7JRO | pdb_00007jro

Plant Mitochondrial complex IV from Vigna radiata


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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: 216.21 kDa 
  • Atom Count: 12,747 
  • Modeled Residue Count: 1,491 
  • Deposited Residue Count: 1,780 
  • Unique protein chains: 10

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
COX1A [auth a]527Vigna radiataMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2B [auth b]251Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3TZB2 (Vigna radiata var. radiata)
Explore A0A1S3TZB2 
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Entity Groups
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UniProt GroupA0A1S3TZB2
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
COX3C [auth c]265Vigna radiataMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
COX4D [auth d]79Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3TNX9 (Vigna radiata var. radiata)
Explore A0A1S3TNX9 
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UniProt GroupA0A1S3TNX9
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
cytochrome c oxidase subunit 5b-2, mitochondrialE [auth e]150Vigna radiata var. radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3U1E4 (Vigna radiata var. radiata)
Explore A0A1S3U1E4 
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UniProt GroupA0A1S3U1E4
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
cytochrome c oxidase subunit 6a, mitochondrialF [auth f]100Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3UMA0 (Vigna radiata var. radiata)
Explore A0A1S3UMA0 
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UniProt GroupA0A1S3UMA0
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
cytochrome c oxidase subunit 6b-1G [auth g]181Vigna radiata var. radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3VV60 (Vigna radiata var. radiata)
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UniProt GroupA0A1S3VV60
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5CH [auth h]64Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3V319 (Vigna radiata var. radiata)
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UniProt GroupA0A1S3V319
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
COX7aI [auth i]67Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3TUX2 (Vigna radiata var. radiata)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
COX7cJ [auth j]96Vigna radiata var. radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3V7C2 (Vigna radiata var. radiata)
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Reference Sequence

Small Molecules

Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

Query on CDL



Download:Ideal Coordinates CCD File
R [auth a]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
HEA

Query on HEA



Download:Ideal Coordinates CCD File
K [auth a],
L [auth a]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PC1

Query on PC1



Download:Ideal Coordinates CCD File
IA [auth i],
O [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]
EA [auth c]
AA [auth c],
BA [auth c],
CA [auth c],
DA [auth c],
EA [auth c],
FA [auth d],
HA [auth h],
KA [auth i],
P [auth a],
Q [auth a],
S [auth a],
T [auth a],
U [auth a],
V [auth a],
X [auth b],
Y [auth b],
Z [auth b]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
LYS

Query on LYS



Download:Ideal Coordinates CCD File
JA [auth i]LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
CUA

Query on CUA



Download:Ideal Coordinates CCD File
W [auth b]DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
GA [auth e]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU

Query on CU



Download:Ideal Coordinates CCD File
M [auth a]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
N [auth a]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary