6TT7 | pdb_00006tt7

Ovine ATP synthase 1a state

PDB DOI: https://doi.org/10.2210/pdb6TT7/pdb
EM Map EMD-10573: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Ovis aries
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2019-12-23 Released: 2020-09-23
Deposition Author(s): Pinke, G., Zhou, L., Sazanov, L.A.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Cryo-EM structure of the entire mammalian F-type ATP synthase.

Pinke, G., Zhou, L., Sazanov, L.A.

(2020) Nat Struct Mol Biol 27: 1077-1085

PubMed: 32929284 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41594-020-0503-8
Primary Citation Related Structures:
6TT7, 6ZA9

PubMed Abstract:
The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo, determined by cryo-electron microscopy. Subunits in the membrane domain are arranged in the 'proton translocation cluster' attached to the c-ring and a more distant 'hook apparatus' holding subunit e. Unexpectedly, this subunit is anchored to a lipid 'plug' capping the c-ring. We present a detailed proton translocation pathway in mammalian Fo and key inter-monomer contacts in F1Fo multimers. Cryo-EM maps of F1Fo exposed to calcium reveal a retracted subunit e and a disassembled c-ring, suggesting permeability transition pore opening. We propose a model for the permeability transition pore opening, whereby subunit e pulls the lipid plug out of the c-ring. Our structure will allow the design of drugs for many emerging applications in medicine.

Organizational Affiliation

Institute of Science and Technology Austria, Klosterneuburg, Austria.

Macromolecule Content

Total Structure Weight: 690.11 kDa
Atom Count: 40,337
Modeled Residue Count: 5,173
Deposited Residue Count: 6,258
Unique protein chains: 17

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit alpha	A [auth B], B [auth C], C [auth A]	553	Ovis aries	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit beta	D [auth E], E [auth D], F	528	Ovis aries	Mutation(s): 0 EC: 7.1.2.2

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit gamma	G	298	Ovis aries	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P05631 (Bos taurus) Explore P05631 Go to UniProtKB: P05631
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05631
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F1 subunit delta	H	168	Ovis aries	Mutation(s): 0

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F1 subunit epsilon	I	51	Ovis aries	Mutation(s): 0

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase peripheral stalk subunit OSCP	J	213	Ovis aries	Mutation(s): 0

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit b	K	256	Ovis aries	Mutation(s): 0

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase-coupling factor 6, mitochondrial	L	108	Ovis aries	Mutation(s): 0

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit d, mitochondrial	M	161	Ovis aries	Mutation(s): 0

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase F(0) complex subunit C1, mitochondrial	N [auth 1] O [auth 2] P [auth 3] Q [auth 4] R [auth 5] N [auth 1], O [auth 2], P [auth 3], Q [auth 4], R [auth 5], S [auth 6], T [auth 7], U [auth 8]	136	Ovis aries	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P17605 (Ovis aries) Explore P17605 Go to UniProtKB: P17605
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17605
Sequence Annotations Expand
Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit a	V [auth N]	226	Ovis aries	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for O78752 (Ovis aries) Explore O78752 Go to UniProtKB: O78752
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O78752
Sequence Annotations Expand
Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Subunit DAPIT	W [auth O]	58	Ovis aries	Mutation(s): 0

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase membrane subunit 6.8PL	X [auth P]	60	Ovis aries	Mutation(s): 0

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase protein 8	Y [auth Q]	66	Ovis aries	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for O78751 (Ovis aries) Explore O78751 Go to UniProtKB: O78751
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O78751
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase membrane subunit f	Z [auth R]	88	Ovis aries	Mutation(s): 0

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit	AA [auth S]	103	Ovis aries	Mutation(s): 0

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| 3D Structure

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Subunit e	BA [auth T]	71	Ovis aries	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain OA [auth R] SDF format, chain PA [auth R] SDF format, chain QA [auth R] MOL2 format, chain OA [auth R] MOL2 format, chain PA [auth R] MOL2 format, chain QA [auth R] mmCIF format, chain OA [auth R] mmCIF format, chain PA [auth R] mmCIF format, chain QA [auth R]	OA [auth R], PA [auth R], QA [auth R]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain OA [auth R] Focus chain PA [auth R] Focus chain QA [auth R] Interactions & Density Focus chain OA [auth R] Focus chain PA [auth R] Focus chain QA [auth R]
P5S Query on P5S Download:Ideal Coordinates CCD File SDF format, chain MA [auth 2] MOL2 format, chain MA [auth 2] mmCIF format, chain MA [auth 2]	MA [auth 2]	O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine C₄₂ H₈₂ N O₁₀ P TZCPCKNHXULUIY-RGULYWFUSA-N		Interactions Focus chain MA [auth 2] Interactions & Density Focus chain MA [auth 2]
LHG Query on LHG Download:Ideal Coordinates CCD File SDF format, chain KA [auth K] SDF format, chain LA [auth K] SDF format, chain NA [auth 2] SDF format, chain RA [auth R] SDF format, chain SA [auth S] SDF format, chain TA [auth S] MOL2 format, chain KA [auth K] MOL2 format, chain LA [auth K] MOL2 format, chain NA [auth 2] MOL2 format, chain RA [auth R] MOL2 format, chain SA [auth S] MOL2 format, chain TA [auth S] mmCIF format, chain KA [auth K] mmCIF format, chain LA [auth K] mmCIF format, chain NA [auth 2] mmCIF format, chain RA [auth R] mmCIF format, chain SA [auth S] mmCIF format, chain TA [auth S]	KA [auth K] LA [auth K] NA [auth 2] RA [auth R] SA [auth S] KA [auth K], LA [auth K], NA [auth 2], RA [auth R], SA [auth S], TA [auth S]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C₃₈ H₇₅ O₁₀ P BIABMEZBCHDPBV-MPQUPPDSSA-N		Interactions Focus chain KA [auth K] Focus chain LA [auth K] Focus chain NA [auth 2] Focus chain RA [auth R] Focus chain SA [auth S] Focus chain TA [auth S] Interactions & Density Focus chain KA [auth K] Focus chain LA [auth K] Focus chain NA [auth 2] Focus chain RA [auth R] Focus chain SA [auth S] Focus chain TA [auth S]
S12 Query on S12 Download:Ideal Coordinates CCD File SDF format, chain UA [auth T] MOL2 format, chain UA [auth T] mmCIF format, chain UA [auth T]	UA [auth T]	O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine C₂₄ H₄₆ N O₉ P JZWNYZVVZXZRRH-VXKWHMMOSA-N		Interactions Focus chain UA [auth T] Interactions & Density Focus chain UA [auth T]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain FA [auth C] SDF format, chain HA [auth A] SDF format, chain IA [auth D] SDF format, chain JA [auth F] MOL2 format, chain DA [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth F] mmCIF format, chain DA [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain HA [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain JA [auth F]	DA [auth B], FA [auth C], HA [auth A], IA [auth D], JA [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain DA [auth B] Focus chain FA [auth C] Focus chain HA [auth A] Focus chain IA [auth D] Focus chain JA [auth F] Interactions & Density Focus chain DA [auth B] Focus chain FA [auth C] Focus chain HA [auth A] Focus chain IA [auth D] Focus chain JA [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain EA [auth C] SDF format, chain GA [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain GA [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain GA [auth A]	CA [auth B], EA [auth C], GA [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain EA [auth C] Focus chain GA [auth A] Interactions & Density Focus chain CA [auth B] Focus chain EA [auth C] Focus chain GA [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0
MODEL REFINEMENT	PHENIX	1.12_2829
MODEL REFINEMENT	PHENIX	1.12_2829

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-09-23

Deposition Author(s):

Pinke, G.

Zhou, L.

Sazanov, L.A.

Revision History (Full details and data files)

Version 1.0: 2020-09-23
Type: Initial release
Version 1.1: 2020-09-30
Changes: Database references
Version 2.0: 2020-12-30
Type: Coordinate replacement
Reason: Model completeness
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
Version 2.1: 2024-05-22
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

6TT7 | pdb_00006tt7

Ovine ATP synthase 1a state

Literature

Cryo-EM structure of the entire mammalian F-type ATP synthase.

Biological Assembly 1

Macromolecules

Entity ID: 1

Entity ID: 2

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 4

Entity ID: 5

Entity ID: 6

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Entity ID: 8

Entity ID: 9

Entity ID: 10

UniProt

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Sequence Annotations

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Entity ID: 11

UniProt

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Sequence Annotations

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Entity ID: 12

Entity ID: 13

Entity ID: 14

UniProt

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Sequence Annotations

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Entity ID: 15

Entity ID: 16

Entity ID: 17

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)