Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 16-mer - ABCDEFGHIJKLMNOP Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 16-mer -A3BCDEFGHIJKLMN 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 16-mer - ABCDEFGHIJKLMNOP Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 16-mer -A3BCDEFGHIJKLMN 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 1080577.25 
• Atom Count: 73998 
• Residue Count: 9796 
• Unique protein chains: 16

4HEA

Crystal structure of the entire respiratory complex I from Thermus thermophilus

• DOI: 10.2210/pdb4HEA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)


• Deposited: 2012-10-03 Released: 2013-02-13 
• Deposition Author(s): Baradaran, R., Berrisford, J.M., Minhas, G.S., Sazanov, L.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.3027 Å
• R-Value Free: 0.239 
• R-Value Work: 0.202 

Literature

Crystal structure of the entire respiratory complex I.

Baradaran, R., Berrisford, J.M., Minhas, G.S., Sazanov, L.A.

(2013) Nature 494: 443-448

• PubMed: 23417064 
• DOI: 10.1038/nature11871
• Primary Citation of Related Structures:  
  4HE8


• PubMed Abstract: 
  

Complex I is the first and largest enzyme of the respiratory chain and has a central role in cellular energy production through the coupling of NADH:ubiquinone electron transfer to proton translocation. It is also implicated in many common human neurodegenerative diseases. Here, we report the first crystal structure of the entire, intact complex I (from Thermus thermophilus) at 3.3 Å resolution. The structure of the 536-kDa complex comprises 16 different subunits, with a total of 64 transmembrane helices and 9 iron-sulphur clusters. The core fold of subunit Nqo8 (ND1 in humans) is, unexpectedly, similar to a half-channel of the antiporter-like subunits. Small subunits nearby form a linked second half-channel, which completes the fourth proton-translocation pathway (present in addition to the channels in three antiporter-like subunits). The quinone-binding site is unusually long, narrow and enclosed. The quinone headgroup binds at the deep end of this chamber, near iron-sulphur cluster N2. Notably, the chamber is linked to the fourth channel by a 'funnel' of charged residues. The link continues over the entire membrane domain as a flexible central axis of charged and polar residues, and probably has a leading role in the propagation of conformational changes, aided by coupling elements. The structure suggests that a unique, out-of-the-membrane quinone-reaction chamber enables the redox energy to drive concerted long-range conformational changes in the four antiporter-like domains, resulting in translocation of four protons per cycle.

---

Organizational Affiliation: 

Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
NADH-quinone oxidoreductase subunit 1	1, B	438	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: nqo1 EC: 7.1.1.-
Membrane protein mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Electron Transport Chain Complexes: Complex I	Protein:  Complex I complete
Find proteins for Q56222 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q56222

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
NADH-quinone oxidoreductase subunit 2	2, C	181	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: nqo2 EC: 7.1.1.-
Membrane protein mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Electron Transport Chain Complexes: Complex I	Protein:  Complex I complete
Find proteins for Q56221 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q56221

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
NADH-quinone oxidoreductase subunit 3	3, D	783	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: nqo3 EC: 7.1.1.-
Membrane protein mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Electron Transport Chain Complexes: Complex I	Protein:  Complex I complete
Find proteins for Q56223 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q56223

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
NADH-quinone oxidoreductase subunit 4	4, E	409	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: nqo4 EC: 7.1.1.-
Membrane protein mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Electron Transport Chain Complexes: Complex I	Protein:  Complex I complete
Find proteins for Q56220 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q56220

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
NADH-quinone oxidoreductase subunit 5	5, F	207	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: nqo5 EC: 7.1.1.-
Membrane protein mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Electron Transport Chain Complexes: Complex I	Protein:  Complex I complete
Find proteins for Q56219 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q56219

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
NADH-quinone oxidoreductase subunit 6	6, G	181	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: nqo6 EC: 7.1.1.-
Membrane protein mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Electron Transport Chain Complexes: Complex I	Protein:  Complex I complete
Find proteins for Q56218 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q56218

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
NADH-quinone oxidoreductase subunit 9	9, O	182	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: nqo9 EC: 7.1.1.-
Membrane protein mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Electron Transport Chain Complexes: Complex I	Protein:  Complex I complete
Find proteins for Q56224 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q56224

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
NADH-quinone oxidoreductase subunit 15	7, I	129	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: nqo15 EC: 7.1.1.-
Membrane protein mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Electron Transport Chain Complexes: Complex I	Protein:  Complex I complete
Find proteins for Q5SKZ7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SKZ7

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
Putative uncharacterized protein TTHA1528	W, X	131	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0
Membrane protein mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Electron Transport Chain Complexes: Complex I	Protein:  Complex I complete
Find proteins for Q5SI52 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SI52

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
NADH-quinone oxidoreductase subunit 7	A, P	119	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: nqo7 EC: 7.1.1.-
Membrane protein mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Electron Transport Chain Complexes: Complex I	Protein:  Complex I complete
Find proteins for Q56217 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q56217

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
NADH-quinone oxidoreductase subunit 10	J, R	176	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: nqo10 EC: 7.1.1.-
Membrane protein mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Electron Transport Chain Complexes: Complex I	Protein:  Complex I complete
Find proteins for Q56225 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q56225

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
NADH-quinone oxidoreductase subunit 11	K, S	95	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: nqo11 EC: 7.1.1.-
Membrane protein mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Electron Transport Chain Complexes: Complex I	Protein:  Complex I complete
Find proteins for Q56226 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q56226

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details
NADH-quinone oxidoreductase subunit 12	L, T	606	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: nqo12 EC: 7.1.1.-
Membrane protein mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Electron Transport Chain Complexes: Complex I	Protein:  Complex I complete
Find proteins for Q56227 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q56227

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details
NADH-quinone oxidoreductase subunit 13	M, U	469	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: nqo13 EC: 7.1.1.-
Membrane protein mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Electron Transport Chain Complexes: Complex I	Protein:  Complex I complete
Find proteins for Q56228 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q56228

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details
NADH-quinone oxidoreductase subunit 14	N, V	427	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: nqo14 EC: 7.1.1.-
Membrane protein mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Electron Transport Chain Complexes: Complex I	Protein:  Complex I complete
Find proteins for Q56229 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q56229

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
NADH-quinone oxidoreductase subunit 8	H, Q	365	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: nqo8 EC: 7.1.1.-
Membrane protein mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Electron Transport Chain Complexes: Complex I	Protein:  Complex I complete
Find proteins for Q60019 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q60019

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SF4	1, 3, 6, 9, B, D, G, O	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
FMN	1, B	FLAVIN MONONUCLEOTIDE RIBOFLAVIN MONOPHOSPHATE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
FES	2, 3, C, D	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.3027 Å
• R-Value Free: 0.239 
• R-Value Work: 0.202 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 96.280	α = 90.00
b = 340.890	β = 100.57
c = 263.300	γ = 90.00

Software Package:

Software Name	Purpose
MOSFLM	data reduction
XSCALE	data scaling
PHENIX	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-10-03 
• Released Date: 2013-02-13 
• Deposition Author(s): Baradaran, R., Berrisford, J.M., Minhas, G.S., Sazanov, L.A.

Revision History 

• Version 1.0: 2013-02-13
  Type: Initial release
• Version 1.1: 2013-03-13
  Type: Database references