8APK

rotational state 3 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


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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
subunit-eA [auth L],
M [auth l]
92Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-gB [auth M],
N [auth m]
144Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit aC [auth a]231Trypanosoma brucei bruceiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-8D [auth c]114Trypanosoma brucei bruceiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-dE [auth d]370Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB1F [auth e]396Trypanosoma brucei bruceiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-fG [auth f]145Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB3H [auth g]269Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB4I [auth h]157Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-i/jJ [auth i]104Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB6K [auth j]169Trypanosoma brucei bruceiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-kL [auth k]124Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB11O [auth n]156Trypanosoma brucei bruceiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB12P [auth o]101Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-bQ [auth p]105Trypanosoma brucei bruceiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
ATPEG3R [auth q]98Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
ATPEG4S [auth r]62Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha, mitochondrialT [auth A1],
U [auth B1],
V [auth C1]
584Trypanosoma brucei bruceiMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9GS23 (Trypanosoma brucei brucei)
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UniProt GroupQ9GS23
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit beta, mitochondrialW [auth D1],
X [auth E1],
Y [auth F1]
519Trypanosoma brucei bruceiMutation(s): 0 
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for Q9GPE9 (Trypanosoma brucei brucei)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase gamma subunitZ [auth G1]305Trypanosoma brucei bruceiMutation(s): 0 
EC: 3.6.3.14
Membrane Entity: Yes 
UniProt
Find proteins for A0A161CM65 (Trypanosoma brucei brucei)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase, epsilon chain, putativeAA [auth H1]182Trypanosoma brucei bruceiMutation(s): 0 
EC: 3.6.3
Membrane Entity: Yes 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit epsilon, mitochondrialBA [auth I1]75Trypanosoma brucei bruceiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0DPG3 (Trypanosoma brucei brucei)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit p18, mitochondrialCA [auth J1],
DA [auth K1],
EA [auth L1]
188Trypanosoma brucei bruceiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
OSCPFA [auth M1]255Trypanosoma brucei bruceiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
ATPase subunit 9, putative118Trypanosoma brucei bruceiMutation(s): 0 
EC: 3.6.3.14
Membrane Entity: Yes 
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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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CB [auth f]
FB [auth j]
IB [auth k]
JB [auth l]
KB [auth m]
CB [auth f],
FB [auth j],
IB [auth k],
JB [auth l],
KB [auth m],
OB [auth q],
QA [auth M],
RA [auth M],
TA [auth a],
VA [auth c],
WA [auth e],
XA [auth e],
YA [auth e],
ZA [auth e]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
Q7G
Query on Q7G

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BB [auth e],
MB [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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EB [auth i],
GB [auth j],
NB [auth p],
UA [auth a]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE (Subject of Investigation/LOI)
Query on 3PE

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DB [auth f],
LB [auth m],
SA [auth M]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
LMT
Query on LMT

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AB [auth e],
HB [auth j]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
ATP (Subject of Investigation/LOI)
Query on ATP

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PB [auth A1],
RB [auth B1],
TB [auth C1],
VB [auth E1]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
UTP (Subject of Investigation/LOI)
Query on UTP

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ZB [auth H1]URIDINE 5'-TRIPHOSPHATE
C9 H15 N2 O15 P3
PGAVKCOVUIYSFO-XVFCMESISA-N
ADP (Subject of Investigation/LOI)
Query on ADP

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XB [auth F1]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

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QB [auth A1],
SB [auth B1],
UB [auth C1],
WB [auth E1],
YB [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