8AP7

membrane region of the Trypanosoma brucei mitochondrial ATP synthase dimer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 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
ATP synthase subunit aA,
P [auth a]
231Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for P24499 (Trypanosoma brucei brucei)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-8B [auth C],
Q [auth c]
114Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q585K5 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-dC [auth D],
R [auth d]
370Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q57ZW9 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB1D [auth E],
S [auth e]
396Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q38CI8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-fE [auth F],
T [auth f]
145Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q57ZE2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-i/jF [auth I],
U [auth i]
104Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q57ZM4 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB6G [auth J],
V [auth j]
169Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for D0A5R7 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-kH [auth K],
W [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: 9
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-eI [auth L],
X [auth l]
92Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q387J1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-gJ [auth M],
Y [auth m]
144Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for C9ZJA0 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB11K [auth N],
Z [auth n]
156Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q582T1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTB12AA [auth o],
L [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: 13
MoleculeChains Sequence LengthOrganismDetailsImage
subunit-bBA [auth p],
M [auth P]
105Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for C9ZLR9 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
ATPEG3CA [auth q],
N [auth Q]
98Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q583U4 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
ATPEG4DA [auth r],
O [auth R]
62Trypanosoma brucei bruceiMutation(s): 0 
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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AB [auth c]
BB [auth e]
CB [auth e]
DB [auth e]
EA [auth C]
AB [auth c],
BB [auth e],
CB [auth e],
DB [auth e],
EA [auth C],
EB [auth e],
FA [auth E],
FB [auth e],
GA [auth E],
HA [auth E],
IA [auth E],
IB [auth f],
JA [auth E],
MA [auth F],
NB [auth j],
OB [auth j],
RA [auth J],
RB [auth l],
SA [auth J],
SB [auth m],
UB [auth q],
VA [auth L],
WA [auth M],
YA [auth Q]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
Q7G
Query on Q7G

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HB [auth e],
LA [auth E],
TB [auth n],
XA [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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KB [auth f]
LB [auth f]
MB [auth i]
OA [auth F]
PA [auth F]
KB [auth f],
LB [auth f],
MB [auth i],
OA [auth F],
PA [auth F],
PB [auth j],
QA [auth I],
TA [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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JB [auth f],
NA [auth F],
VB [auth r],
ZA [auth R]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
LMT
Query on LMT

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GB [auth e],
KA [auth E],
QB [auth j],
UA [auth J]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 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