6TMH | pdb_00006tmh

Cryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase dimer, OSCP/F1/c-ring model

PDB DOI: https://doi.org/10.2210/pdb6TMH/pdb
EM Map EMD-10521: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Toxoplasma gondii GT1
Mutation(s): No

Deposited: 2019-12-04 Released: 2020-12-16
Deposition Author(s): Muhleip, A., Kock Flygaard, R., Amunts, A.
Funding Organization(s): Swedish Research Council, European Research Council, Knut and Alice Wallenberg Foundation, European Molecular Biology Organization

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 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

PubMed: 33402698 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-020-20381-z
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 649.93 kDa
Atom Count: 32,410
Modeled Residue Count: 4,264
Deposited Residue Count: 6,002
Unique protein chains: 8

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inhibitor of F1	A [auth i]	145	Toxoplasma gondii GT1	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
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Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit alpha,subunit alpha	B [auth A], C [auth E], D [auth C]	565	Toxoplasma gondii GT1	Mutation(s): 0
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit beta	E [auth B], F, G [auth D]	560	Toxoplasma gondii GT1	Mutation(s): 0 EC: 7.1.2.2
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit gamma	H [auth g]	314	Toxoplasma gondii GT1	Mutation(s): 0
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit delta	I [auth d]	183	Toxoplasma gondii GT1	Mutation(s): 0
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit epsilon	J [auth e]	73	Toxoplasma gondii GT1	Mutation(s): 0
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligomycin sensitivity conferring protein (OSCP)	K [auth G]	252	Toxoplasma gondii GT1	Mutation(s): 0
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
subunit c	L [auth H] M [auth I] N [auth J] O [auth K] P [auth L] L [auth H], M [auth I], N [auth J], O [auth K], P [auth L], Q [auth M], R [auth N], S [auth O], T [auth P], U [auth Q]	166	Toxoplasma gondii GT1	Mutation(s): 0
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Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain X [auth E] SDF format, chain V [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain X [auth E] MOL2 format, chain V [auth A] mmCIF format, chain Z [auth C] mmCIF format, chain X [auth E] mmCIF format, chain V [auth A]	V [auth A], X [auth E], Z [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain V [auth A] Focus chain X [auth E] Focus chain Z [auth C] Interactions & Density Focus chain V [auth A] Focus chain X [auth E] Focus chain Z [auth C]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain BA [auth B] MOL2 format, chain DA [auth D] MOL2 format, chain BA [auth B] mmCIF format, chain DA [auth D] mmCIF format, chain BA [auth B]	BA [auth B], DA [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain BA [auth B] Focus chain DA [auth D] Interactions & Density Focus chain BA [auth B] Focus chain DA [auth D]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain W [auth A] SDF format, chain EA [auth D] SDF format, chain CA [auth B] SDF format, chain AA [auth C] MOL2 format, chain Y [auth E] MOL2 format, chain W [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain AA [auth C] mmCIF format, chain Y [auth E] mmCIF format, chain W [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain AA [auth C]	AA [auth C], CA [auth B], EA [auth D], W [auth A], Y [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain CA [auth B] Focus chain EA [auth D] Focus chain W [auth A] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth C] Focus chain CA [auth B] Focus chain EA [auth D] Focus chain W [auth A] Focus chain Y [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.17rc2-3612
RECONSTRUCTION	RELION	3.0

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-12-16

Deposition Author(s):

Muhleip, A.

Kock Flygaard, R.

Amunts, A.

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	NT_2015-04107
European Research Council	Sweden	ERC-2018-StG-805230
Knut and Alice Wallenberg Foundation	Sweden	2018.0080
European Molecular Biology Organization	Sweden	ALTF 260-2017