8E73

Vigna radiata supercomplex I+III2 (full bridge)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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

Plant-specific features of respiratory supercomplex I + III 2 from Vigna radiata.

Maldonado, M.Fan, Z.Abe, K.M.Letts, J.A.

(2023) Nat Plants 9: 157-168

  • DOI: https://doi.org/10.1038/s41477-022-01306-8
  • Primary Citation of Related Structures:  
    8E73

  • PubMed Abstract: 

    The last steps of cellular respiration-an essential metabolic process in plants-are carried out by mitochondrial oxidative phosphorylation. This process involves a chain of multi-subunit membrane protein complexes (complexes I-V) that form higher-order assemblies called supercomplexes. Although supercomplexes are the most physiologically relevant form of the oxidative phosphorylation complexes, their functions and structures remain mostly unknown. Here we present the cryogenic electron microscopy structure of the supercomplex I + III 2 from Vigna radiata (mung bean). The structure contains the full subunit complement of complex I, including a newly assigned, plant-specific subunit. It also shows differences in the mitochondrial processing peptidase domain of complex III 2 relative to a previously determined supercomplex with complex IV. The supercomplex interface, while reminiscent of that in other organisms, is plant specific, with a major interface involving complex III 2 's mitochondrial processing peptidase domain and no participation of complex I's bridge domain. The complex I structure suggests that the bridge domain sets the angle between the enzyme's two arms, limiting large-scale conformational changes. Moreover, complex I's catalytic loops and its response in active-to-deactive assays suggest that, in V. radiata, the resting complex adopts a non-canonical state and can sample deactive- or open-like conformations even in the presence of substrate. This study widens our understanding of the possible conformations and behaviour of complex I and supercomplex I + III 2 . Further studies of complex I and its supercomplexes in diverse organisms are needed to determine the universal and clade-specific mechanisms of respiration.


  • Organizational Affiliation

    Department of Molecular and Cellular Biology, University of California, Davis, CA, USA. mmaldo@ucdavis.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MPP-betaA,
K [auth M]
527Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3TWG4 (Vigna radiata var. radiata)
Explore A0A1S3TWG4 
Go to UniProtKB:  A0A1S3TWG4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3TWG4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MPP-alpha (protomer 1)510Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3UHF9 (Vigna radiata var. radiata)
Explore A0A1S3UHF9 
Go to UniProtKB:  A0A1S3UHF9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3UHF9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
COB (cyt b)C,
M [auth O]
394Vigna radiataMutation(s): 0 
UniProt
Find proteins for E9KZM1 (Vigna radiata var. radiata)
Explore E9KZM1 
Go to UniProtKB:  E9KZM1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9KZM1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CYC1 (cyt c1)D,
N [auth P]
306Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3W199 (Vigna radiata var. radiata)
Explore A0A1S3W199 
Go to UniProtKB:  A0A1S3W199
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3W199
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
UCR1 (Rieske iron-sulfur protein subunit)E,
O [auth Q]
271Vigna radiataMutation(s): 0 
EC: 7.1.1.8
UniProt
Find proteins for A0A1S3TB49 (Vigna radiata var. radiata)
Explore A0A1S3TB49 
Go to UniProtKB:  A0A1S3TB49
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3TB49
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
QCR7F,
P [auth R]
122Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3U9J1 (Vigna radiata var. radiata)
Explore A0A1S3U9J1 
Go to UniProtKB:  A0A1S3U9J1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3U9J1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
QCR8G,
Q [auth S]
72Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3U9S5 (Vigna radiata var. radiata)
Explore A0A1S3U9S5 
Go to UniProtKB:  A0A1S3U9S5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3U9S5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
QCR6H,
R [auth T]
69Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3VHC0 (Vigna radiata var. radiata)
Explore A0A1S3VHC0 
Go to UniProtKB:  A0A1S3VHC0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3VHC0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
QCR9I [auth J],
S [auth V]
72Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3TQD2 (Vigna radiata var. radiata)
Explore A0A1S3TQD2 
Go to UniProtKB:  A0A1S3TQD2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3TQD2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
QCR10 (UCRY)J [auth K],
T [auth W]
81Vigna radiataMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
MPP-alpha (protomer 2)L [auth N]506Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3VF71 (Vigna radiata var. radiata)
Explore A0A1S3VF71 
Go to UniProtKB:  A0A1S3VF71
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3VF71
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Nad1U [auth 1M]325Vigna radiataMutation(s): 0 
UniProt
Find proteins for E9KZL0 (Vigna radiata var. radiata)
Explore E9KZL0 
Go to UniProtKB:  E9KZL0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9KZL0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Nad2V [auth 2M]488Vigna radiataMutation(s): 0 
UniProt
Find proteins for E9KZK9 (Vigna radiata var. radiata)
Explore E9KZK9 
Go to UniProtKB:  E9KZK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9KZK9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Nad3W [auth 3M]118Vigna radiataMutation(s): 0 
UniProt
Find proteins for Q9XPB4 (Vigna radiata var. radiata)
Explore Q9XPB4 
Go to UniProtKB:  Q9XPB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XPB4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Nad4X [auth 4M]495Vigna radiataMutation(s): 0 
UniProt
Find proteins for E9KZL8 (Vigna radiata var. radiata)
Explore E9KZL8 
Go to UniProtKB:  E9KZL8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9KZL8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Nad4LY [auth 4L]100Vigna radiataMutation(s): 0 
UniProt
Find proteins for E9KZN8 (Vigna radiata var. radiata)
Explore E9KZN8 
Go to UniProtKB:  E9KZN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9KZN8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Nad5Z [auth 5M]673Vigna radiataMutation(s): 0 
UniProt
Find proteins for E9KZL1 (Vigna radiata var. radiata)
Explore E9KZL1 
Go to UniProtKB:  E9KZL1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9KZL1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Nad6AA [auth 6M]205Vigna radiataMutation(s): 0 
UniProt
Find proteins for E9KZM5 (Vigna radiata var. radiata)
Explore E9KZM5 
Go to UniProtKB:  E9KZM5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9KZM5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NDUA1BA [auth A1]65Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3TU57 (Vigna radiata var. radiata)
Explore A0A1S3TU57 
Go to UniProtKB:  A0A1S3TU57
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3TU57
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NDUA2CA [auth A2]98Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3TVC7 (Vigna radiata var. radiata)
Explore A0A1S3TVC7 
Go to UniProtKB:  A0A1S3TVC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3TVC7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NDUA3DA [auth A3]63Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3TCK0 (Vigna radiata var. radiata)
Explore A0A1S3TCK0 
Go to UniProtKB:  A0A1S3TCK0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3TCK0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NDUA5EA [auth A5]169Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3U023 (Vigna radiata var. radiata)
Explore A0A1S3U023 
Go to UniProtKB:  A0A1S3U023
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3U023
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NDUA6FA [auth A6]132Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3W1K8 (Vigna radiata var. radiata)
Explore A0A1S3W1K8 
Go to UniProtKB:  A0A1S3W1K8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3W1K8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NDUA7GA [auth A7]127Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3UVC7 (Vigna radiata var. radiata)
Explore A0A1S3UVC7 
Go to UniProtKB:  A0A1S3UVC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3UVC7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NDUA8HA [auth A8]106Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3VVN6 (Vigna radiata var. radiata)
Explore A0A1S3VVN6 
Go to UniProtKB:  A0A1S3VVN6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3VVN6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NDUA9IA [auth A9]396Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3V8W7 (Vigna radiata var. radiata)
Explore A0A1S3V8W7 
Go to UniProtKB:  A0A1S3V8W7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3V8W7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NDUA11JA [auth AK]160Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3TLY8 (Vigna radiata var. radiata)
Explore A0A1S3TLY8 
Go to UniProtKB:  A0A1S3TLY8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3TLY8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NDUA12KA [auth AL]156Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3VNK7 (Vigna radiata var. radiata)
Explore A0A1S3VNK7 
Go to UniProtKB:  A0A1S3VNK7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3VNK7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NDUA13LA [auth AM]143Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3UYW0 (Vigna radiata var. radiata)
Explore A0A1S3UYW0 
Go to UniProtKB:  A0A1S3UYW0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3UYW0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NDUAB1-betaMA [auth AC]116Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3TW35 (Vigna radiata var. radiata)
Explore A0A1S3TW35 
Go to UniProtKB:  A0A1S3TW35
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3TW35
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NDUAB1-alphaNA [auth AB]128Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3VXS7 (Vigna radiata var. radiata)
Explore A0A1S3VXS7 
Go to UniProtKB:  A0A1S3VXS7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3VXS7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
NDUB2OA [auth B2]66Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3TFG6 (Vigna radiata var. radiata)
Explore A0A1S3TFG6 
Go to UniProtKB:  A0A1S3TFG6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3TFG6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NDUB3PA [auth B3]68Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3UVV0 (Vigna radiata var. radiata)
Explore A0A1S3UVV0 
Go to UniProtKB:  A0A1S3UVV0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3UVV0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NDUB4QA [auth B4]71Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3ULL3 (Vigna radiata var. radiata)
Explore A0A1S3ULL3 
Go to UniProtKB:  A0A1S3ULL3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3ULL3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NDUB7RA [auth B7]98Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3V2B8 (Vigna radiata var. radiata)
Explore A0A1S3V2B8 
Go to UniProtKB:  A0A1S3V2B8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3V2B8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NDUB8SA [auth B8]125Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3UJ95 (Vigna radiata var. radiata)
Explore A0A1S3UJ95 
Go to UniProtKB:  A0A1S3UJ95
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3UJ95
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NDUB9TA [auth B9]115Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3U1J6 (Vigna radiata var. radiata)
Explore A0A1S3U1J6 
Go to UniProtKB:  A0A1S3U1J6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3U1J6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NDUB10UA [auth BJ]106Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3VGT1 (Vigna radiata var. radiata)
Explore A0A1S3VGT1 
Go to UniProtKB:  A0A1S3VGT1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3VGT1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NDUB11VA [auth BK]118Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3V2Z3 (Vigna radiata var. radiata)
Explore A0A1S3V2Z3 
Go to UniProtKB:  A0A1S3V2Z3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3V2Z3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NDUFXWA [auth FD]158Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3VXN7 (Vigna radiata var. radiata)
Explore A0A1S3VXN7 
Go to UniProtKB:  A0A1S3VXN7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3VXN7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NDUC2XA [auth C2]82Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3UPL8 (Vigna radiata var. radiata)
Explore A0A1S3UPL8 
Go to UniProtKB:  A0A1S3UPL8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3UPL8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
NDUP2YA [auth P2]115Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3TGE7 (Vigna radiata var. radiata)
Explore A0A1S3TGE7 
Go to UniProtKB:  A0A1S3TGE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3TGE7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
NDUCA1ZA [auth G1]270Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3VT00 (Vigna radiata var. radiata)
Explore A0A1S3VT00 
Go to UniProtKB:  A0A1S3VT00
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3VT00
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
NDUCA2AB [auth G2]273Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3U544 (Vigna radiata var. radiata)
Explore A0A1S3U544 
Go to UniProtKB:  A0A1S3U544
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3U544
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
NDUCAL2BB [auth L2]256Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3UI49 (Vigna radiata var. radiata)
Explore A0A1S3UI49 
Go to UniProtKB:  A0A1S3UI49
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3UI49
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
NDUS1CB [auth S1]746Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3TQ85 (Vigna radiata var. radiata)
Explore A0A1S3TQ85 
Go to UniProtKB:  A0A1S3TQ85
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3TQ85
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
NDUS2DB [auth S2]394Vigna radiataMutation(s): 0 
UniProt
Find proteins for E9KZN6 (Vigna radiata var. radiata)
Explore E9KZN6 
Go to UniProtKB:  E9KZN6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9KZN6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
NDUS3EB [auth S3]190Vigna radiataMutation(s): 0 
UniProt
Find proteins for E9KZM7 (Vigna radiata var. radiata)
Explore E9KZM7 
Go to UniProtKB:  E9KZM7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9KZM7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
NDUS4FB [auth S4]146Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3UIW7 (Vigna radiata var. radiata)
Explore A0A1S3UIW7 
Go to UniProtKB:  A0A1S3UIW7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3UIW7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
NDUS5GB [auth S5]83Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3TQ33 (Vigna radiata var. radiata)
Explore A0A1S3TQ33 
Go to UniProtKB:  A0A1S3TQ33
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3TQ33
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
NDUS6HB [auth S6]103Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3VYF3 (Vigna radiata var. radiata)
Explore A0A1S3VYF3 
Go to UniProtKB:  A0A1S3VYF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3VYF3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
NDUS7IB [auth S7]213Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3U8J5 (Vigna radiata var. radiata)
Explore A0A1S3U8J5 
Go to UniProtKB:  A0A1S3U8J5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3U8J5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
NDUS8JB [auth S8]222Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3VGS8 (Vigna radiata var. radiata)
Explore A0A1S3VGS8 
Go to UniProtKB:  A0A1S3VGS8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3VGS8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
NDUP1KB [auth P1]91Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3U2B9 (Vigna radiata var. radiata)
Explore A0A1S3U2B9 
Go to UniProtKB:  A0A1S3U2B9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3U2B9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
NDUP4LB [auth P4]61Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3UND4 (Vigna radiata var. radiata)
Explore A0A1S3UND4 
Go to UniProtKB:  A0A1S3UND4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3UND4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
NDUB6MB [auth C1]87Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3TTD7 (Vigna radiata var. radiata)
Explore A0A1S3TTD7 
Go to UniProtKB:  A0A1S3TTD7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3TTD7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
NDUV1NB [auth V1]492Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3V7V2 (Vigna radiata var. radiata)
Explore A0A1S3V7V2 
Go to UniProtKB:  A0A1S3V7V2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3V7V2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
NDUV2OB [auth V2]251Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3U769 (Vigna radiata var. radiata)
Explore A0A1S3U769 
Go to UniProtKB:  A0A1S3U769
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3U769
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
NDUX1PB [auth X1]101Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3VI15 (Vigna radiata var. radiata)
Explore A0A1S3VI15 
Go to UniProtKB:  A0A1S3VI15
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3VI15
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
CC [auth M]
HC [auth O]
KC [auth O]
LC [auth O]
RB [auth A]
CC [auth M],
HC [auth O],
KC [auth O],
LC [auth O],
RB [auth A],
SB [auth C],
XB [auth C],
ZB [auth D]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
U10
Query on U10

Download Ideal Coordinates CCD File 
QC [auth 1M]UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
PC1
Query on PC1

Download Ideal Coordinates CCD File 
DC [auth M]
GD [auth P4]
OC [auth S]
PC [auth 1M]
QB [auth A]
DC [auth M],
GD [auth P4],
OC [auth S],
PC [auth 1M],
QB [auth A],
VC [auth G1],
WC [auth G1],
XC [auth G2]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE
Query on 3PE

Download Ideal Coordinates CCD File 
AC [auth G]
BC [auth M]
EC [auth O]
IC [auth O]
JC [auth O]
AC [auth G],
BC [auth M],
EC [auth O],
IC [auth O],
JC [auth O],
NC [auth R],
VB [auth C],
WB [auth C]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP
Query on NDP

Download Ideal Coordinates CCD File 
RC [auth A9]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
HEC
Query on HEC

Download Ideal Coordinates CCD File 
MC [auth P],
YB [auth D]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
FC [auth O],
GC [auth O],
TB [auth C],
UB [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
ZMP
Query on ZMP

Download Ideal Coordinates CCD File 
SC [auth AC],
TC [auth AB]
S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
C25 H49 N2 O8 P S
HDTINWYIVVMRIN-HSZRJFAPSA-N
FMN
Query on FMN

Download Ideal Coordinates CCD File 
HD [auth V1]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
BD [auth S1]
DD [auth S7]
ED [auth S8]
FD [auth S8]
ID [auth V1]
BD [auth S1],
DD [auth S7],
ED [auth S8],
FD [auth S8],
ID [auth V1],
ZC [auth S1]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
AD [auth S1],
JD [auth V2]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CD [auth S6],
YC [auth G2]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
UC [auth FD]FE (III) ION
Fe
VTLYFUHAOXGGBS-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 & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-SC0022293

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release
  • Version 1.1: 2023-02-08
    Changes: Database references