3VR8 | pdb_00003vr8

Mitochondrial rhodoquinol-fumarate reductase from the parasitic nematode Ascaris suum

PDB DOI: https://doi.org/10.2210/pdb3VR8/pdb

Classification: OXIDOREDUCTASE
Organism(s): Ascaris suum
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 2012-04-07 Released: 2012-07-11
Deposition Author(s): Shimizu, H., Shiba, T., Inaoka, D.K., Osanai, A., Kita, K., Sakamoto, K., Harada, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free:
0.297 (Depositor), 0.286 (DCC)
R-Value Work:
0.231 (Depositor), 0.223 (DCC)
R-Value Observed:
0.234 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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

PubMed: 22577165 Search on PubMed
DOI: https://doi.org/10.1093/jb/mvs051
Primary Citation Related Structures:
3VR8, 3VRB

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 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.

Macromolecule Content

Total Structure Weight: 288.92 kDa
Atom Count: 18,232
Modeled Residue Count: 2,285
Deposited Residue Count: 2,542
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavoprotein subunit of complex II	A, E	645	Ascaris suum	Mutation(s): 0 EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for Q33862 (Ascaris suum) Explore Q33862 Go to UniProtKB: Q33862
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q33862
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron-sulfur subunit of succinate dehydrogenase	B, F	282	Ascaris suum	Mutation(s): 0 EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for O44074 (Ascaris suum) Explore O44074 Go to UniProtKB: O44074
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O44074
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-large subunit	C, G	188	Ascaris suum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P92506 (Ascaris suum) Explore P92506 Go to UniProtKB: P92506
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P92506
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial	D, H	156	Ascaris suum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P92507 (Ascaris suum) Explore P92507 Go to UniProtKB: P92507
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P92507
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain R [auth E] SDF format, chain J [auth A] MOL2 format, chain R [auth E] MOL2 format, chain J [auth A] mmCIF format, chain R [auth E] mmCIF format, chain J [auth A]	J [auth A], R [auth E]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain J [auth A] Focus chain R [auth E] Interactions & Density Focus chain J [auth A] Focus chain R [auth E]
EPH Query on EPH Download:Ideal Coordinates CCD File SDF format, chain X [auth H] SDF format, chain P [auth D] MOL2 format, chain X [auth H] MOL2 format, chain P [auth D] mmCIF format, chain X [auth H] mmCIF format, chain P [auth D]	P [auth D], X [auth H]	L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE C₃₉ H₆₈ N O₈ P MABRTXOVHMDVAT-AAEGOEIASA-N		Interactions Focus chain P [auth D] Focus chain X [auth H] Interactions & Density Focus chain P [auth D] Focus chain X [auth H]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain V [auth G] SDF format, chain N [auth C] MOL2 format, chain V [auth G] MOL2 format, chain N [auth C] mmCIF format, chain V [auth G] mmCIF format, chain N [auth C]	N [auth C], V [auth G]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain N [auth C] Focus chain V [auth G] Interactions & Density Focus chain N [auth C] Focus chain V [auth G]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain T [auth F] SDF format, chain L [auth B] MOL2 format, chain T [auth F] MOL2 format, chain L [auth B] mmCIF format, chain T [auth F] mmCIF format, chain L [auth B]	L [auth B], T [auth F]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain T [auth F] Interactions & Density Focus chain L [auth B] Focus chain T [auth F]
F3S Query on F3S Download:Ideal Coordinates CCD File SDF format, chain U [auth F] SDF format, chain M [auth B] MOL2 format, chain U [auth F] MOL2 format, chain M [auth B] mmCIF format, chain U [auth F] mmCIF format, chain M [auth B]	M [auth B], U [auth F]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain U [auth F] Interactions & Density Focus chain M [auth B] Focus chain U [auth F]
RQX Query on RQX Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain W [auth G] MOL2 format, chain O [auth C] MOL2 format, chain W [auth G] mmCIF format, chain O [auth C] mmCIF format, chain W [auth G]	O [auth C], W [auth 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		Interactions Focus chain O [auth C] Focus chain W [auth G] Interactions & Density Focus chain O [auth C] Focus chain W [auth G]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain S [auth F] SDF format, chain K [auth B] MOL2 format, chain S [auth F] MOL2 format, chain K [auth B] mmCIF format, chain S [auth F] mmCIF format, chain K [auth B]	K [auth B], S [auth F]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain S [auth F] Interactions & Density Focus chain K [auth B] Focus chain S [auth F]
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain Q [auth E] SDF format, chain I [auth A] MOL2 format, chain Q [auth E] MOL2 format, chain I [auth A] mmCIF format, chain Q [auth E] mmCIF format, chain I [auth A]	I [auth A], Q [auth E]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain Q [auth E] Interactions & Density Focus chain I [auth A] Focus chain Q [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free: 0.297 (Depositor), 0.286 (DCC)
R-Value Work: 0.231 (Depositor), 0.223 (DCC)
R-Value Observed: 0.234 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.707	α = 90
b = 129.09	β = 90
c = 221.167	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-07-11

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.3: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-16
Changes: Structure summary