7ARD | pdb_00007ard

Cryo-EM structure of Polytomella Complex-I (complete composition)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7ARD

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

  • 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: 1,095.47 kDa 
  • Atom Count: 70,559 
  • Modeled Residue Count: 8,747 
  • Deposited Residue Count: 9,636 
  • Unique protein chains: 51

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
PSST164Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ND9217Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ND7395Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
24 kDa276Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
51 kDa469Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
75 kDa720Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
ND1293Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
TYKY229Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
ND6145Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
ND4L127Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
ND5536Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
ND4438Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
ND2375Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
C1-FDX200Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
39 kDa370Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
18 kDa185Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
13 kDa132Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
B898Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
SDAP1123Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
SDAP2122Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
B13159Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
B14137Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
PGIV100Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
B14.7206Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
B16.6142Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
MWFEAA [auth a]71Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
B9BA [auth b]54Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
KFYICA [auth c]110Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
B14.5bDA [auth d]83Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
15 kDaEA [auth e]75Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
MNLLFA [auth f]121Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
ESSSGA [auth g]172Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
NUOP4HA [auth h]81Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
NUOP5IA [auth i]128Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
AGGGJA [auth j]87Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
B12KA [auth k]55Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
ASHILA [auth l]151Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
B15MA [auth m]138Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
Complex I-B22NA [auth n]121Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A024FSS5 (Polytomella sp. Pringsheim 198.80)
Explore A0A024FSS5 
Go to UniProtKB:  A0A024FSS5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A024FSS5
Sequence Annotations
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Reference Sequence
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
B18OA [auth o]85Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
PDSWPA [auth p]156Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
B17.2QA [auth q]155Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
B14.5aRA [auth r]121Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
NUOP7SA [auth s]118Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
NUOP8TA [auth t]134Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
unknownUA [auth u]50Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
unknownVA [auth w]41Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
CALWA [auth x]280Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
CA2XA [auth y]310Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 51
MoleculeChains  Sequence LengthOrganismDetailsImage
CA3YA [auth z]227Polytomella sp. Pringsheim 198.80Mutation(s): 0 

Small Molecules

Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

Query on CDL



Download:Ideal Coordinates CCD File
DC [auth t],
KB [auth L],
OB [auth M],
RB [auth N],
ZB [auth d]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PC7

Query on PC7



Download:Ideal Coordinates CCD File
EC [auth z]
LB [auth L]
PB [auth M]
QB [auth M]
SB [auth N]
EC [auth z],
LB [auth L],
PB [auth M],
QB [auth M],
SB [auth N],
TB [auth N],
ZA [auth A]
(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
NDP

Query on NDP



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

Query on PTY



Download:Ideal Coordinates CCD File
AC [auth m]
BC [auth m]
HB [auth H]
MB [auth L]
NB [auth M]
AC [auth m],
BC [auth m],
HB [auth H],
MB [auth L],
NB [auth M],
UB [auth N],
YB [auth Y]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
8Q1

Query on 8Q1



Download:Ideal Coordinates CCD File
CC [auth n],
XB [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
CB [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
AB [auth B]
DB [auth F]
FB [auth G]
GB [auth G]
IB [auth I]
AB [auth B],
DB [auth F],
FB [auth G],
GB [auth G],
IB [auth I],
JB [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES

Query on FES



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

Query on ZN



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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 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 SocietyGermany1

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
  • Version 1.2: 2025-07-02
    Changes: Data collection