Crystal structure of human STEP (PTPN5) at cryogenic temperature (100 K) and high pressure (205 MPa)

Experimental Data Snapshot

  • Resolution: 1.84 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report

This is version 2.0 of the entry. See complete history


Pushed to extremes: distinct effects of high temperature vs. pressure on the structure of an atypical phosphatase.

Guerrero, L.Ebrahim, A.Riley, B.T.Kim, M.Huang, Q.Finke, A.D.Keedy, D.A.

(2023) Biorxiv 

  • DOI: https://doi.org/10.1101/2023.05.02.538097
  • Primary Citation of Related Structures:  
    8SLS, 8SLT, 8SLU

  • PubMed Abstract: 

    Protein function hinges on small shifts of three-dimensional structure. Elevating temperature or pressure may provide experimentally accessible insights into such shifts, but the effects of these distinct perturbations on protein structures have not been compared in atomic detail. To quantitatively explore these two axes, we report the first pair of structures at physiological temperature vs. high pressure for the same protein, STEP (PTPN5). We show that these perturbations have distinct and surprising effects on protein volume, patterns of ordered solvent, and local backbone and side-chain conformations. This includes novel interactions between key catalytic loops only at physiological temperature, and a distinct conformational ensemble for another active-site loop only at high pressure. Strikingly, in torsional space, physiological temperature shifts STEP toward previously reported active-like states, while high pressure shifts it toward a previously uncharted region. Together, our work argues that temperature and pressure are complementary, powerful, fundamental macromolecular perturbations.

  • Organizational Affiliation

    Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 5282Homo sapiensMutation(s): 0 
Gene Names: PTPN5
UniProt & NIH Common Fund Data Resources
Find proteins for P54829 (Homo sapiens)
Explore P54829 
Go to UniProtKB:  P54829
PHAROS:  P54829
GTEx:  ENSG00000110786 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54829
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.143α = 90
b = 63.466β = 90
c = 134.198γ = 90
Software Package:
Software NamePurpose
xia2data scaling
DIMPLEdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM133769

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 2.0: 2023-09-27
    Type: Coordinate replacement
    Reason: Atoms with unrealistic or zero occupancies
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary