7AR9 | pdb_00007ar9

Cryo-EM structure of Polytomella Complex-I (membrane arm)

PDB DOI: https://doi.org/10.2210/pdb7AR9/pdb
EM Map EMD-11877: EMDB EMDataResource

Classification: ELECTRON TRANSPORT
Organism(s): Polytomella sp. Pringsheim 198.80
Mutation(s): No

Deposited: 2020-10-23 Released: 2021-12-08
Deposition Author(s): Klusch, N., Kuehlbrandt, W., Yildiz, O.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.97 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

A ferredoxin bridge connects the two arms of plant mitochondrial complex I.

Klusch, N., Senkler, J., Yildiz, O., Kuhlbrandt, W., Braun, H.P.

(2021) Plant Cell 33: 2072-2091

PubMed: 33768254 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/plcell/koab092
Primary Citation Related Structures:
7AQQ, 7AQR, 7AQW, 7AR7, 7AR8, 7AR9, 7ARB, 7ARC, 7ARD

PubMed Abstract:
Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two arms, which form a conserved L-shape. We report the structures of the intact, 47-subunit mitochondrial complex I from Arabidopsis thaliana and the 51-subunit complex I from the green alga Polytomella sp., both at around 2.9 Å resolution. In both complexes, a heterotrimeric γ-carbonic anhydrase domain is attached to the membrane arm on the matrix side. Two states are resolved in A. thaliana complex I, with different angles between the two arms and different conformations of the ND1 (NADH dehydrogenase subunit 1) loop near the quinol binding site. The angle appears to depend on a bridge domain, which links the peripheral arm to the membrane arm and includes an unusual ferredoxin. We propose that the bridge domain participates in regulating the activity of plant complex I.

Organizational Affiliation

Department of Structural Biology, Max-Planck-Institute of Biophysics, Frankfurt 60438, Germany.

Macromolecule Content

Total Structure Weight: 650.64 kDa
Atom Count: 42,861
Modeled Residue Count: 5,291
Deposited Residue Count: 5,687
Unique protein chains: 35

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ND3	A	154	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ND1	B [auth H]	293	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ND6	C [auth J]	145	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ND4L	D [auth K]	127	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ND5	E [auth L]	536	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
ND4	F [auth M]	438	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
ND2	G [auth N]	375	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
C1-FDX	H [auth O]	200	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
SDAP1	I [auth T]	123	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
PGIV	J [auth X]	100	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
B14.7	K [auth Y]	206	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
B16.6	L [auth Z]	142	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
MWFE	M [auth a]	71	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
B9	N [auth b]	54	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
KFYI	O [auth c]	110	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
B14.5b	P [auth d]	83	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
15 kDa	Q [auth e]	75	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
MNLL	R [auth f]	121	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
ESSS	S [auth g]	172	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
NUOP4	T [auth h]	81	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
NUOP5	U [auth i]	128	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
AGGG	V [auth j]	87	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
B12	W [auth k]	55	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
ASHI	X [auth l]	151	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
B15	Y [auth m]	138	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
B22	Z [auth n]	121	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
B18	AA [auth o]	85	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
PDSW	BA [auth p]	156	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
NUOP7	CA [auth s]	118	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
NUOP8	DA [auth t]	134	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
unknown	EA [auth u]	50	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
unknown	FA [auth w]	41	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
CAL	GA [auth x]	280	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
CA2	HA [auth y]	310	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
CA3	IA [auth z]	227	Polytomella sp. Pringsheim 198.80	Mutation(s): 0
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Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain XA [auth d] SDF format, chain SA [auth N] SDF format, chain RA [auth M] SDF format, chain LA [auth L] SDF format, chain BB [auth t] MOL2 format, chain XA [auth d] MOL2 format, chain SA [auth N] MOL2 format, chain RA [auth M] MOL2 format, chain LA [auth L] MOL2 format, chain BB [auth t] mmCIF format, chain XA [auth d] mmCIF format, chain SA [auth N] mmCIF format, chain RA [auth M] mmCIF format, chain LA [auth L] mmCIF format, chain BB [auth t]	BB [auth t], LA [auth L], RA [auth M], SA [auth N], XA [auth d]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain BB [auth t] Focus chain LA [auth L] Focus chain RA [auth M] Focus chain SA [auth N] Focus chain XA [auth d] Interactions & Density Focus chain BB [auth t] Focus chain LA [auth L] Focus chain RA [auth M] Focus chain SA [auth N] Focus chain XA [auth d]
PC7 Query on PC7 Download:Ideal Coordinates CCD File SDF format, chain UA [auth N] SDF format, chain TA [auth N] SDF format, chain OA [auth L] SDF format, chain NA [auth L] SDF format, chain MA [auth L] SDF format, chain JA [auth A] SDF format, chain CB [auth z] MOL2 format, chain UA [auth N] MOL2 format, chain TA [auth N] MOL2 format, chain OA [auth L] MOL2 format, chain NA [auth L] MOL2 format, chain MA [auth L] MOL2 format, chain JA [auth A] MOL2 format, chain CB [auth z] mmCIF format, chain UA [auth N] mmCIF format, chain TA [auth N] mmCIF format, chain OA [auth L] mmCIF format, chain NA [auth L] mmCIF format, chain MA [auth L] mmCIF format, chain JA [auth A] mmCIF format, chain CB [auth z]	CB [auth z] JA [auth A] MA [auth L] NA [auth L] OA [auth L] CB [auth z], JA [auth A], MA [auth L], NA [auth L], OA [auth L], TA [auth N], UA [auth N]	(7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE C₄₂ H₈₅ N O₈ P PZNPLUBHRSSFHT-FAIXQHPJSA-O		Interactions Focus chain CB [auth z] Focus chain JA [auth A] Focus chain MA [auth L] Focus chain NA [auth L] Focus chain OA [auth L] Focus chain TA [auth N] Focus chain UA [auth N] Interactions & Density Focus chain CB [auth z] Focus chain JA [auth A] Focus chain MA [auth L] Focus chain NA [auth L] Focus chain OA [auth L] Focus chain TA [auth N] Focus chain UA [auth N]
PTY Query on PTY Download:Ideal Coordinates CCD File SDF format, chain ZA [auth m] SDF format, chain YA [auth m] SDF format, chain WA [auth Y] SDF format, chain VA [auth N] SDF format, chain QA [auth M] SDF format, chain PA [auth L] SDF format, chain KA [auth H] MOL2 format, chain ZA [auth m] MOL2 format, chain YA [auth m] MOL2 format, chain WA [auth Y] MOL2 format, chain VA [auth N] MOL2 format, chain QA [auth M] MOL2 format, chain PA [auth L] MOL2 format, chain KA [auth H] mmCIF format, chain ZA [auth m] mmCIF format, chain YA [auth m] mmCIF format, chain WA [auth Y] mmCIF format, chain VA [auth N] mmCIF format, chain QA [auth M] mmCIF format, chain PA [auth L] mmCIF format, chain KA [auth H]	KA [auth H] PA [auth L] QA [auth M] VA [auth N] WA [auth Y] KA [auth H], PA [auth L], QA [auth M], VA [auth N], WA [auth Y], YA [auth m], ZA [auth m]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain KA [auth H] Focus chain PA [auth L] Focus chain QA [auth M] Focus chain VA [auth N] Focus chain WA [auth Y] Focus chain YA [auth m] Focus chain ZA [auth m] Interactions & Density Focus chain KA [auth H] Focus chain PA [auth L] Focus chain QA [auth M] Focus chain VA [auth N] Focus chain WA [auth Y] Focus chain YA [auth m] Focus chain ZA [auth m]
8Q1 Query on 8Q1 Download:Ideal Coordinates CCD File SDF format, chain AB [auth n] MOL2 format, chain AB [auth n] mmCIF format, chain AB [auth n]	AB [auth n]	S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate C₂₃ H₄₅ N₂ O₈ P S MVHUOSAYFQKAMT-NRFANRHFSA-N		Interactions Focus chain AB [auth n] Interactions & Density Focus chain AB [auth n]