7ZKP

Late assembly intermediate of the proximal proton pumping module of complex I with assembly factors NDUFAF1 and CIA84

PDB DOI: https://doi.org/10.2210/pdb7ZKP/pdb
EM Map EMD-14764: EMDB EMDataResource

Classification: ELECTRON TRANSPORT
Organism(s): Yarrowia lipolytica
Expression System: Yarrowia lipolytica
Mutation(s): No
Membrane Protein: Yes OPMPDBTM

Deposited: 2022-04-13 Released: 2022-11-23
Deposition Author(s): Schiller, J., Laube, E., Vonck, J., Zickermann, V.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Insights into complex I assembly: Function of NDUFAF1 and a link with cardiolipin remodeling.

Schiller, J., Laube, E., Wittig, I., Kuhlbrandt, W., Vonck, J., Zickermann, V.

(2022) Sci Adv 8: eadd3855-eadd3855

PubMed: 36383672 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/sciadv.add3855
Primary Citation of Related Structures:
7ZKP, 7ZKQ

PubMed Abstract:
Respiratory complex I is a ~1-MDa proton pump in mitochondria. Its structure has been revealed in great detail, but the structural basis of its assembly, in humans involving at least 15 assembly factors, is essentially unknown. We determined cryo-electron microscopy structures of assembly intermediates associated with assembly factor NDUFAF1 in a yeast model system. Subunits ND2 and NDUFC2 together with assembly factors NDUFAF1 and CIA84 form the nucleation point of the NDUFAF1-dependent assembly pathway. Unexpectedly, the cardiolipin remodeling enzyme tafazzin is an integral component of this core complex. In a later intermediate, all 12 subunits of the proximal proton pump module have assembled. NDUFAF1 locks the central ND3 subunit in an assembly-competent conformation, and major rearrangements of central subunits are required for complex I maturation.

Organizational Affiliation

Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany.

Macromolecule Content

Total Structure Weight: 361.54 kDa
Atom Count: 19,929
Modelled Residue Count: 2,451
Deposited Residue Count: 3,146
Unique protein chains: 14

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)	A [auth D]	87	Yarrowia lipolytica	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for B5FVD3 (Yarrowia lipolytica (strain CLIB 122 / E 150)) Explore B5FVD3 Go to UniProtKB: B5FVD3
Entity Groups
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UniProt Group	B5FVD3
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 4L	B [auth L]	89	Yarrowia lipolytica	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for Q9B6D4 (Yarrowia lipolytica (strain CLIB 122 / E 150)) Explore Q9B6D4 Go to UniProtKB: Q9B6D4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9B6D4
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)	C [auth U]	172	Yarrowia lipolytica	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q6CGB4 (Yarrowia lipolytica (strain CLIB 122 / E 150)) Explore Q6CGB4 Go to UniProtKB: Q6CGB4
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6CGB4
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)	D [auth W]	123	Yarrowia lipolytica	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for B5FVF8 (Yarrowia lipolytica (strain CLIB 122 / E 150)) Explore B5FVF8 Go to UniProtKB: B5FVF8
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UniProt Group	B5FVF8
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit-domain-containing protein	E [auth X]	169	Yarrowia lipolytica	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q6C4A6 (Yarrowia lipolytica (strain CLIB 122 / E 150)) Explore Q6C4A6 Go to UniProtKB: Q6C4A6
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UniProt Group	Q6C4A6
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 1	F [auth 1]	341	Yarrowia lipolytica	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
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UniProt Group	Q9B6E8
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase subunit 2	G [auth 2]	469	Yarrowia lipolytica	Mutation(s): 0 EC: 1.6.5.3 Membrane Entity: Yes
UniProt
Find proteins for Q9B6C8 (Yarrowia lipolytica (strain CLIB 122 / E 150)) Explore Q9B6C8 Go to UniProtKB: Q9B6C8
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UniProt Group	Q9B6C8
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 3	H [auth 3]	128	Yarrowia lipolytica	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for Q9B6C7 (Yarrowia lipolytica (strain CLIB 122 / E 150)) Explore Q9B6C7 Go to UniProtKB: Q9B6C7
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UniProt Group	Q9B6C7
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 6	I [auth 6]	185	Yarrowia lipolytica	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for Q9B6E9 (Yarrowia lipolytica (strain CLIB 122 / E 150)) Explore Q9B6E9 Go to UniProtKB: Q9B6E9
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UniProt Group	Q9B6E9
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)	J [auth g]	78	Yarrowia lipolytica	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for B5FVF3 (Yarrowia lipolytica (strain CLIB 122 / E 150)) Explore B5FVF3 Go to UniProtKB: B5FVF3
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B5FVF3
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)	K [auth b]	74	Yarrowia lipolytica	Mutation(s): 0
UniProt
Find proteins for A0A1D8NGI5 (Yarrowia lipolytica) Explore A0A1D8NGI5 Go to UniProtKB: A0A1D8NGI5
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UniProt Group	A0A1D8NGI5
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)	L [auth 9]	89	Yarrowia lipolytica	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for B5RSL7 (Yarrowia lipolytica (strain CLIB 122 / E 150)) Explore B5RSL7 Go to UniProtKB: B5RSL7
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UniProt Group	B5RSL7
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
assembly factor CIA84	M [auth C]	852	Yarrowia lipolytica	Mutation(s): 0
UniProt
Find proteins for Q6CG31 (Yarrowia lipolytica (strain CLIB 122 / E 150)) Explore Q6CG31 Go to UniProtKB: Q6CG31
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UniProt Group	Q6CG31
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
CIA30 domain-containing protein	N [auth A]	290	Yarrowia lipolytica	Mutation(s): 0 Gene Names: YALI1_D17795g
UniProt
Find proteins for A0A1D8NEL0 (Yarrowia lipolytica) Explore A0A1D8NEL0 Go to UniProtKB: A0A1D8NEL0
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UniProt Group	A0A1D8NEL0
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Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download Ideal Coordinates CCD File SDF format, chain O [auth X] SDF format, chain R [auth g] MOL2 format, chain O [auth X] MOL2 format, chain R [auth g]	O [auth X], R [auth g]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain O [auth X] Focus chain R [auth g] Interactions & Density Focus chain O [auth X] Focus chain R [auth g]
T7X Query on T7X Download Ideal Coordinates CCD File SDF format, chain T [auth b] MOL2 format, chain T [auth b]	T [auth b]	Phosphatidylinositol C₄₇ H₈₃ O₁₃ P KRTOMQDUKGRFDJ-TWUHCGEESA-N		Interactions Focus chain T [auth b] Interactions & Density Focus chain T [auth b]
CPL Query on CPL Download Ideal Coordinates CCD File SDF format, chain Q [auth 2] MOL2 format, chain Q [auth 2]	Q [auth 2]	1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₂ H₈₀ N O₈ P JLPULHDHAOZNQI-ZTIMHPMXSA-N		Interactions Focus chain Q [auth 2] Interactions & Density Focus chain Q [auth 2]
3PE Query on 3PE Download Ideal Coordinates CCD File SDF format, chain S [auth g] MOL2 format, chain S [auth g]	S [auth g]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain S [auth g] Interactions & Density Focus chain S [auth g]
PLC Query on PLC Download Ideal Coordinates CCD File SDF format, chain P [auth 1] MOL2 format, chain P [auth 1]	P [auth 1]	DIUNDECYL PHOSPHATIDYL CHOLINE C₃₂ H₆₅ N O₈ P IJFVSSZAOYLHEE-SSEXGKCCSA-O		Interactions Focus chain P [auth 1] Interactions & Density Focus chain P [auth 1]