7JRO

Plant Mitochondrial complex IV from Vigna radiata


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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

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: 10.7554/eLife.62047
  • Primary Citation of 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 ...

    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.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COX1A [auth a]527Vigna radiataMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2B [auth b]251Vigna radiata var. radiataMutation(s): 0 
Gene Names: LOC106760164
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3TZB2 (Vigna radiata var. radiata)
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UniProt GroupA0A1S3TZB2
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
COX3C [auth c]265Vigna radiataMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
COX4D [auth d]79Vigna radiata var. radiataMutation(s): 0 
Gene Names: LOC106757297
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3TNX9 (Vigna radiata var. radiata)
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UniProt GroupA0A1S3TNX9
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
cytochrome c oxidase subunit 5b-2, mitochondrialE [auth e]150Vigna radiata var. radiataMutation(s): 0 
Gene Names: LOC106760900
UniProt
Find proteins for A0A1S3U1E4 (Vigna radiata var. radiata)
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UniProt GroupA0A1S3U1E4
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
cytochrome c oxidase subunit 6a, mitochondrialF [auth f]100Vigna radiata var. radiataMutation(s): 0 
Gene Names: LOC106766916
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3UMA0 (Vigna radiata var. radiata)
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UniProt GroupA0A1S3UMA0
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
cytochrome c oxidase subunit 6b-1G [auth g]181Vigna radiata var. radiataMutation(s): 0 
Gene Names: LOC106778794
UniProt
Find proteins for A0A1S3VV60 (Vigna radiata var. radiata)
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UniProt GroupA0A1S3VV60
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5CH [auth h]64Vigna radiata var. radiataMutation(s): 0 
Gene Names: LOC106771138
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3V319 (Vigna radiata var. radiata)
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UniProt GroupA0A1S3V319
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
COX7aI [auth i]67Vigna radiata var. radiataMutation(s): 0 
Gene Names: LOC106759053
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3TUX2 (Vigna radiata var. radiata)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
COX7cJ [auth j]96Vigna radiata var. radiataMutation(s): 0 
Gene Names: LOC106772338
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3V7C2 (Vigna radiata var. radiata)
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UniProt GroupA0A1S3V7C2
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Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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R [auth a]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
HEA
Query on HEA

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K [auth a],
L [auth a]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
PC1
Query on PC1

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IA [auth i],
O [auth a]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
 Ligand Interaction
3PE
Query on 3PE

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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
 Ligand Interaction
LYS
Query on LYS

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JA [auth i]LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
CUA
Query on CUA

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W [auth b]DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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GA [auth e]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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M [auth a]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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N [auth a]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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