6R10 | pdb_00006r10

Thermus thermophilus V/A-type ATPase/synthase, rotational state 1R

PDB DOI: https://doi.org/10.2210/pdb6R10/pdb
EM Map EMD-4703: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Thermus thermophilus HB8
Mutation(s): No
Membrane Protein: Yes PDBTM mpstruc

Deposited: 2019-03-13 Released: 2019-08-28
Deposition Author(s): Zhou, L., Sazanov, L.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase.

Zhou, L., Sazanov, L.A.

(2019) Science 365

PubMed: 31439765 Search on PubMed
DOI: https://doi.org/10.1126/science.aaw9144
Primary Citation Related Structures:
6QUM, 6R0W, 6R0Y, 6R0Z, 6R10

PubMed Abstract:
V (vacuolar)/A (archaeal)-type adenosine triphosphatases (ATPases), found in archaea and eubacteria, couple ATP hydrolysis or synthesis to proton translocation across the plasma membrane using the rotary-catalysis mechanism. They belong to the V-type ATPase family, which differs from the mitochondrial/chloroplast F-type ATP synthases in overall architecture. We solved cryo-electron microscopy structures of the intact Thermus thermophilus V/A-ATPase, reconstituted into lipid nanodiscs, in three rotational states and two substates. These structures indicate substantial flexibility between V ₁ and V _o in a working enzyme, which results from mechanical competition between central shaft rotation and resistance from the peripheral stalks. We also describe details of adenosine diphosphate inhibition release, V ₁-V _o torque transmission, and proton translocation, which are relevant for the entire V-type ATPase family.

Organizational Affiliation

Institute of Science and Technology Austria, Klosterneuberg 3400, Austria.

Macromolecule Content

Total Structure Weight: 681.54 kDa
Atom Count: 38,522
Modeled Residue Count: 5,842
Deposited Residue Count: 6,274
Unique protein chains: 9

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type ATP synthase alpha chain	A, B, C	578	Thermus thermophilus HB8	Mutation(s): 0 EC: 7.1.2.2
UniProt
Find proteins for Q56403 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q56403 Go to UniProtKB: Q56403
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q56403
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type ATP synthase beta chain	D, E, F	478	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q56404 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q56404 Go to UniProtKB: Q56404
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q56404
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type ATP synthase subunit D	G	223	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for O87880 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore O87880 Go to UniProtKB: O87880
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O87880
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type ATP synthase subunit F	H	104	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P74903 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P74903 Go to UniProtKB: P74903
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P74903
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type ATP synthase, subunit (VAPC-THERM)	I, K	120	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SIT5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIT5 Go to UniProtKB: Q5SIT5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SIT5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type ATP synthase subunit E	J, L	188	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P74901 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P74901 Go to UniProtKB: P74901
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P74901
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type ATP synthase subunit C	M	323	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P74902 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P74902 Go to UniProtKB: P74902
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P74902
Sequence Annotations Expand
Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type ATP synthase subunit I	N	652	Thermus thermophilus HB8	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q5SIT6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIT6 Go to UniProtKB: Q5SIT6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SIT6
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type ATP synthase, subunit K	O, P, Q, R, S O, P, Q, R, S, T, U, V, W, X, Y, Z	99	Thermus thermophilus HB8	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q5SIT7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIT7 Go to UniProtKB: Q5SIT7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SIT7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain BA [auth A] MOL2 format, chain CA [auth F] MOL2 format, chain BA [auth A] mmCIF format, chain CA [auth F] mmCIF format, chain BA [auth A]	BA [auth A], CA [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain BA [auth A] Focus chain CA [auth F] Interactions & Density Focus chain BA [auth A] Focus chain CA [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain AA [auth A]	AA [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Interactions & Density Focus chain AA [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-08-28

Deposition Author(s):

Zhou, L.

Sazanov, L.

Revision History (Full details and data files)

Version 1.0: 2019-08-28
Type: Initial release
Version 1.1: 2019-09-04
Changes: Data collection, Database references
Version 1.2: 2019-12-18
Changes: Other
Version 1.3: 2020-09-30
Changes: Database references
Version 1.4: 2024-05-15
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.

6R10 | pdb_00006r10

Thermus thermophilus V/A-type ATPase/synthase, rotational state 1R

Literature

Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)