7AR7

Cryo-EM structure of Arabidopsis thaliana complex-I (open conformation)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.72 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.Kuehlbrandt, 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
NADH-ubiquinone oxidoreductase chain 3119Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P92533 (Arabidopsis thaliana)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial157Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q42577 (Arabidopsis thaliana)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3185Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q95748 (Arabidopsis thaliana)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2385Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for P93306 (Arabidopsis thaliana)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial192Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for O22769 (Arabidopsis thaliana)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial434Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial688Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q9FGI6 (Arabidopsis thaliana)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1324Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P92558 (Arabidopsis thaliana)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial169Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q42599 (Arabidopsis thaliana)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6205Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P60497 (Arabidopsis thaliana)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4L88Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q04614 (Arabidopsis thaliana)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5615Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P29388 (Arabidopsis thaliana)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4487Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P93313 (Arabidopsis thaliana)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2488Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for O05000 (Arabidopsis thaliana)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrialO [auth P]331Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialP [auth Q]119Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9FJW4 (Arabidopsis thaliana)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialQ [auth R]62Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9M9M6 (Arabidopsis thaliana)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2R [auth S]93Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9FIJ2 (Arabidopsis thaliana)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein 1, mitochondrialS [auth T]84Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P53665 (Arabidopsis thaliana)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein 2, mitochondrialT [auth U]83Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O80800 (Arabidopsis thaliana)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrialU [auth V]140Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9FLX7 (Arabidopsis thaliana)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6V [auth W]133Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9LHI0 (Arabidopsis thaliana)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-BW [auth X]96Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q8LGE7 (Arabidopsis thaliana)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-AX [auth Z]125Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8RWA7 (Arabidopsis thaliana)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1Y [auth a]58Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9C9Z5 (Arabidopsis thaliana)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
At2g46540/F11C10.23Z [auth b]40Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9ZPY5 (Arabidopsis thaliana)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane proteinAA [auth c]76Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8VZT9 (Arabidopsis thaliana)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Excitatory amino acid transporterBA [auth d]75Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q94AL6 (Arabidopsis thaliana)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-ACA [auth e]64Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O82238 (Arabidopsis thaliana)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
At4g16450DA [auth f]100Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q84W12 (Arabidopsis thaliana)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) proteinEA [auth g]72Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9SLC8 (Arabidopsis thaliana)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
At1g67350FA [auth i]85Arabidopsis thalianaMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2GA [auth j]51Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-AHA [auth k]47Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialIA [auth l]46Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
AT2G31490 proteinJA [auth m]67Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9KA [auth n]109Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q945M1 (Arabidopsis thaliana)
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7LA [auth o]80Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9SKC9 (Arabidopsis thaliana)
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-BMA [auth p]93Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12NA [auth q]63Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9M9M9 (Arabidopsis thaliana)
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
B14.5aOA [auth r]10Arabidopsis thalianaMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
unknownPA [auth u]30Arabidopsis thalianaMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein At2g27730, mitochondrialQA [auth v]30Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9ZUX4 (Arabidopsis thaliana)
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma carbonic anhydrase-like 2, mitochondrialRA [auth x]214Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SMN1 (Arabidopsis thaliana)
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma carbonic anhydrase 2, mitochondrialSA [auth y]268Arabidopsis thalianaMutation(s): 0 
EC: 4.2.1
Membrane Entity: Yes 
UniProt
Find proteins for Q9C6B3 (Arabidopsis thaliana)
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Go to UniProtKB:  Q9C6B3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9C6B3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma carbonic anhydrase 1, mitochondrialTA [auth z]233Arabidopsis 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 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMN
Query on LMN

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HB [auth M]Lauryl Maltose Neopentyl Glycol
C47 H88 O22
MADJBYLAYPCCOO-XYPZXBMFSA-N
T7X
Query on T7X

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RB [auth z]Phosphatidylinositol
C47 H83 O13 P
KRTOMQDUKGRFDJ-TWUHCGEESA-N
UQ9
Query on UQ9

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BB [auth H]Ubiquinone-9
C54 H82 O4
UUGXJSBPSRROMU-YJKFELPISA-N
PC7
Query on PC7

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FB [auth M],
MB [auth f]
(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

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PB [auth y](1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C40 H79 O10 P
KBPVYRBBONZJHF-AMAPPZPBSA-N
NDP
Query on NDP

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JB [auth P]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
PTY
Query on PTY

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EB [auth I],
GB [auth M],
IB [auth N]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
8Q1
Query on 8Q1

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LB [auth W],
NB [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
FMN
Query on FMN

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WA [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
PSF
Query on PSF

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QB [auth z]1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE
C18 H34 N O10 P
MIQYPPGTNIFAPO-CABCVRRESA-N
SF4
Query on SF4

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AB [auth G]
CB [auth I]
DB [auth I]
UA [auth B]
XA [auth F]
AB [auth G],
CB [auth I],
DB [auth I],
UA [auth B],
XA [auth F],
ZA [auth G]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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VA [auth E],
YA [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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KB [auth R],
OB [auth y]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.72 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: 2022-03-02
    Type: Initial release