7ARC

Cryo-EM structure of Polytomella Complex-I (peripheral arm)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

A ferredoxin bridge connects the two arms of plant mitochondrial complex I.

Klusch, N.Senkler, J.Yildiz, O.Kuhlbrandt, W.Braun, H.P.

(2021) Plant Cell 33: 2072-2091

  • DOI: 10.1093/plcell/koab092
  • Primary Citation of Related Structures:  
    7AQQ, 7AQR, 7AQW, 7AR7, 7AR8, 7AR9, 7ARB, 7ARC, 7ARD

  • PubMed Abstract: 
  • Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two arms, which form a conserved L-shape. We report the structures of the intact, 47-subunit mitochondrial complex I from Arabidopsis thaliana and the 51-subunit complex I from the green alga Polytomella sp ...

    Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two arms, which form a conserved L-shape. We report the structures of the intact, 47-subunit mitochondrial complex I from Arabidopsis thaliana and the 51-subunit complex I from the green alga Polytomella sp., both at around 2.9 Å resolution. In both complexes, a heterotrimeric γ-carbonic anhydrase domain is attached to the membrane arm on the matrix side. Two states are resolved in A. thaliana complex I, with different angles between the two arms and different conformations of the ND1 (NADH dehydrogenase subunit 1) loop near the quinol binding site. The angle appears to depend on a bridge domain, which links the peripheral arm to the membrane arm and includes an unusual ferredoxin. We propose that the bridge domain participates in regulating the activity of plant complex I.


    Organizational Affiliation

    Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover 30419, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PSSTA [auth B]164Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for A0A7S0V8A9 (Polytomella parva)
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UniProt GroupA0A7S0V8A9
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ND9B [auth C]217Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for A0A7S0VFV2 (Polytomella parva)
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UniProt GroupA0A7S0VFV2
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ND7C [auth D]395Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for A0A7S0VKR5 (Polytomella parva)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
24 kDaD [auth E]276Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
51 kDaE [auth F]469Polytomella sp. Pringsheim 198.80Mutation(s): 0 
EC: 7.1.1.2
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Find proteins for A0A7S0V3A3 (Polytomella parva)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
75 kDaF [auth G]720Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
TYKYG [auth I]229Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for A0A7S0UQ60 (Polytomella parva)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
39 kDaH [auth P]370Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
18 kDaI [auth Q]185Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
13 kDaJ [auth R]132Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
B8K [auth S]98Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
SDAP2L [auth U]122Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for A0A7S0UWZ2 (Polytomella parva)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
B13M [auth V]159Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
B14N [auth W]137Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for A0A7S0UM40 (Polytomella parva)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
B17.2O [auth q]155Polytomella sp. Pringsheim 198.80Mutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
B14.5aP [auth r]121Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for A0A7S0YAP9 (Polytomella parva)
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Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

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Z [auth P]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
8Q1
Query on 8Q1

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BA [auth W]S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
C23 H45 N2 O8 P S
MVHUOSAYFQKAMT-NRFANRHFSA-N
 Ligand Interaction
FMN
Query on FMN

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

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Q [auth B],
T [auth F],
V [auth G],
W [auth G],
X [auth I],
Q [auth B],
T [auth F],
V [auth G],
W [auth G],
X [auth I],
Y [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

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R [auth E],
U [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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AA [auth R]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-08
    Type: Initial release