7AR9

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 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

  • DOI: https://doi.org/10.1093/plcell/koab092
  • Primary Citation of 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ND3154Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ND1B [auth H]293Polytomella sp. Pringsheim 198.80Mutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for E5Q323 (Polytomella sp. SAG 198.80)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ND6C [auth J]145Polytomella sp. Pringsheim 198.80Mutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ND4LD [auth K]127Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ND5E [auth L]536Polytomella sp. Pringsheim 198.80Mutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ND4F [auth M]438Polytomella sp. Pringsheim 198.80Mutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ND2G [auth N]375Polytomella sp. Pringsheim 198.80Mutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
C1-FDXH [auth O]200Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
SDAP1I [auth T]123Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
PGIVJ [auth X]100Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for A0A7S0UMB8 (Polytomella parva)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
B14.7K [auth Y]206Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
B16.6L [auth Z]142Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
MWFEM [auth a]71Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
B9N [auth b]54Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
KFYIO [auth c]110Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
B14.5bP [auth d]83Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
15 kDaQ [auth e]75Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
MNLLR [auth f]121Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
ESSSS [auth g]172Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NUOP4T [auth h]81Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NUOP5U [auth i]128Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
AGGGV [auth j]87Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
B12W [auth k]55Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
ASHIX [auth l]151Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for A0A7S0YPK2 (Polytomella parva)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
B15Y [auth m]138Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for A0A7S0Y945 (Polytomella parva)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
B22Z [auth n]121Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A024FSS5 (Polytomella sp. Pringsheim 198.80)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
B18AA [auth o]85Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
PDSWBA [auth p]156Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NUOP7CA [auth s]118Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A7S0VJV3 (Polytomella parva)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NUOP8DA [auth t]134Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
unknownEA [auth u]50Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
unknownFA [auth w]41Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
CALGA [auth x]280Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
CA2HA [auth y]310Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
CA3IA [auth z]227Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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BB [auth t],
LA [auth L],
RA [auth M],
SA [auth N],
XA [auth d]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PC7
Query on PC7

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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
PTY
Query on PTY

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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
8Q1
Query on 8Q1

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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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-08
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Structure summary