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 5TSJ | pdb_00005tsj

Thermus thermophilus V/A-ATPase bound to VH dAbs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history. 

Literature

Cryo-EM analysis of a domain antibody bound rotary ATPase complex.

Davies, R.B., Smits, C., Wong, A.S., Stock, D., Christie, M., Sandin, S., Stewart, A.G.

(2017) J Struct Biol 197: 350-353

  • DOI: https://doi.org/10.1016/j.jsb.2017.01.002
  • Primary Citation Related Structures: 
    5TSJ

  • PubMed Abstract: 

    The bacterial A/V-type ATPase/synthase rotary motor couples ATP hydrolysis/synthesis with proton translocation across biological membranes. The A/V-type ATPase/synthase from Thermus thermophilus has been extensively studied both structurally and functionally for many years. Here we provide an 8.7Å resolution cryo-electron microscopy 3D reconstruction of this complex bound to single-domain antibody fragments, small monomeric antibodies containing just the variable heavy domain. Docking of known structures into the density revealed the molecular orientation of the domain antibodies, suggesting that structure determination of co-domain antibody:protein complexes could be a useful avenue for unstable or smaller proteins. Although previous studies suggested that the presence of fluoroaluminate in this complex could change the rotary state of this enzyme, we observed no gross structural rearrangements under these conditions.


  • Organizational Affiliation: 
    • Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia.

Macromolecule Content 

  • Total Structure Weight: 701.11 kDa 
  • Atom Count: 24,625 
  • Modeled Residue Count: 6,112 
  • Deposited Residue Count: 6,455 
  • Unique protein chains: 10

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type ATP synthase alpha chain
A, B, C
577Thermus thermophilus HB8Mutation(s): 0 
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
UniProt
Find proteins for Q56403 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ56403
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type ATP synthase beta chain
D, E, F
457Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q72J73 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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UniProt GroupQ72J73
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type ATP synthase subunit E
G, H
186Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P74901 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type ATPase subunit G
I, J
105Thermus thermophilus HB8Mutation(s): 0 
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type ATP synthase subunit D210Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q72J74 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type ATP synthase subunit F100Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P74903 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type ATP synthase subunit C323Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P74902 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Archaeal/vacuolar-type H+-ATPase subunit I652Thermus thermophilus HB8Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for H9ZQR4 (Thermus thermophilus JL-18)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Vacuolar type ATP synthase subunit
O, P, Q, R, S
O, P, Q, R, S, T, U, V, W, X, Y, Z
99Thermus thermophilus HB8Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P74900 (Thermus thermophilus)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Human heavy chain domain antibodyAA [auth 1],
BA [auth 2]
149Homo sapiensMutation(s): 0 
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1022143
National Health and Medical Research Council (NHMRC, Australia)Australia1047004

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2017-02-08
    Changes: Database references
  • Version 1.2: 2017-04-05
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2020-01-15
    Changes: Author supporting evidence
  • Version 1.5: 2024-03-13
    Changes: Data collection, Database references