8BEL

Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CIII membrane domain)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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. Niklas.Klusch@biophys.mpg.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bA [auth C],
H [auth M]
393Arabidopsis thalianaMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for P42792 (Arabidopsis thaliana)
Explore P42792 
Go to UniProtKB:  P42792
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42792
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske-1, mitochondrialB [auth D],
I [auth N]
272Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for Q94JS0 (Arabidopsis thaliana)
Explore Q94JS0 
Go to UniProtKB:  Q94JS0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94JS0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1 2, heme protein, mitochondrialC [auth E],
J [auth O]
307Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9FKS5 (Arabidopsis thaliana)
Explore Q9FKS5 
Go to UniProtKB:  Q9FKS5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FKS5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8-1, mitochondrialD [auth G],
K [auth Q]
72Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SG91 (Arabidopsis thaliana)
Explore Q9SG91 
Go to UniProtKB:  Q9SG91
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SG91
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6-1, mitochondrialE [auth H],
L [auth R]
69Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q0WWE3 (Arabidopsis thaliana)
Explore Q0WWE3 
Go to UniProtKB:  Q0WWE3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0WWE3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9, mitochondrialF [auth I],
M [auth S]
72Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9LXJ2 (Arabidopsis thaliana)
Explore Q9LXJ2 
Go to UniProtKB:  Q9LXJ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LXJ2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10, mitochondrialG [auth J],
N [auth T]
57Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q94K78 (Arabidopsis thaliana)
Explore Q94K78 
Go to UniProtKB:  Q94K78
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94K78
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

Download Ideal Coordinates CCD File 
DA [auth G]
OA [auth M]
TA [auth N]
V [auth C]
W [auth C]
DA [auth G],
OA [auth M],
TA [auth N],
V [auth C],
W [auth C],
WA [auth O],
XA [auth Q]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
Q7G (Subject of Investigation/LOI)
Query on Q7G

Download Ideal Coordinates CCD File 
QA [auth M],
RA [auth M]
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
PC7 (Subject of Investigation/LOI)
Query on PC7

Download Ideal Coordinates CCD File 
EA [auth G],
PA [auth M],
UA [auth N],
X [auth C],
Z [auth D]
(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 (Subject of Investigation/LOI)
Query on PGT

Download Ideal Coordinates CCD File 
CA [auth G],
MA [auth M],
T [auth C],
U [auth C]
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C40 H79 O10 P
KBPVYRBBONZJHF-AMAPPZPBSA-N
PTY (Subject of Investigation/LOI)
Query on PTY

Download Ideal Coordinates CCD File 
AB [auth T],
GA [auth J],
NA [auth M]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
3PH (Subject of Investigation/LOI)
Query on 3PH

Download Ideal Coordinates CCD File 
BA [auth G]
FA [auth I]
LA [auth M]
S [auth C]
YA [auth T]
BA [auth G],
FA [auth I],
LA [auth M],
S [auth C],
YA [auth T],
ZA [auth T]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
UQ7 (Subject of Investigation/LOI)
Query on UQ7

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

Download Ideal Coordinates CCD File 
AA [auth E]
HA [auth M]
IA [auth M]
O [auth C]
P [auth C]
AA [auth E],
HA [auth M],
IA [auth M],
O [auth C],
P [auth C],
VA [auth O]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
UQ5 (Subject of Investigation/LOI)
Query on UQ5

Download Ideal Coordinates CCD File 
JA [auth M],
Q [auth C],
R [auth C]
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
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
SA [auth N],
Y [auth D]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1.3
MODEL REFINEMENTPHENIX1.20.1-4487

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: 2023-01-11
    Type: Initial release
  • Version 1.1: 2023-02-01
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary