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

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Architecture of Mammalian Respiratory Complex I.

Vinothkumar, K.R., Zhu, J., Hirst, J.

(2014) Nature 515: 80

PubMed: 25209663 Search on PubMedSearch on PubMed Central
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 Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.

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

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

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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
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN 2, MITOCHONDRIAL	E	159	Bos taurus	Mutation(s): 0
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN 1, MITOCHONDRIAL	F	411	Bos taurus	Mutation(s): 0
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-UBIQUINONE OXIDOREDUCTASE 75 KDA SUBUNIT, MITOCHONDRIAL	G	538	Bos taurus	Mutation(s): 0
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE CHAIN 1	H	313	Bos taurus	Mutation(s): 0
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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
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE CHAIN 6	J	171	Bos taurus	Mutation(s): 0
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE CHAIN 4L	K	84	Bos taurus	Mutation(s): 0
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE CHAIN 5	L	601	Bos taurus	Mutation(s): 0
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE CHAIN 4	M	453	Bos taurus	Mutation(s): 0
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE CHAIN 2	N	345	Bos taurus	Mutation(s): 0
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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
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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
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH DEHYDROGENASE [UBIQUINONE] SUBUNIT 4	Q	85	Bos taurus	Mutation(s): 0
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH DEHYDROGENASE [UBIQUINONE] SUBUNIT 6	R	47	Bos taurus	Mutation(s): 0
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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
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
ACYL CARRIER PROTEIN, MITOCHONDRIAL	T	75	Bos taurus	Mutation(s): 0
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE DEHYDROGENASE	U	79	Bos taurus	Mutation(s): 0
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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
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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
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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
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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
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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
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	AA [auth a]	29	Bos taurus	Mutation(s): 0
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	BA [auth b]	42	Bos taurus	Mutation(s): 0
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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
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	DA [auth d]	39	Bos taurus	Mutation(s): 0
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	EA [auth e]	20	Bos taurus	Mutation(s): 0
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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
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	GA [auth g]	22	Bos taurus	Mutation(s): 0
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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
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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
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	MA [auth m]	34	Bos taurus	Mutation(s): 0
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	NA [auth n]	59	Bos taurus	Mutation(s): 0
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	OA [auth o]	21	Bos taurus	Mutation(s): 0
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	QA [auth q]	25	Bos taurus	Mutation(s): 0
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	RA [auth r]	26	Bos taurus	Mutation(s): 0
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	TA [auth t]	57	Bos taurus	Mutation(s): 0
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	UA [auth u]	43	Bos taurus	Mutation(s): 0
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH UBIQUINONE OXIDOREDUCTASE	VA [auth v]	32	Bos taurus	Mutation(s): 0
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Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain AB [auth G] SDF format, chain BB [auth G] SDF format, chain DB [auth I] SDF format, chain EB [auth I] SDF format, chain XA [auth B] SDF format, chain ZA [auth F] MOL2 format, chain AB [auth G] MOL2 format, chain BB [auth G] MOL2 format, chain DB [auth I] MOL2 format, chain EB [auth I] MOL2 format, chain XA [auth B] MOL2 format, chain ZA [auth F]	AB [auth G] BB [auth G] DB [auth I] EB [auth I] XA [auth B] AB [auth G], BB [auth G], DB [auth I], EB [auth I], XA [auth B], ZA [auth F]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AB [auth G] Focus chain BB [auth G] Focus chain DB [auth I] Focus chain EB [auth I] Focus chain XA [auth B] Focus chain ZA [auth F] Interactions & Density Focus chain AB [auth G] Focus chain BB [auth G] Focus chain DB [auth I] Focus chain EB [auth I] Focus chain XA [auth B] Focus chain ZA [auth F]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain CB [auth G] SDF format, chain YA [auth E] MOL2 format, chain CB [auth G] MOL2 format, chain YA [auth E]	CB [auth G], YA [auth E]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain CB [auth G] Focus chain YA [auth E] Interactions & Density Focus chain CB [auth G] Focus chain YA [auth E]

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

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Entry History

Deposition Data

Released Date: 2014-10-01

Deposition Author(s):

Vinothkumar, K.R.

Zhu, J.

Hirst, J.

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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Help and Resources

4UQ8

Electron cryo-microscopy of bovine Complex I

Architecture of Mammalian Respiratory Complex I.

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