6TMK

Cryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase dimer, composite model


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

ATP synthase hexamer assemblies shape cristae of Toxoplasma mitochondria.

Muhleip, A.Kock Flygaard, R.Ovciarikova, J.Lacombe, A.Fernandes, P.Sheiner, L.Amunts, A.

(2021) Nat Commun 12: 120-120

  • DOI: https://doi.org/10.1038/s41467-020-20381-z
  • Primary Citation of Related Structures:  
    6TMG, 6TMH, 6TMI, 6TMJ, 6TMK, 6TML

  • PubMed Abstract: 

    Mitochondrial ATP synthase plays a key role in inducing membrane curvature to establish cristae. In Apicomplexa causing diseases such as malaria and toxoplasmosis, an unusual cristae morphology has been observed, but its structural basis is unknown. Here, we report that the apicomplexan ATP synthase assembles into cyclic hexamers, essential to shape their distinct cristae. Cryo-EM was used to determine the structure of the hexamer, which is held together by interactions between parasite-specific subunits in the lumenal region. Overall, we identified 17 apicomplexan-specific subunits, and a minimal and nuclear-encoded subunit-a. The hexamer consists of three dimers with an extensive dimer interface that includes bound cardiolipins and the inhibitor IF 1 . Cryo-ET and subtomogram averaging revealed that hexamers arrange into ~20-megadalton pentagonal pyramids in the curved apical membrane regions. Knockout of the linker protein ATPTG11 resulted in the loss of pentagonal pyramids with concomitant aberrantly shaped cristae. Together, this demonstrates that the unique macromolecular arrangement is critical for the maintenance of cristae morphology in Apicomplexa.


  • Organizational Affiliation

    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTG11A [auth q],
Y [auth Q]
134Toxoplasma gondii GT1Mutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTG7B [auth i],
Z [auth I]
236Toxoplasma gondii GT1Mutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTG14AA [auth T],
C [auth t]
133Toxoplasma gondii GT1Mutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTG5BA [auth G],
D [auth g]
252Toxoplasma gondii GT1Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
subunit kCA [auth O],
E [auth o]
157Toxoplasma gondii GT1Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
subunit aDA [auth K],
F [auth k]
224Toxoplasma gondii GT1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
subunit i/jEA [auth J],
G [auth j]
229Toxoplasma gondii GT1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTG13FA [auth S],
H [auth s]
128Toxoplasma gondii GT1Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTG15GA [auth U],
I [auth u]
126Toxoplasma gondii GT1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTG6HA [auth H],
J [auth h]
239Toxoplasma gondii GT1Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTG3IA [auth E],
K [auth e]
325Toxoplasma gondii GT1Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTG17JA [auth X],
L [auth x]
83Toxoplasma gondii GT1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
subunit bKA [auth B],
M [auth b]
571Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTG12LA [auth R],
N [auth r]
134Toxoplasma gondii GT1Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTG10MA [auth P],
O [auth p]
138Toxoplasma gondii GT1Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
subunit fNA [auth V],
P [auth v]
111Toxoplasma gondii GT1Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTG8OA [auth L],
Q [auth l]
208Toxoplasma gondii GT1Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTG1PA [auth C],
R [auth c]
398Toxoplasma gondii GT1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTG2QA [auth D],
S [auth d]
310Toxoplasma gondii GT1Mutation(s): 0 
UniProt
Find proteins for A0A125YV76 (Toxoplasma gondii (strain ATCC 50853 / GT1))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
subunit 8RA [auth M],
T [auth m]
205Toxoplasma gondii GT1Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTG9SA [auth N],
U [auth n]
166Toxoplasma gondii GT1Mutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTG4TA [auth F],
V [auth f]
267Toxoplasma gondii GT1Mutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
ATPTG16UA [auth W],
W [auth w]
106Toxoplasma gondii GT1Mutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
subunit dVA [auth A],
X [auth a]
536Toxoplasma gondii GT1Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Inhibitor of F1RB [auth i1],
WA [auth i2]
145Toxoplasma gondii GT1Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha,subunit alpha565Toxoplasma gondii GT1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit beta560Toxoplasma gondii GT1Mutation(s): 0 
EC: 7.1.2.2
Membrane Entity: Yes 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit gammaDB [auth g2],
YB [auth g1]
314Toxoplasma gondii GT1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit deltaEB [auth d2],
ZB [auth d1]
183Toxoplasma gondii GT1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit epsilonAC [auth e1],
FB [auth e2]
73Toxoplasma gondii GT1Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Oligomycin sensitivity conferring protein (OSCP)BC [auth G1],
GB [auth G2]
252Toxoplasma gondii GT1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
subunit c166Toxoplasma gondii GT1Mutation(s): 0 
Membrane Entity: Yes 
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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AD [auth v]
BD [auth c]
CE [auth D]
GD [auth d]
KD [auth O]
AD [auth v],
BD [auth c],
CE [auth D],
GD [auth d],
KD [auth O],
OC [auth o],
OD [auth U],
QD [auth H],
RD [auth E],
SC [auth u],
TD [auth B],
UC [auth h],
UD [auth B],
VC [auth e],
WD [auth V],
XC [auth b],
XD [auth C],
YC [auth b]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PC1 (Subject of Investigation/LOI)
Query on PC1

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ID [auth O]
LD [auth O]
MC [auth o]
PC [auth o]
VD [auth V]
ID [auth O],
LD [auth O],
MC [auth o],
PC [auth o],
VD [auth V],
ZC [auth v]
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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DD [auth c]
MD [auth J]
ND [auth J]
QC [auth j]
RC [auth j]
DD [auth c],
MD [auth J],
ND [auth J],
QC [auth j],
RC [auth j],
ZD [auth C]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
LMT
Query on LMT

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AE [auth C]
BE [auth D]
CD [auth c]
DE [auth D]
ED [auth c]
AE [auth C],
BE [auth D],
CD [auth c],
DE [auth D],
ED [auth c],
FD [auth d],
HD [auth d],
JD [auth O],
NC [auth o],
PD [auth H],
SD [auth X],
TC [auth h],
WC [auth x],
YD [auth C]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
ATP (Subject of Investigation/LOI)
Query on ATP

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EE [auth A2]
FE [auth E2]
GE [auth C2]
JE [auth A1]
KE [auth E1]
EE [auth A2],
FE [auth E2],
GE [auth C2],
JE [auth A1],
KE [auth E1],
LE [auth C1]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

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HE [auth B2],
IE [auth D2],
ME [auth B1],
NE [auth D1]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX1.17rc2-3612

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSwedenNT_2015-04107
European Research CouncilSwedenERC-2018-StG-805230
Knut and Alice Wallenberg FoundationSweden2018.0080
European Molecular Biology OrganizationSwedenALTF 260-2017

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2021-01-20
    Changes: Database references