7ARC | pdb_00007arc

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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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 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: 444.83 kDa 
  • Atom Count: 27,699 
  • Modeled Residue Count: 3,456 
  • Deposited Residue Count: 3,949 
  • Unique protein chains: 16

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PSSTA [auth B]164Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for A0A7S0V8A9 (Polytomella parva)
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UniProt GroupA0A7S0V8A9
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ND9B [auth C]217Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for A0A7S0VFV2 (Polytomella parva)
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UniProt GroupA0A7S0VFV2
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ND7C [auth D]395Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for A0A7S0VKR5 (Polytomella parva)
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UniProt GroupA0A7S0VKR5
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
24 kDaD [auth E]276Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
51 kDaE [auth F]469Polytomella sp. Pringsheim 198.80Mutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for A0A7S0V3A3 (Polytomella parva)
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UniProt GroupA0A7S0V3A3
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
75 kDaF [auth G]720Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
TYKYG [auth I]229Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for A0A7S0UQ60 (Polytomella parva)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
39 kDaH [auth P]370Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
18 kDaI [auth Q]185Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
13 kDaJ [auth R]132Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
B8K [auth S]98Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
SDAP2L [auth U]122Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for A0A7S0UWZ2 (Polytomella parva)
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
B13M [auth V]159Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
B14N [auth W]137Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A7S0UM40 (Polytomella parva)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
B17.2O [auth q]155Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
B14.5aP [auth r]121Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for A0A7S0YAP9 (Polytomella parva)
Explore A0A7S0YAP9 
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP

Query on NDP



Download:Ideal Coordinates CCD File
Z [auth P]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
8Q1

Query on 8Q1



Download:Ideal Coordinates CCD File
BA [auth W]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
FMN

Query on FMN



Download:Ideal Coordinates CCD File
S [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
Q [auth B]
T [auth F]
V [auth G]
W [auth G]
X [auth I]
Q [auth B],
T [auth F],
V [auth G],
W [auth G],
X [auth I],
Y [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES

Query on FES



Download:Ideal Coordinates CCD File
R [auth E],
U [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
AA [auth R]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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: 2024-07-10
    Changes: Data collection
  • Version 1.2: 2025-07-09
    Changes: Data collection, Structure summary