6X89

Vigna radiata mitochondrial complex I*


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Atomic structure of a mitochondrial complex I intermediate from vascular plants.

Maldonado, M.Padavannil, A.Zhou, L.Guo, F.Letts, J.A.

(2020) Elife 9

  • DOI: 10.7554/eLife.56664
  • Primary Citation of Related Structures:  
    6X89

  • PubMed Abstract: 
  • Respiration, an essential metabolic process, provides cells with chemical energy. In eukaryotes, respiration occurs via the mitochondrial electron transport chain (mETC) composed of several large membrane-protein complexes. Complex I (CI) is the main entry point for electrons into the mETC ...

    Respiration, an essential metabolic process, provides cells with chemical energy. In eukaryotes, respiration occurs via the mitochondrial electron transport chain (mETC) composed of several large membrane-protein complexes. Complex I (CI) is the main entry point for electrons into the mETC. For plants, limited availability of mitochondrial material has curbed detailed biochemical and structural studies of their mETC. Here, we present the cryoEM structure of the known CI assembly intermediate CI* from Vigna radiata at 3.9 Å resolution. CI* contains CI's NADH-binding and CoQ-binding modules, the proximal-pumping module and the plant-specific γ-carbonic-anhydrase domain (γCA). Our structure reveals significant differences in core and accessory subunits of the plant complex compared to yeast, mammals and bacteria, as well as the details of the γCA domain subunit composition and membrane anchoring. The structure sheds light on differences in CI assembly across lineages and suggests potential physiological roles for CI* beyond assembly.


    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
Unknown PeptideA18Vigna radiataMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2B [auth A2]98Vigna radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3TVC7 (Vigna radiata var. radiata)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrialC [auth A5]169Vigna radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3U023 (Vigna radiata var. radiata)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6D [auth A6]132Vigna radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3W1K8 (Vigna radiata var. radiata)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NDUA7E [auth A7]127Vigna radiataMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial isoform X1F [auth A9]396Vigna radiataMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12G [auth AL]156Vigna radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrialH [auth S1]746Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3TQ85 (Vigna radiata var. radiata)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
NDUS2I [auth S2]394Vigna radiataMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
NDUS3J [auth S3]190Vigna radiataMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialK [auth S4]146Vigna radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialL [auth S6]103Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3VYF3 (Vigna radiata var. radiata)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialM [auth S7]213Vigna radiataMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrialN [auth S8]222Vigna radiataMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialO [auth V1]491Vigna radiataMutation(s): 0 
EC: 1.6.99.3 (PDB Primary Data), 7.1.1.2 (PDB Primary Data)
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3V7V2 (Vigna radiata var. radiata)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialP [auth V2]251Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3U769 (Vigna radiata var. radiata)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
NU1MQ [auth 1M]325Vigna radiataMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
NU2MR [auth 2M]488Vigna radiataMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
NU3MS [auth 3M]118Vigna radiataMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
NU4LT [auth 4L]100Vigna radiataMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
NU6MU [auth 6M]205Vigna radiataMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1V [auth A1]65Vigna radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3TU57 (Vigna radiata var. radiata)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
uncharacterized protein LOC106754061W [auth A3]63Vigna radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3TCK0 (Vigna radiata var. radiata)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-BX [auth A8]106Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3VVN6 (Vigna radiata var. radiata)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-AY [auth AM]143Vigna radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3UYW0 (Vigna radiata var. radiata)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown PeptideZ [auth B]25Vigna radiataMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown PeptideAA [auth C]43Vigna radiataMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
NDUC2BA [auth C2]81Vigna radiataMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Protein At2g27730, mitochondrialCA [auth P2]115Vigna radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3TGE7 (Vigna radiata var. radiata)
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
serine/arginine-rich-splicing factor SR34 isoform X2DA [auth S5]399Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3TQ33 (Vigna radiata var. radiata)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
NDUX1EA [auth X1]101Vigna radiataMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1S3VI15 (Vigna radiata var. radiata)
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
gamma carbonic anhydrase 1, mitochondrialFA [auth G1]270Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3VT00 (Vigna radiata var. radiata)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
gamma carbonic anhydrase 1, mitochondrial-likeGA [auth G2]273Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3U544 (Vigna radiata var. radiata)
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
gamma carbonic anhydrase-like 2, mitochondrialHA [auth L2]256Vigna radiataMutation(s): 0 
UniProt
Find proteins for A0A1S3UI49 (Vigna radiata var. radiata)
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Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PC1
Query on PC1

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JA [auth AL], NA [auth S2], VA [auth A1], WA [auth C2], XA [auth G1], YA [auth G1]1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
 Ligand Interaction
NAP
Query on NAP

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IA [auth A9]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
FMN
Query on FMN

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TA [auth V1]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SF4
Query on SF4

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KA [auth S1], LA [auth S1], PA [auth S7], QA [auth S8], RA [auth S8], SA [auth V1]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

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MA [auth S1], UA [auth V2]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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OA [auth S6], ZA [auth G1]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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: 2020-09-02
    Type: Initial release