8BPX

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.09 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: 10.1038/s41477-022-01308-6
  • Primary Citation of Related Structures:  
    8BED, 8BEE, 8BEF, 8BEH, 8BEL, 8BEP, 8BPX

  • 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 ...

    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

    Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, Germany. braun@genetik.uni-hannover.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3A119Arabidopsis thalianaMutation(s): 0 
Gene Names: ND3NAD3AtMg00990
EC: 7.1.1.2
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Entity ID: 2
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialB218Arabidopsis thalianaMutation(s): 0 
Gene Names: At5g11770T22P22_160
EC: 7.1.1.2
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Entity ID: 3
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 3C190Arabidopsis thalianaMutation(s): 0 
Gene Names: NAD9AtMg00070
EC: 7.1.1.2
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Entity ID: 4
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 2D394Arabidopsis thalianaMutation(s): 0 
Gene Names: NAD7AtMg00510
EC: 7.1.1.2
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Entity ID: 5
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NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialE255Arabidopsis thalianaMutation(s): 0 
Gene Names: At4g02580T10P11.14
EC: 7.1.1.2
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Entity ID: 6
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NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialF486Arabidopsis thalianaMutation(s): 0 
Gene Names: At5g08530MAH20.9
EC: 7.1.1.2
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Entity ID: 7
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrialG748Arabidopsis thalianaMutation(s): 0 
Gene Names: EMB1467At5g37510MPA22.5
EC: 7.1.1.2
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Entity ID: 8
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NADH-ubiquinone oxidoreductase chain 1H325Arabidopsis thalianaMutation(s): 0 
Gene Names: ND1NAD1AtMg00516/AtMg01120/AtMg01275At2g07785At2g07786
EC: 7.1.1.2
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Entity ID: 9
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrialI222Arabidopsis thalianaMutation(s): 0 
Gene Names: At1g79010YUP8H12R.37YUP8H12R_21
EC: 7.1.1.2
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Entity ID: 10
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NADH-ubiquinone oxidoreductase chain 6J205Arabidopsis thalianaMutation(s): 0 
Gene Names: ND6NAD6AtMg00270
EC: 7.1.1.2
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Entity ID: 11
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NADH-ubiquinone oxidoreductase chain 4LK100Arabidopsis thalianaMutation(s): 0 
Gene Names: ND4LNAD4LAtMg00650
EC: 7.1.1.2
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NADH-ubiquinone oxidoreductase chain 5L669Arabidopsis thalianaMutation(s): 3 
Gene Names: ND5NAD5NAD5CAtMg00060/AtMg00513/AtMg00665
EC: 7.1.1.2
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NADH-ubiquinone oxidoreductase chain 4M495Arabidopsis thalianaMutation(s): 3 
Gene Names: ND4NAD4AtMg00580
EC: 7.1.1.2
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Entity ID: 14
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NADH-ubiquinone oxidoreductase chain 2N499Arabidopsis thalianaMutation(s): 0 
Gene Names: ND2NAD2AtMg00285/AtMg01320
EC: 7.1.1.2
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Entity ID: 15
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2Fe-2S ferredoxin-like superfamily proteinO159Arabidopsis thalianaMutation(s): 0 
Gene Names: F21O3.19At3g07480
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Entity ID: 16
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrialP402Arabidopsis thalianaMutation(s): 0 
Gene Names: At2g20360F11A3.9
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Entity ID: 17
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialQ154Arabidopsis thalianaMutation(s): 0 
Gene Names: FRO1At5g67590K9I9.16
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Entity ID: 18
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialR110Arabidopsis thalianaMutation(s): 0 
Gene Names: At3g03070T17B22_24
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Entity ID: 19
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2S97Arabidopsis thalianaMutation(s): 0 
Gene Names: At5g47890MCA23_23
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Entity ID: 20
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Acyl carrier protein 1, mitochondrialT122Arabidopsis thalianaMutation(s): 0 
Gene Names: MTACP1At2g44620F16B22.11
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Entity ID: 21
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Acyl carrier protein 2, mitochondrialU126Arabidopsis thalianaMutation(s): 0 
Gene Names: MTACP2At1g65290T8F5.6
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Entity ID: 22
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Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrialV169Arabidopsis thalianaMutation(s): 0 
Gene Names: At5g52840MXC20.6
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Find proteins for Q9FLX7 (Arabidopsis thaliana)
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Entity ID: 23
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6W133Arabidopsis thalianaMutation(s): 0 
Gene Names: At3g12260F28J15.12MQC3.9
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Entity ID: 24
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-BX106Arabidopsis thalianaMutation(s): 0 
Gene Names: At5g18800F17K4.50
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Entity ID: 25
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Outer envelope pore protein 16-3, chloroplastic/mitochondrialY159Arabidopsis thalianaMutation(s): 0 
Gene Names: OEP163B14.7At2g42210T24P15.12
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Entity ID: 26
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-AZ143Arabidopsis thalianaMutation(s): 0 
Gene Names: MEE4At1g04630T1G11.12
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Entity ID: 27
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1AA [auth a]65Arabidopsis thalianaMutation(s): 0 
Gene Names: At3g08610F17O14.8
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Entity ID: 28
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At2g46540/F11C10.23BA [auth b]65Arabidopsis thalianaMutation(s): 0 
Gene Names: At2g46540F13A10.7F13A10_7
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Entity ID: 29
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Transmembrane proteinCA [auth c]88Arabidopsis thalianaMutation(s): 0 
Gene Names: At4g00585
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Entity ID: 30
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Excitatory amino acid transporterDA [auth d]81Arabidopsis thalianaMutation(s): 0 
Gene Names: At4g20150F1C12.70F1C12_70
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Entity ID: 31
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-BEA [auth e]83Arabidopsis thalianaMutation(s): 0 
Gene Names: At3g62790F26K9_220
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At4g16450FA [auth f]106Arabidopsis thalianaMutation(s): 0 
Gene Names: At4g16450Dl4250WFCAALL.388
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Entity ID: 33
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ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) proteinGA [auth g]114Arabidopsis thalianaMutation(s): 0 
Gene Names: MHK10.3MHK10_3At2g42310
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At1g67350HA [auth i]98Arabidopsis thalianaMutation(s): 0 
Gene Names: At1g67350F1N21.17
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Entity ID: 35
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2IA [auth j]69Arabidopsis thalianaMutation(s): 0 
Gene Names: At1g76200T23E18.30
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Entity ID: 36
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-AJA [auth k]72Arabidopsis thalianaMutation(s): 0 
Gene Names: At2g02510T8K22.19
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Entity ID: 37
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialKA [auth l]125Arabidopsis thalianaMutation(s): 0 
Gene Names: At5g47570MNJ7.16
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Entity ID: 38
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AT2G31490 proteinLA [auth m]71Arabidopsis thalianaMutation(s): 0 
Gene Names: At2g31490T28P16.2T28P16_2
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Entity ID: 39
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9MA [auth n]117Arabidopsis thalianaMutation(s): 0 
Gene Names: CIB22At4g34700T4L20_280
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Entity ID: 40
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7NA [auth o]103Arabidopsis thalianaMutation(s): 0 
Gene Names: At2g02050F14H20.12
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Entity ID: 41
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-BOA [auth p]106Arabidopsis thalianaMutation(s): 0 
Gene Names: At3g18410MYF24_12
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12PA [auth q]159Arabidopsis thalianaMutation(s): 0 
Gene Names: At3g03100T17B22.21
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein At1g67785QA [auth u]63Arabidopsis thalianaMutation(s): 0 
Gene Names: At1g67785AT1G67785
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein At2g27730, mitochondrialRA [auth v]113Arabidopsis thalianaMutation(s): 0 
Gene Names: At2g27730F15K20.17
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
Gamma carbonic anhydrase-like 2, mitochondrialSA [auth x]256Arabidopsis thalianaMutation(s): 0 
Gene Names: GAMMACAL2At3g48680T8P19.190
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
Gamma carbonic anhydrase 2, mitochondrialTA [auth y]278Arabidopsis thalianaMutation(s): 0 
Gene Names: GAMMACA2APFIAt1g47260F8G22.2
EC: 4.2.1
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
Gamma carbonic anhydrase 1, mitochondrialUA [auth z]275Arabidopsis thalianaMutation(s): 0 
Gene Names: GAMMACA1At1g19580F14P1.8F18O14.34
EC: 4.2.1
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
Probable mitochondrial-processing peptidase subunit alpha-1, mitochondrialVA [auth AA],
FB [auth BA]
503Arabidopsis thalianaMutation(s): 0 
Gene Names: MPPalpha1At1g51980F5F19.4
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
Probable mitochondrial-processing peptidase subunit beta, mitochondrialWA [auth AB],
GB [auth BB]
531Arabidopsis thalianaMutation(s): 0 
Gene Names: MPPbetaAt3g02090F1C9.12
EC: 3.4.24.64
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bXA [auth AC],
HB [auth BC]
393Arabidopsis thalianaMutation(s): 1 
Gene Names: MT-CYBCOBCYTBMTCYBAtMg00220At2g07727
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske-1, mitochondrialYA [auth AD],
IB [auth BD]
272Arabidopsis thalianaMutation(s): 0 
Gene Names: UCR1-1At5g13430T22N19.80
EC: 7.1.1.8
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c1 2, heme protein, mitochondrialZA [auth AE],
JB [auth BE]
307Arabidopsis thalianaMutation(s): 0 
Gene Names: CYC1-2At5g40810MHK7.4
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7-2, mitochondrialAB [auth AF],
KB [auth BF]
122Arabidopsis thalianaMutation(s): 0 
Gene Names: QCR7-2At5g25450F18G18.190T14C9.20
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8-1, mitochondrialBB [auth AG],
LB [auth BG]
72Arabidopsis thalianaMutation(s): 0 
Gene Names: UCRQ-1At3g10860T7M13.6
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6-1, mitochondrialCB [auth AH],
MB [auth BH]
69Arabidopsis thalianaMutation(s): 0 
Gene Names: QCR6-1At1g15120F9L1.5
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9, mitochondrialDB [auth AI],
NB [auth BI]
72Arabidopsis thalianaMutation(s): 0 
Gene Names: QCR9At3g52730F3C22.130
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10, mitochondrialEB [auth AJ],
OB [auth BJ]
57Arabidopsis thalianaMutation(s): 0 
Gene Names: UCRYAt2g40765
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Small Molecules
Ligands 18 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

Download Ideal Coordinates CCD File 
DE [auth AE],
HD [auth u],
ID [auth u],
PE [auth BC],
QE [auth BC],
DE [auth AE],
HD [auth u],
ID [auth u],
PE [auth BC],
QE [auth BC],
XE [auth BE],
YD [auth AC],
ZD [auth AC],
ZE [auth BG]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
Q7G (Subject of Investigation/LOI)
Query on Q7G

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CC [auth K],
OC [auth M],
SE [auth BC],
TE [auth BC],
ZB [auth H],
CC [auth K],
OC [auth M],
SE [auth BC],
TE [auth BC],
ZB [auth H],
ZC [auth a]
2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside
C56 H92 O25
LKBFXDNKNZXHHW-NXLTVWPKSA-N
 Ligand Interaction
COO (Subject of Investigation/LOI)
Query on COO

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

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YB [auth H]Ubiquinone-9
C54 H82 O4
UUGXJSBPSRROMU-YJKFELPISA-N
 Ligand Interaction
PC7 (Subject of Investigation/LOI)
Query on PC7

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AE [auth AC],
BD [auth d],
ED [auth f],
FE [auth AG],
IC [auth L],
AE [auth AC],
BD [auth d],
ED [auth f],
FE [auth AG],
IC [auth L],
JD [auth v],
QD [auth AB],
RE [auth BC],
VE [auth BD]
(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
 Ligand Interaction
PGT (Subject of Investigation/LOI)
Query on PGT

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EC [auth L],
EE [auth AF],
FC [auth L],
GC [auth L],
LC [auth M],
EC [auth L],
EE [auth AF],
FC [auth L],
GC [auth L],
LC [auth M],
MD [auth y],
OE [auth BC],
PB [auth A],
WD [auth AC],
XD [auth AC]
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C40 H79 O10 P
KBPVYRBBONZJHF-AMAPPZPBSA-N
 Ligand Interaction
NDP (Subject of Investigation/LOI)
Query on NDP

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

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AD [auth d],
GD [auth m],
HC [auth L],
IE [auth BB],
MC [auth M],
AD [auth d],
GD [auth m],
HC [auth L],
IE [auth BB],
MC [auth M],
NC [auth M],
ND [auth z],
PC [auth N],
PD [auth AB],
QC [auth N],
RB [auth D],
RC [auth N],
YC [auth Y],
YE [auth BF]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
 Ligand Interaction
3PH (Subject of Investigation/LOI)
Query on 3PH

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AF [auth BJ],
BF [auth BJ],
CD [auth f],
DC [auth L],
DD [auth f],
AF [auth BJ],
BF [auth BJ],
CD [auth f],
DC [auth L],
DD [auth f],
FD [auth l],
GE [auth AI],
KC [auth M],
NE [auth BC],
VD [auth AC],
XC [auth Y]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
 Ligand Interaction
UQ7 (Subject of Investigation/LOI)
Query on UQ7

Download Ideal Coordinates CCD File 
ME [auth BC]UBIQUINONE-7
C44 H66 O4
DBESHHFMIFSNRV-RJYQSXAYSA-N
 Ligand Interaction
HEM (Subject of Investigation/LOI)
Query on HEM

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CE [auth AE],
JE [auth BC],
KE [auth BC],
RD [auth AC],
SD [auth AC],
CE [auth AE],
JE [auth BC],
KE [auth BC],
RD [auth AC],
SD [auth AC],
WE [auth BE]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
8Q1 (Subject of Investigation/LOI)
Query on 8Q1

Download Ideal Coordinates CCD File 
VC [auth T],
WC [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
 Ligand Interaction
UQ5 (Subject of Investigation/LOI)
Query on UQ5

Download Ideal Coordinates CCD File 
JC [auth L],
LE [auth BC],
TD [auth AC],
UD [auth AC]
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
 Ligand Interaction
FMN (Subject of Investigation/LOI)
Query on FMN

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

Download Ideal Coordinates CCD File 
AC [auth I],
BC [auth I],
QB [auth B],
UB [auth F],
WB [auth G],
AC [auth I],
BC [auth I],
QB [auth B],
UB [auth F],
WB [auth G],
XB [auth G]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
BE [auth AD],
SB [auth E],
UE [auth BD],
VB [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
HE [auth BB],
KD [auth y],
OD [auth AB],
UC [auth R]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
SC [auth O]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
A L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.09 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: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-02-01
    Changes: Database references