1NEK

Complex II (Succinate Dehydrogenase) From E. Coli with ubiquinone bound

PDB DOI: https://doi.org/10.2210/pdb1NEK/pdb

Classification: OXIDOREDUCTASE/ELECTRON TRANSPORT
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 2002-12-11 Released: 2003-02-25
Deposition Author(s): Yankovskaya, V., Horsefield, R., Tornroth, S., Luna-Chavez, C., Miyoshi, H., Leger, C., Byrne, B., Cecchini, G., Iwata, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.289
R-Value Work: 0.247
R-Value Observed: 0.247

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Architecture of succinate dehydrogenase and reactive oxygen species generation.

Yankovskaya, V., Horsefield, R., Tornroth, S., Luna-Chavez, C., Miyoshi, H., Leger, C., Byrne, B., Cecchini, G., Iwata, S.

(2003) Science 299: 700-704

PubMed: 12560550 Search on PubMed
DOI: https://doi.org/10.1126/science.1079605
Primary Citation of Related Structures:
1NEK, 1NEN

PubMed Abstract:
The structure of Escherichia coli succinate dehydrogenase (SQR), analogous to the mitochondrial respiratory complex II, has been determined, revealing the electron transport pathway from the electron donor, succinate, to the terminal electron acceptor, ubiquinone. It was found that the SQR redox centers are arranged in a manner that aids the prevention of reactive oxygen species (ROS) formation at the flavin adenine dinucleotide. This is likely to be the main reason SQR is expressed during aerobic respiration rather than the related enzyme fumarate reductase, which produces high levels of ROS. Furthermore, symptoms of genetic disorders associated with mitochondrial SQR mutations may be a result of ROS formation resulting from impaired electron transport in the enzyme.

Organizational Affiliation

Molecular Biology Division, VA Medical Center, San Francisco, CA 94121, USA.

Macromolecule Content

Total Structure Weight: 123.11 kDa
Atom Count: 8,698
Modelled Residue Count: 1,068
Deposited Residue Count: 1,070
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase flavoprotein subunit	A	588	Escherichia coli	Mutation(s): 0 Gene Names: SDHA OR B0723 OR Z0877 OR ECS0748 EC: 1.3.99.1 (PDB Primary Data), 1.3.5.1 (PDB Primary Data) Membrane Entity: Yes
UniProt
Find proteins for P0AC41 (Escherichia coli (strain K12)) Explore P0AC41 Go to UniProtKB: P0AC41
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AC41
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase iron-sulfur protein	B	238	Escherichia coli	Mutation(s): 0 Gene Names: SDHB OR B0724 EC: 1.3.99.1 (PDB Primary Data), 1.3.5.1 (PDB Primary Data) Membrane Entity: Yes
UniProt
Find proteins for P07014 (Escherichia coli (strain K12)) Explore P07014 Go to UniProtKB: P07014
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07014
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase cytochrome b-556 subunit	C	129	Escherichia coli	Mutation(s): 0 Gene Names: SDHC OR CYBA OR B0721 OR Z0875 OR ECS0746 Membrane Entity: Yes
UniProt
Find proteins for P69054 (Escherichia coli (strain K12)) Explore P69054 Go to UniProtKB: P69054
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P69054
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase hydrophobic membrane anchor protein	D	115	Escherichia coli	Mutation(s): 0 Gene Names: SDHD OR B0722 Membrane Entity: Yes
UniProt
Find proteins for P0AC44 (Escherichia coli (strain K12)) Explore P0AC44 Go to UniProtKB: P0AC44
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AC44
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDN Query on CDN Download Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	CARDIOLIPIN C₅₈ H₁₂₀ O₁₇ P₂ GKRASOJOCMJQMF-DUXRJKJQSA-N		Interactions Focus chain M [auth C]
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain G [auth A]
EPH Query on EPH Download Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C] mmCIF format, chain N [auth C]	N [auth C]	L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE C₃₉ H₆₈ N O₈ P MABRTXOVHMDVAT-AAEGOEIASA-N		Interactions Focus chain N [auth C]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain L [auth C]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain J [auth B]
UQ2 Query on UQ2 Download Ideal Coordinates CCD File SDF format, chain O [auth D] MOL2 format, chain O [auth D] mmCIF format, chain O [auth D]	O [auth D]	UBIQUINONE-2 C₁₉ H₂₆ O₄ SQQWBSBBCSFQGC-JLHYYAGUSA-N		Interactions Focus chain O [auth D]
F3S Query on F3S Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain K [auth B]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain I [auth B]
OAA Query on OAA Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	OXALOACETATE ION C₄ H₃ O₅ KHPXUQMNIQBQEV-UHFFFAOYSA-M		Interactions Focus chain E [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B]	F [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.289
R-Value Work: 0.247
R-Value Observed: 0.247
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.8	α = 90
b = 138.8	β = 90
c = 521.9	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
CNS	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2003-02-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-02-25
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary