8APA

rotational state 1a of the Trypanosoma brucei mitochondrial ATP synthase dimer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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

An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases.

Gahura, O.Muhleip, A.Hierro-Yap, C.Panicucci, B.Jain, M.Hollaus, D.Slapnickova, M.Zikova, A.Amunts, A.

(2022) Nat Commun 13: 5989-5989

  • DOI: https://doi.org/10.1038/s41467-022-33588-z
  • Primary Citation of Related Structures:  
    8AP6, 8AP7, 8AP8, 8AP9, 8APA, 8APB, 8APC, 8APD, 8APE, 8APF, 8APG, 8APH, 8APJ, 8APK

  • PubMed Abstract: 

    Mitochondrial ATP synthase forms stable dimers arranged into oligomeric assemblies that generate the inner-membrane curvature essential for efficient energy conversion. Here, we report cryo-EM structures of the intact ATP synthase dimer from Trypanosoma brucei in ten different rotational states. The model consists of 25 subunits, including nine lineage-specific, as well as 36 lipids. The rotary mechanism is influenced by the divergent peripheral stalk, conferring a greater conformational flexibility. Proton transfer in the lumenal half-channel occurs via a chain of five ordered water molecules. The dimerization interface is formed by subunit-g that is critical for interactions but not for the catalytic activity. Although overall dimer architecture varies among eukaryotes, we find that subunit-g together with subunit-e form an ancestral oligomerization motif, which is shared between the trypanosomal and mammalian lineages. Therefore, our data defines the subunit-g/e module as a structural component determining ATP synthase oligomeric assemblies.


  • Organizational Affiliation

    Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha, mitochondrialA [auth A1],
B [auth B1],
C [auth C1]
584Trypanosoma brucei bruceiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit beta, mitochondrialD [auth D1],
E [auth E1],
F [auth F1]
519Trypanosoma brucei bruceiMutation(s): 0 
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase gamma subunitG [auth G1]305Trypanosoma brucei bruceiMutation(s): 0 
EC: 3.6.3.14
Membrane Entity: Yes 
UniProt
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UniProt GroupA0A161CM65
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase, epsilon chain, putativeH [auth H1]182Trypanosoma brucei bruceiMutation(s): 0 
EC: 3.6.3
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit epsilon, mitochondrialI [auth I1]75Trypanosoma brucei bruceiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit p18, mitochondrialJ [auth J1],
K [auth K1],
M [auth L1]
188Trypanosoma brucei bruceiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-eJA [auth l],
L
92Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-gKA [auth m],
N [auth M]
144Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
OSCPO [auth M1]255Trypanosoma brucei bruceiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ATPase subunit 9, putative118Trypanosoma brucei bruceiMutation(s): 0 
EC: 3.6.3.14
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit aZ [auth a]231Trypanosoma brucei bruceiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-8AA [auth c]114Trypanosoma brucei bruceiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-dBA [auth d]370Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB1CA [auth e]396Trypanosoma brucei bruceiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-fDA [auth f]145Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB3EA [auth g]269Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for A0A3L6KRX7 (Trypanosoma brucei equiperdum)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB4FA [auth h]157Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-i/jGA [auth i]104Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB6HA [auth j]169Trypanosoma brucei bruceiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0A5R7 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-kIA [auth k]124Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q57VT0 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB11LA [auth n]156Trypanosoma brucei bruceiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB12MA [auth o]101Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q57Z84 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-bNA [auth p]105Trypanosoma brucei bruceiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
ATPEG3OA [auth q]98Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
ATPEG4PA [auth r]62Trypanosoma brucei bruceiMutation(s): 0 
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Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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BB [auth L]
DB [auth c]
EB [auth e]
FB [auth e]
GB [auth e]
BB [auth L],
DB [auth c],
EB [auth e],
FB [auth e],
GB [auth e],
HB [auth e],
IB [auth e],
LB [auth f],
QB [auth j],
TB [auth l],
UB [auth m],
XB [auth p],
YB [auth q],
ZB [auth q]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
Q7G
Query on Q7G

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KB [auth e],
WB [auth n]
2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside
C56 H92 O25
LKBFXDNKNZXHHW-NXLTVWPKSA-N
PC1 (Subject of Investigation/LOI)
Query on PC1

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NB [auth f],
OB [auth f],
PB [auth i],
RB [auth j]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
PEE (Subject of Investigation/LOI)
Query on PEE

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CB [auth M],
MB [auth f],
VB [auth m]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
LMT
Query on LMT

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JB [auth e],
SB [auth j]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
ATP
Query on ATP

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QA [auth A1],
SA [auth B1],
UA [auth C1],
YA [auth F1]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
UTP (Subject of Investigation/LOI)
Query on UTP

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AB [auth H1]URIDINE 5'-TRIPHOSPHATE
C9 H15 N2 O15 P3
PGAVKCOVUIYSFO-XVFCMESISA-N
ADP
Query on ADP

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WA [auth D1]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

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RA [auth A1],
TA [auth B1],
VA [auth C1],
XA [auth D1],
ZA [auth F1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-26
    Type: Initial release