4UQ8

Electron cryo-microscopy of bovine Complex I

• PDB DOI:  https://doi.org/10.2210/pdb4UQ8/pdb
• EM Map EMD-2676: EMDB EMDataResource

• Classification: OXIDOREDUCTASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2014-06-21 Released: 2014-10-01 
• Deposition Author(s): Vinothkumar, K.R., Zhu, J., Hirst, J.

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.95 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Architecture of Mammalian Respiratory Complex I.

Vinothkumar, K.R., Zhu, J., Hirst, J.

(2014) Nature 515: 80

• PubMed: 25209663 
• DOI: https://doi.org/10.1038/nature13686
• Primary Citation of Related Structures:  
  4UQ8


• PubMed Abstract: 
  

Complex I (NADH:ubiquinone oxidoreductase) is essential for oxidative phosphorylation in mammalian mitochondria. It couples electron transfer from NADH to ubiquinone with proton translocation across the energy-transducing inner membrane, providing electrons for respiration and driving ATP synthesis. Mammalian complex I contains 44 different nuclear- and mitochondrial-encoded subunits, with a combined mass of 1 MDa. The 14 conserved 'core' subunits have been structurally defined in the minimal, bacterial complex, but the structures and arrangement of the 30 'supernumerary' subunits are unknown. Here we describe a 5 Å resolution structure of complex I from Bos taurus heart mitochondria, a close relative of the human enzyme, determined by single-particle electron cryo-microscopy. We present the structures of the mammalian core subunits that contain eight iron-sulphur clusters and 60 transmembrane helices, identify 18 supernumerary transmembrane helices, and assign and model 14 supernumerary subunits. Thus, we considerably advance knowledge of the structure of mammalian complex I and the architecture of its supernumerary ensemble around the core domains. Our structure provides insights into the roles of the supernumerary subunits in regulation, assembly and homeostasis, and a basis for understanding the effects of mutations that cause a diverse range of human diseases.

---

Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 49-mer - A13B10C8D6E5F3G2H1I1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 49-mer - A5B2C2D2E2F2G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 517.64 kDa 
• Atom Count: 28,647 
• Modelled Residue Count: 5,711 
• Deposited Residue Count: 6,036 
• Unique protein chains: 43

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE CHAIN 3	A	111	Bos taurus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN 7, MITOCHONDRIAL	B	143	Bos taurus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN 3, MITOCHONDRIAL	C	154	Bos taurus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN 2, MITOCHONDRIAL	D	384	Bos taurus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN 2, MITOCHONDRIAL	E	159	Bos taurus	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN 1, MITOCHONDRIAL	F	411	Bos taurus	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-UBIQUINONE OXIDOREDUCTASE 75 KDA SUBUNIT, MITOCHONDRIAL	G	538	Bos taurus	Mutation(s): 0

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE CHAIN 1	H	313	Bos taurus	Mutation(s): 0

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN 8, MITOCHONDRIAL	I	162	Bos taurus	Mutation(s): 0

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE CHAIN 6	J	171	Bos taurus	Mutation(s): 0

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE CHAIN 4L	K	84	Bos taurus	Mutation(s): 0

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE CHAIN 5	L	601	Bos taurus	Mutation(s): 0

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE CHAIN 4	M	453	Bos taurus	Mutation(s): 0

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE CHAIN 2	N	345	Bos taurus	Mutation(s): 0

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT 10	O	220	Bos taurus	Mutation(s): 0

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT 9, MITOCHONDRIAL	P	303	Bos taurus	Mutation(s): 0

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH DEHYDROGENASE [UBIQUINONE] SUBUNIT 4	Q	85	Bos taurus	Mutation(s): 0

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH DEHYDROGENASE [UBIQUINONE] SUBUNIT 6	R	47	Bos taurus	Mutation(s): 0

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT 2	S	80	Bos taurus	Mutation(s): 0

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
ACYL CARRIER PROTEIN, MITOCHONDRIAL	T	75	Bos taurus	Mutation(s): 0

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE DEHYDROGENASE	U	79	Bos taurus	Mutation(s): 0

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT; 5	V	71	Bos taurus	Mutation(s): 0

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT; 6	W	72	Bos taurus	Mutation(s): 0

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT 8	X	79	Bos taurus	Mutation(s): 0

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT; 11	Y	106	Bos taurus	Mutation(s): 0

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT 13	Z	65	Bos taurus	Mutation(s): 0

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	AA [auth a]	29	Bos taurus	Mutation(s): 0

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	BA [auth b]	42	Bos taurus	Mutation(s): 0

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	CA [auth c], WA [auth w]	27	Bos taurus	Mutation(s): 0

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	DA [auth d]	39	Bos taurus	Mutation(s): 0

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	EA [auth e]	20	Bos taurus	Mutation(s): 0

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	FA [auth f], HA [auth h], IA [auth i]	30	Bos taurus	Mutation(s): 0

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	GA [auth g]	22	Bos taurus	Mutation(s): 0

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	JA [auth j], LA [auth l]	24	Bos taurus	Mutation(s): 0

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	KA [auth k], PA [auth p], SA [auth s]	28	Bos taurus	Mutation(s): 0

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	MA [auth m]	34	Bos taurus	Mutation(s): 0

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	NA [auth n]	59	Bos taurus	Mutation(s): 0

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	OA [auth o]	21	Bos taurus	Mutation(s): 0

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	QA [auth q]	25	Bos taurus	Mutation(s): 0

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	RA [auth r]	26	Bos taurus	Mutation(s): 0

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	TA [auth t]	57	Bos taurus	Mutation(s): 0

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	UA [auth u]	43	Bos taurus	Mutation(s): 0

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	VA [auth v]	32	Bos taurus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	AB [auth G], BB [auth G], DB [auth I], EB [auth I], XA [auth B], ZA [auth F]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
FES	CB [auth G], YA [auth E]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.95 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-01 
Deposition Author(s): Vinothkumar, K.R., Zhu, J., Hirst, J.

Revision History  

• Version 1.0: 2014-10-01
  Type: Initial release
  
• Version 1.1: 2014-11-12
  Changes: Database references
• Version 1.2: 2017-08-02
  Changes: Data collection