7JRG | pdb_00007jrg

Plant Mitochondrial complex III2 from Vigna radiata


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Atomic structures of respiratory complex III 2 , complex IV, and supercomplex III 2 -IV from vascular plants.

Maldonado, M.Guo, F.Letts, J.A.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.62047
  • Primary Citation Related Structures: 
    7JRG, 7JRO, 7JRP

  • PubMed Abstract: 

    Mitochondrial complex III (CIII 2 ) and complex IV (CIV), which can associate into a higher-order supercomplex (SC III 2 +IV), play key roles in respiration. However, structures of these plant complexes remain unknown. We present atomic models of CIII 2 , CIV, and SC III 2 +IV from Vigna radiata determined by single-particle cryoEM. The structures reveal plant-specific differences in the MPP domain of CIII 2 and define the subunit composition of CIV. Conformational heterogeneity analysis of CIII 2 revealed long-range, coordinated movements across the complex, as well as the motion of CIII 2 's iron-sulfur head domain. The CIV structure suggests that, in plants, proton translocation does not occur via the H channel. The supercomplex interface differs significantly from that in yeast and bacteria in its interacting subunits, angle of approach and limited interactions in the mitochondrial matrix. These structures challenge long-standing assumptions about the plant complexes and generate new mechanistic hypotheses.


  • Organizational Affiliation
    • Department of Molecular and Cellular Biology, University of California Davis, Davis, United States.

Macromolecule Content 

  • Total Structure Weight: 570.54 kDa 
  • Atom Count: 32,930 
  • Modeled Residue Count: 3,983 
  • Deposited Residue Count: 4,838 
  • Unique protein chains: 10

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1A,
K [auth M]
527Vigna radiata var. radiataMutation(s): 0 
EC: 3.4.24.64
UniProt
Find proteins for A0A1S3TWG4 (Vigna radiata var. radiata)
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Entity Groups
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UniProt GroupA0A1S3TWG4
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-MPPB,
L [auth N]
506Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3VF71 (Vigna radiata var. radiata)
Explore A0A1S3VF71 
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UniProt GroupA0A1S3VF71
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
COBC,
M [auth O]
393Vigna radiata var. radiataMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
cytochrome c1-2, heme protein, mitochondrialD,
N [auth P]
306Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3W199 (Vigna radiata var. radiata)
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UniProt GroupA0A1S3W199
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE,
O [auth Q]
271Vigna radiata var. radiataMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3TB49 (Vigna radiata var. radiata)
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UniProt GroupA0A1S3TB49
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7F,
P [auth R]
122Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3U9J1 (Vigna radiata var. radiata)
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UniProt GroupA0A1S3U9J1
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
cytochrome b-c1 complex subunit 8G,
Q [auth S]
72Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3U9S5 (Vigna radiata var. radiata)
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UniProt GroupA0A1S3U9S5
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6H,
R [auth T]
69Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3VHC0 (Vigna radiata var. radiata)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
cytochrome b-c1 complex subunit 9I [auth J],
S [auth V]
72Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3TQD2 (Vigna radiata var. radiata)
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UniProt GroupA0A1S3TQD2
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
QCR10J [auth K],
T [auth W]
81Vigna radiata var. radiataMutation(s): 0 

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

Query on CDL



Download:Ideal Coordinates CCD File
AB [auth P]
CB [auth S]
GA [auth C]
IA [auth D]
OA [auth M]
AB [auth P],
CB [auth S],
GA [auth C],
IA [auth D],
OA [auth M],
RA [auth O],
VA [auth O],
W [auth A],
X [auth C]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PC1

Query on PC1



Download:Ideal Coordinates CCD File
BB [auth S],
PA [auth M],
V [auth A]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE

Query on 3PE



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
DB [auth W]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
DB [auth W],
EA [auth C],
EB [auth W],
FA [auth C],
JA [auth F],
KA [auth F],
LA [auth G],
NA [auth M],
QA [auth O],
UA [auth O],
WA [auth O],
XA [auth O],
YA [auth O]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
HEC

Query on HEC



Download:Ideal Coordinates CCD File
HA [auth D],
ZA [auth P]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
SA [auth O],
TA [auth O],
Y [auth C],
Z [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
ZN

Query on ZN



Download:Ideal Coordinates CCD File
MA [auth M],
U [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2021-02-03
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary