6B90

Multiconformer model of apo WT PTP1B with glycerol at 100 K (ALTERNATIVE REFINEMENT OF PDB 1SUG showing conformational heterogeneity)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering.

Keedy, D.A.Hill, Z.B.Biel, J.T.Kang, E.Rettenmaier, T.J.Brandao-Neto, J.Pearce, N.M.von Delft, F.Wells, J.A.Fraser, J.S.

(2018) Elife 7

  • DOI: 10.7554/eLife.36307
  • Primary Citation of Related Structures:  
    5QDE, 5QDG, 5QDF, 5QEB, 5QEA, 5QED, 5QEC, 5QEF, 5QEE, 5QEH

  • PubMed Abstract: 
  • Allostery is an inherent feature of proteins, but it remains challenging to reveal the mechanisms by which allosteric signals propagate. A clearer understanding of this intrinsic circuitry would afford new opportunities to modulate protein function. Here ...

    Allostery is an inherent feature of proteins, but it remains challenging to reveal the mechanisms by which allosteric signals propagate. A clearer understanding of this intrinsic circuitry would afford new opportunities to modulate protein function. Here, we have identified allosteric sites in protein tyrosine phosphatase 1B (PTP1B) by combining multiple-temperature X-ray crystallography experiments and structure determination from hundreds of individual small-molecule fragment soaks. New modeling approaches reveal 'hidden' low-occupancy conformational states for protein and ligands. Our results converge on allosteric sites that are conformationally coupled to the active-site WPD loop and are hotspots for fragment binding. Targeting one of these sites with covalently tethered molecules or mutations allosterically inhibits enzyme activity. Overall, this work demonstrates how the ensemble nature of macromolecular structure, revealed here by multitemperature crystallography, can elucidate allosteric mechanisms and open new doors for long-range control of protein function.


    Related Citations: 
    • Water-molecule network and active-site flexibility of apo protein tyrosine phosphatase 1B.
      Pedersen, A.K., Peters G, G.u., Moller, K.B., Iversen, L.F., Kastrup, J.S.
      (2004) Acta Crystallogr D Biol Crystallogr 60: 1527

    Organizational Affiliation

    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 1 A321Homo sapiensMutation(s): 0 
Gene Names: PTPN1PTP1B
EC: 3.1.3.48
Find proteins for P18031 (Homo sapiens)
Explore P18031 
Go to UniProtKB:  P18031
NIH Common Fund Data Resources
PHAROS:  P18031
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.118α = 90
b = 88.118β = 90
c = 103.9γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Author supporting evidence, Data collection