6GCS image
Deposition Date 2018-04-19
Release Date 2018-10-10
Last Version Date 2024-10-09
Entry Detail
PDB ID:
6GCS
Keywords:
OXIDOREDUCTASE
Title:
Cryo-EM structure of respiratory complex I from Yarrowia lipolytica
Biological Source:
Source Organism:
Yarrowia lipolytica (Taxon ID: 4952)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.32 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6GCS validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ND1 SUBUNIT (NU1M)
Gene (Uniprot):ND1
Chain IDs:IA (auth: 1)
Chain Length:341
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q9B6E8 Pfam ID:PF00146
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ND2 SUBUNIT (NU2M)
Gene (Uniprot):ND2
Chain IDs:JA (auth: 2)
Chain Length:469
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q9B6C8 Pfam ID:PF00361
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ND3 SUBUNIT (NU3M)
Gene (Uniprot):ND3
Chain IDs:KA (auth: 3)
Chain Length:128
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q9B6C7 Pfam ID:PF00507
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ND4 SUBUNIT (NU4M)
Gene (Uniprot):ND4
Chain IDs:LA (auth: 4)
Chain Length:486
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q9B6D6 Pfam ID:PF00361
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ND5 SUBUNIT (NU5M)
Gene (Uniprot):ND5
Chain IDs:MA (auth: 5)
Chain Length:655
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q9B6D3 Pfam ID:PF00662, PF00361
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ND6 SUBUNIT (NU6M)
Gene (Uniprot):ND6
Chain IDs:NA (auth: 6)
Chain Length:185
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q9B6E9 Pfam ID:PF00499
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NB8M SUBUNIT
Chain IDs:OA (auth: 8)
Chain Length:99
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:B5FVG1 Pfam ID:PF05676
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NIPM SUBUNIT
Chain IDs:PA (auth: 9)
Chain Length:89
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:B5RSL7 Pfam ID:PF10200
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:75-KDA PROTEIN (NUAM)
Gene (Uniprot):nuam
Chain IDs:A
Chain Length:728
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q9UUU3 Pfam ID:PF13510, PF10588, PF22117, PF22151, PF00384, PF09326
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:51-KDA PROTEIN (NUBM)
Gene (Uniprot):nubm
Chain IDs:B
Chain Length:64
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q9UUU2 Pfam ID:PF01512, PF22461, PF10589
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:49-KDA PROTEIN (NUCM)
Gene (Uniprot):nucm
Chain IDs:C
Chain Length:466
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q9UUU1 Pfam ID:PF00346
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NIMM SUBUNIT
Chain IDs:D
Chain Length:92
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:B5FVD3 Pfam ID:PF15879
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NUEM SUBUNIT
Gene (Uniprot):YALI0_D24585g
Chain IDs:E
Chain Length:45
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q6C7X4 Pfam ID:PF01370
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NUFM SUBUNIT
Gene (Uniprot):YALI0_E23089g
Chain IDs:F
Chain Length:144
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q6C4W9 Pfam ID:PF04716
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30-KDA PROTEIN (NUGM)
Gene (Uniprot):nugm
Chain IDs:G
Chain Length:281
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q9UUU0 Pfam ID:PF00329 EC:7.1.1.2
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:24-KDA SUBUNIT (NUHM)
Gene (Uniprot):nuhm
Chain IDs:H
Chain Length:243
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q9UUT9 Pfam ID:PF01257
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:TYKY SUBUNIT (NUIM)
Gene (Uniprot):nuim
Chain IDs:I
Chain Length:53
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q9UUT8 Pfam ID:PF12838
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NUJM SUBUNIT
Gene (Uniprot):YALI0_E11891g
Chain IDs:J
Chain Length:93
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q6C674
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:PSST SUBUNIT (NUKM)
Gene (Uniprot):nukm
Chain IDs:K
Chain Length:210
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q9UUT7 Pfam ID:PF01058
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ND4L SUBUNIT (NULM)
Gene (Uniprot):ND4L
Chain IDs:L
Chain Length:86
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q9B6D4 Pfam ID:PF00420
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NUMM SUBUNIT
Chain IDs:M
Chain Length:136
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q6C8J9 Pfam ID:PF10276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ACPM1 SUBUNIT
Chain IDs:N (auth: O)
Chain Length:109
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q6C926 Pfam ID:PF00550
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NB4M SUBUNIT
Chain IDs:O (auth: P)
Chain Length:124
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q6CI60 Pfam ID:PF13233
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ACPM2 SUBUNIT
Chain IDs:P (auth: Q)
Chain Length:132
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q6C7X2 Pfam ID:PF00550
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NI2M SUBUNIT
Chain IDs:Q (auth: R)
Chain Length:109
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q6C9Z1
Polymer Type:polypeptide(L)
Molecule:NESM SUBUNIT
Chain IDs:R (auth: S)
Chain Length:159
Number of Molecules:1
Biological Source:Yarrowia lipolytica
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NUPM SUBUNIT
Gene (Uniprot):YALI0_A20680g
Chain IDs:S (auth: U)
Chain Length:172
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q6CGB4 Pfam ID:PF06747
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NB6M SUBUNIT
Chain IDs:T (auth: W)
Chain Length:123
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:B5FVF8 Pfam ID:PF06212
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NUXM SUBUNIT
Chain IDs:U (auth: X)
Chain Length:169
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q6C4A6 Pfam ID:PF10785, PF12853
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NUYM SUBUNIT
Chain IDs:V (auth: Y)
Chain Length:161
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q6CEK9 Pfam ID:PF04800
Polymer Type:polypeptide(L)
Molecule:NUZM SUBUNIT
Chain IDs:W (auth: Z)
Chain Length:137
Number of Molecules:1
Biological Source:Yarrowia lipolytica
Polymer Type:polypeptide(L)
Molecule:NIAM SUBUNIT
Chain IDs:X (auth: a)
Chain Length:728
Number of Molecules:1
Biological Source:Yarrowia lipolytica
Polymer Type:polypeptide(L)
Molecule:NEBM SUBUNIT
Chain IDs:Y (auth: b)
Chain Length:64
Number of Molecules:1
Biological Source:Yarrowia lipolytica
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NB2M SUBUNIT
Gene (Uniprot):YALI0_D10274g
Chain IDs:Z (auth: c)
Chain Length:466
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:B5FVE5 Pfam ID:PF08122
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NIDM SUBUNIT
Chain IDs:AA (auth: d)
Chain Length:92
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:B5RSK3 Pfam ID:PF10249
Polymer Type:polypeptide(L)
Molecule:NUUM SUBUNIT
Chain IDs:BA (auth: e)
Chain Length:45
Number of Molecules:1
Biological Source:Yarrowia lipolytica
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NI8M SUBUNIT
Chain IDs:CA (auth: f)
Chain Length:144
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q6CD73 Pfam ID:PF05047
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NI9M SUBUNIT
Chain IDs:DA (auth: g)
Chain Length:281
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:B5FVF3
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:N7BM SUBUNIT
Gene (Uniprot):N7BM
Chain IDs:EA (auth: h)
Chain Length:243
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q6CG53 Pfam ID:PF05071
Polymer Type:polypeptide(L)
Molecule:UNKNOWN SUBUNIT
Chain IDs:FA (auth: i)
Chain Length:53
Number of Molecules:1
Biological Source:Yarrowia lipolytica
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NB5M SUBUNIT
Gene (Uniprot):nuvm
Chain IDs:GA (auth: j)
Chain Length:93
Number of Molecules:1
Biological Source:Yarrowia lipolytica
UniProt ID:Q6ZY24
Polymer Type:polypeptide(L)
Molecule:NUNM SUBUNIT
Chain IDs:HA (auth: n)
Chain Length:93
Number of Molecules:1
Biological Source:Yarrowia lipolytica
Ligand Molecules
3PE
CDL
FES
FMN
NDP
SF4
ZMP
ZN
Primary Citation
Cryo-EM structure of respiratory complex I at work.
Elife 7 ? ? (2018)
PMID: 30277212 DOI: 10.7554/eLife.39213

Abstact

Mitochondrial complex I has a key role in cellular energy metabolism, generating a major portion of the proton motive force that drives aerobic ATP synthesis. The hydrophilic arm of the L-shaped ~1 MDa membrane protein complex transfers electrons from NADH to ubiquinone, providing the energy to drive proton pumping at distant sites in the membrane arm. The critical steps of energy conversion are associated with the redox chemistry of ubiquinone. We report the cryo-EM structure of complete mitochondrial complex I from the aerobic yeast Yarrowia lipolytica both in the deactive form and after capturing the enzyme during steady-state activity. The site of ubiquinone binding observed during turnover supports a two-state stabilization change mechanism for complex I.

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Disease

Primary Citation of related structures
6GCS