8IGW

Hexameric Ring Complex of Engineered V1-ATPase bound to 4 ADPs: A3(De)3_(ADP)3cat,1non-cat, Hexameric Ring Complex of Engineered V1-ATPase bound to 5 ADPs: A3(De)3_(ADP)3cat,2non-cat


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7COS


Literature

Design of allosteric sites into rotary motor V 1 -ATPase by restoring lost function of pseudo-active sites.

Kosugi, T.Iida, T.Tanabe, M.Iino, R.Koga, N.

(2023) Nat Chem 15: 1591-1598

  • DOI: https://doi.org/10.1038/s41557-023-01256-4
  • Primary Citation of Related Structures:  
    8IGU, 8IGV, 8IGW

  • PubMed Abstract: 

    Allostery produces concerted functions of protein complexes by orchestrating the cooperative work between the constituent subunits. Here we describe an approach to create artificial allosteric sites in protein complexes. Certain protein complexes contain subunits with pseudo-active sites, which are believed to have lost functions during evolution. Our hypothesis is that allosteric sites in such protein complexes can be created by restoring the lost functions of pseudo-active sites. We used computational design to restore the lost ATP-binding ability of the pseudo-active site in the B subunit of a rotary molecular motor, V 1 -ATPase. Single-molecule experiments with X-ray crystallography analyses revealed that binding of ATP to the designed allosteric site boosts this V 1 's activity compared with the wild-type, and the rotation rate can be tuned by modulating ATP's binding affinity. Pseudo-active sites are widespread in nature, and our approach shows promise as a means of programming allosteric control over concerted functions of protein complexes.


  • Organizational Affiliation

    Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science (IMS), National Institutes of Natural Sciences (NINS), Okazaki, Japan. takahirokosugi@ims.ac.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
V-type sodium ATPase catalytic subunit A
A, B, C, G, H
A, B, C, G, H, I
596Enterococcus hirae ATCC 9790Mutation(s): 0 
Gene Names: ntpAEHR_08260
EC: 7.2.2.1
UniProt
Find proteins for Q08636 (Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258 / NCTC 12367 / WDCM 00089 / R))
Explore Q08636 
Go to UniProtKB:  Q08636
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08636
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
V-type sodium ATPase subunit B
D, E, F, J, K
D, E, F, J, K, L
458Enterococcus hirae ATCC 9790Mutation(s): 10 
Gene Names: ntpBEHR_08265
UniProt
Find proteins for Q08637 (Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258 / NCTC 12367 / WDCM 00089 / R))
Explore Q08637 
Go to UniProtKB:  Q08637
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08637
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
AA [auth J]
CA [auth L]
M [auth A]
O [auth B]
Q [auth C]
AA [auth J],
CA [auth L],
M [auth A],
O [auth B],
Q [auth C],
S [auth D],
U [auth G],
W [auth H],
Y [auth I]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BA [auth J]
DA [auth L]
N [auth A]
P [auth B]
R [auth C]
BA [auth J],
DA [auth L],
N [auth A],
P [auth B],
R [auth C],
T [auth D],
V [auth G],
X [auth H],
Z [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 179.407α = 90
b = 125.077β = 93.826
c = 180.914γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan18H05420
Japan Agency for Medical Research and Development (AMED)JapanJP20am0101071
Japan Science and TechnologyJapanJPMJPR13AD
Japan Science and TechnologyJapanJPMJPR20E6

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-07-19
    Changes: Database references
  • Version 1.2: 2023-11-15
    Changes: Data collection, Database references