8BQ6

Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Complete conformation 2 composition)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of the respiratory I + III 2 supercomplex from Arabidopsis thaliana at 2 angstrom resolution.

Klusch, N.Dreimann, M.Senkler, J.Rugen, N.Kuhlbrandt, W.Braun, H.P.

(2023) Nat Plants 9: 142-156

  • DOI: https://doi.org/10.1038/s41477-022-01308-6
  • Primary Citation of Related Structures:  
    8BED, 8BEE, 8BEF, 8BEH, 8BEL, 8BEP, 8BPX, 8BQ5, 8BQ6

  • PubMed Abstract: 

    Protein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis respiratory supercomplex consisting of complex I and a complex III dimer, with a total of 68 protein subunits and numerous bound cofactors. A complex I-ferredoxin, subunit B14.7 and P9, a newly defined subunit of plant complex I, mediate supercomplex formation. The component complexes stabilize one another, enabling new detailed insights into their structure. We describe (1) an interrupted aqueous passage for proton translocation in the membrane arm of complex I; (2) a new coenzyme A within the carbonic anhydrase module of plant complex I defining a second catalytic centre; and (3) the water structure at the proton exit pathway of complex III 2 with a co-purified ubiquinone in the Q O site. We propose that the main role of the plant supercomplex is to stabilize its components in the membrane.


  • Organizational Affiliation

    Department of Structural Biology, Max-Planck-Institute of Biophysics, Frankfurt, Germany. [email protected].


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, mitochondrial218Arabidopsis 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 3190Arabidopsis 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 2394Arabidopsis 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, mitochondrial255Arabidopsis 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, mitochondrial486Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q9FNN5 (Arabidopsis thaliana)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial748Arabidopsis 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 1325Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for B5TM92 (Arabidopsis thaliana)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial222Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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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 dehydrogenase subunit 4L100Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Find proteins for Q04614 (Arabidopsis thaliana)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5669Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4495Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2499Arabidopsis 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
AT3G07480.1159Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for A0A384LA38 (Arabidopsis thaliana)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial402Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SK66 (Arabidopsis thaliana)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial154Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9FJW4 (Arabidopsis thaliana)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial110Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9M9M6 (Arabidopsis thaliana)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 297Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9FIJ2 (Arabidopsis thaliana)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein 1, mitochondrial122Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P53665 (Arabidopsis thaliana)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein 2, mitochondrial126Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O80800 (Arabidopsis thaliana)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial169Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9FLX7 (Arabidopsis thaliana)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6133Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9LHI0 (Arabidopsis thaliana)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B106Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Outer envelope pore protein 16-3, chloroplastic/mitochondrial159Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for O48528 (Arabidopsis thaliana)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A143Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q8RWA7 (Arabidopsis thaliana)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1AA [auth a]65Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9C9Z5 (Arabidopsis thaliana)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
At2g46540/F11C10.23BA [auth b]65Arabidopsis thalianaMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane proteinCA [auth c]88Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Excitatory amino acid transporterDA [auth d]81Arabidopsis thalianaMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-BEA [auth e]83Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9LZI6 (Arabidopsis thaliana)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
At4g16450FA [auth f]106Arabidopsis thalianaMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) proteinGA [auth g]114Arabidopsis thalianaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
P1HA [auth i]98Arabidopsis thalianaMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2IA [auth j]69Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-AJA [auth k]72Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialKA [auth l]125Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
B15 -- 1 beta subcomplex subunit 4LA [auth m]71Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for A0A178VZI4 (Arabidopsis thaliana)
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9MA [auth n]117Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7NA [auth o]103Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-BOA [auth p]106Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12PA [auth q]159Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein At1g67785QA [auth u]63Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein At2g27730, mitochondrialRA [auth v]113Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9ZUX4 (Arabidopsis thaliana)
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma carbonic anhydrase-like 2, mitochondrialSA [auth x]256Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SMN1 (Arabidopsis thaliana)
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma carbonic anhydrase 2, mitochondrialTA [auth y]278Arabidopsis thalianaMutation(s): 0 
EC: 4.2.1
Membrane Entity: Yes 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma carbonic anhydrase 1, mitochondrialUA [auth z]275Arabidopsis thalianaMutation(s): 0 
EC: 4.2.1
Membrane Entity: Yes 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Probable mitochondrial-processing peptidase subunit alpha-1, mitochondrialFB [auth BA],
VA [auth AA]
503Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9ZU25 (Arabidopsis thaliana)
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Probable mitochondrial-processing peptidase subunit beta, mitochondrialGB [auth BB],
WA [auth AB]
531Arabidopsis thalianaMutation(s): 0 
EC: 3.4.24.64
Membrane Entity: Yes 
UniProt
Find proteins for Q42290 (Arabidopsis thaliana)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bHB [auth BC],
XA [auth AC]
393Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P42792 (Arabidopsis thaliana)
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske-1, mitochondrialIB [auth BD],
YA [auth AD]
272Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1 2, heme protein, mitochondrialJB [auth BE],
ZA [auth AE]
307Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7-2, mitochondrialAB [auth AF],
KB [auth BF]
122Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8-1, mitochondrialBB [auth AG],
LB [auth BG]
72Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9SG91 (Arabidopsis thaliana)
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6-1, mitochondrialCB [auth AH],
MB [auth BH]
69Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q0WWE3 (Arabidopsis thaliana)
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9, mitochondrialDB [auth AI],
NB [auth BI]
72Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10, mitochondrialEB [auth AJ],
OB [auth BJ]
57Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COO (Subject of Investigation/LOI)
Query on COO

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FC [auth y]CROTONYL COENZYME A
C25 H40 N7 O17 P3 S
KFWWCMJSYSSPSK-XBTRWLRFSA-N
UQ9 (Subject of Investigation/LOI)
Query on UQ9

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WB [auth H]Ubiquinone-9
C54 H82 O4
UUGXJSBPSRROMU-YJKFELPISA-N
NDP (Subject of Investigation/LOI)
Query on NDP

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AC [auth P]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
UQ7 (Subject of Investigation/LOI)
Query on UQ7

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RC [auth BC]UBIQUINONE-7
C44 H66 O4
DBESHHFMIFSNRV-RJYQSXAYSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

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HC [auth AC]
IC [auth AC]
MC [auth AE]
OC [auth BC]
PC [auth BC]
HC [auth AC],
IC [auth AC],
MC [auth AE],
OC [auth BC],
PC [auth BC],
TC [auth BE]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
8Q1 (Subject of Investigation/LOI)
Query on 8Q1

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CC [auth W],
DC [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
UQ5 (Subject of Investigation/LOI)
Query on UQ5

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JC [auth AC],
KC [auth AC],
QC [auth BC]
2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE
C34 H50 O4
NYFAQDMDAFCWPU-UVCHAVPFSA-N
FMN (Subject of Investigation/LOI)
Query on FMN

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RB [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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PB [auth B]
SB [auth F]
UB [auth G]
VB [auth G]
XB [auth I]
PB [auth B],
SB [auth F],
UB [auth G],
VB [auth G],
XB [auth I],
YB [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

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LC [auth AD],
QB [auth E],
SC [auth BD],
TB [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

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BC [auth R],
EC [auth y],
GC [auth AB],
NC [auth BB]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)
Query on FE

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ZB [auth O]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1-4487
RECONSTRUCTIONRELION3.1.3

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: 2023-05-10
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Structure summary