7AQQ

Cryo-EM structure of Arabidopsis thaliana Complex-I (membrane core)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3119Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P92533 (Arabidopsis thaliana)
Explore P92533 
Go to UniProtKB:  P92533
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP92533
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1B [auth H]325Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P92558 (Arabidopsis thaliana)
Explore P92558 
Go to UniProtKB:  P92558
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP92558
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6C [auth J]205Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P60497 (Arabidopsis thaliana)
Explore P60497 
Go to UniProtKB:  P60497
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60497
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 4LD [auth K]100Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q04614 (Arabidopsis thaliana)
Explore Q04614 
Go to UniProtKB:  Q04614
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04614
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5E [auth L]669Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P29388 (Arabidopsis thaliana)
Explore P29388 
Go to UniProtKB:  P29388
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29388
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4F [auth M]495Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P93313 (Arabidopsis thaliana)
Explore P93313 
Go to UniProtKB:  P93313
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP93313
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2G [auth N]499Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for O05000 (Arabidopsis thaliana)
Explore O05000 
Go to UniProtKB:  O05000
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO05000
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
AT3G07480.1H [auth O]159Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9SRR8 (Arabidopsis thaliana)
Explore Q9SRR8 
Go to UniProtKB:  Q9SRR8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SRR8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-BI [auth X]106Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q8LGE7 (Arabidopsis thaliana)
Explore Q8LGE7 
Go to UniProtKB:  Q8LGE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8LGE7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-AJ [auth Z]143Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8RWA7 (Arabidopsis thaliana)
Explore Q8RWA7 
Go to UniProtKB:  Q8RWA7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RWA7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1K [auth a]65Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9C9Z5 (Arabidopsis thaliana)
Explore Q9C9Z5 
Go to UniProtKB:  Q9C9Z5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9C9Z5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
At2g46540/F11C10.23L [auth b]65Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9ZPY5 (Arabidopsis thaliana)
Explore Q9ZPY5 
Go to UniProtKB:  Q9ZPY5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZPY5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Excitatory amino acid transporterM [auth d]81Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q94AL6 (Arabidopsis thaliana)
Explore Q94AL6 
Go to UniProtKB:  Q94AL6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94AL6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-BN [auth e]83Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9LZI6 (Arabidopsis thaliana)
Explore Q9LZI6 
Go to UniProtKB:  Q9LZI6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LZI6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
At4g16450O [auth f]106Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q84W12 (Arabidopsis thaliana)
Explore Q84W12 
Go to UniProtKB:  Q84W12
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84W12
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
P1P [auth i]98Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9FYF8 (Arabidopsis thaliana)
Explore Q9FYF8 
Go to UniProtKB:  Q9FYF8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FYF8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
unknownQ [auth u]30Arabidopsis thalianaMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein At2g27730, mitochondrialR [auth v]113Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9ZUX4 (Arabidopsis thaliana)
Explore Q9ZUX4 
Go to UniProtKB:  Q9ZUX4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZUX4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma carbonic anhydrase-like 2, mitochondrialS [auth x]256Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SMN1 (Arabidopsis thaliana)
Explore Q9SMN1 
Go to UniProtKB:  Q9SMN1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SMN1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma carbonic anhydrase 2, mitochondrialT [auth y]278Arabidopsis thalianaMutation(s): 0 
EC: 4.2.1
Membrane Entity: Yes 
UniProt
Find proteins for Q9C6B3 (Arabidopsis thaliana)
Explore Q9C6B3 
Go to UniProtKB:  Q9C6B3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9C6B3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma carbonic anhydrase 1, mitochondrialU [auth z]275Arabidopsis thalianaMutation(s): 0 
EC: 4.2.1
Membrane Entity: Yes 
UniProt
Find proteins for Q9FWR5 (Arabidopsis thaliana)
Explore Q9FWR5 
Go to UniProtKB:  Q9FWR5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FWR5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMN
Query on LMN

Download Ideal Coordinates CCD File 
X [auth M]Lauryl Maltose Neopentyl Glycol
C47 H88 O22
MADJBYLAYPCCOO-XYPZXBMFSA-N
T7X
Query on T7X

Download Ideal Coordinates CCD File 
EA [auth z]Phosphatidylinositol
C47 H83 O13 P
KRTOMQDUKGRFDJ-TWUHCGEESA-N
UQ9
Query on UQ9

Download Ideal Coordinates CCD File 
V [auth H]Ubiquinone-9
C54 H82 O4
UUGXJSBPSRROMU-YJKFELPISA-N
PC7
Query on PC7

Download Ideal Coordinates CCD File 
AA [auth v](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
PGT
Query on PGT

Download Ideal Coordinates CCD File 
CA [auth y](1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C40 H79 O10 P
KBPVYRBBONZJHF-AMAPPZPBSA-N
PTY
Query on PTY

Download Ideal Coordinates CCD File 
W [auth H],
Y [auth N]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
PSF
Query on PSF

Download Ideal Coordinates CCD File 
DA [auth z]1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE
C18 H34 N O10 P
MIQYPPGTNIFAPO-CABCVRRESA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth y]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
Z [auth O]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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