of fumarate to the oxidation of rhodoquinol, a reverse reaction catalyzed by mammalian complex II. In this study, the first structure of anaer ...

    In the anaerobic respiratory chain of the parasitic nematode Ascaris suum, complex II couples the reduction of fumarate to the oxidation of rhodoquinol, a reverse reaction catalyzed by mammalian complex II. In this study, the first structure of anaerobic complex II of mitochondria was determined. The structure, composed of four subunits and five co-factors, is similar to that of aerobic complex II, except for an extra peptide found in the smallest anchor subunit of the A. suum enzyme. We discuss herein the structure-function relationship of the enzyme and the critical role of the low redox potential of rhodoquinol in the fumarate reduction of A. suum complex II.


    Organizational Affiliation

    Department of Biomedical Chemistry, Graduate School of Medicine, University of Tokyo, Tokyo, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Iron-sulfur subunit of succinate dehydrogenaseB, F282Ascaris suumMutation(s): 0 
EC: 1.3.5.1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
Mitochondrial rhodoquinol-fumarate reductase
Find proteins for O44074 (Ascaris suum)
Explore O44074 
Go to UniProtKB:  O44074
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-large subunitC, G188Ascaris suumMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
Mitochondrial rhodoquinol-fumarate reductase
Find proteins for P92506 (Ascaris suum)
Explore P92506 
Go to UniProtKB:  P92506
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Flavoprotein subunit of complex IIA, E645Ascaris suumMutation(s): 0 
EC: 1.3.5.1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
Mitochondrial rhodoquinol-fumarate reductase
Find proteins for Q33862 (Ascaris suum)
Explore Q33862 
Go to UniProtKB:  Q33862
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrialD, H156Ascaris suumMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
Mitochondrial rhodoquinol-fumarate reductase
Find proteins for P92507 (Ascaris suum)
Explore P92507 
Go to UniProtKB:  P92507
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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A, E
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
EPH
Query on EPH

Download CCD File 
D, H
L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
C39 H68 N O8 P
MABRTXOVHMDVAT-AAEGOEIASA-N
 Ligand Interaction
HEM
Query on HEM

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

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B, F
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

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B, F
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
RQX
Query on RQX

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C, G
2-amino-3-methoxy-6-methyl-5-[(2E)-3-methylhex-2-en-1-yl]cyclohexa-2,5-diene-1,4-dione
C15 H21 N O3
FKFYBWHBXHCWCD-VQHVLOKHSA-N
 Ligand Interaction
FES
Query on FES

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

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A, E
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.707α = 90
b = 129.09β = 90
c = 221.167γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
DENZOdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-11
    Type: Initial release
  • Version 1.1: 2012-10-17
    Changes: Atomic model
  • Version 1.2: 2017-11-22
    Changes: Refinement description