8SLT | pdb_00008slt

Crystal structure of human STEP (PTPN5) at physiological temperature (310 K) and ambient pressure (0.1 MPa)

• PDB DOI: https://doi.org/10.2210/pdb8SLT/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-04-24 Released: 2023-06-21 
• Deposition Author(s): Ebrahim, A., Guerrero, L., Riley, B.T., Kim, M., Huang, Q., Finke, A.D., Keedy, D.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.206 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Pushed to extremes: distinct effects of high temperature versus pressure on the structure of STEP.

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

(2024) Commun Biol 7: 59-59

• PubMed: 38216663 
• DOI: https://doi.org/10.1038/s42003-023-05609-0
• Primary Citation 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 versus. 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 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. Altogether, our work indicates that temperature and pressure are complementary, powerful, fundamental macromolecular perturbations.

---

Organizational Affiliation: 
• Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA.
PhD Program in Biochemistry, CUNY Graduate Center, New York, NY, 10016, USA.
Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY, 14853, USA.
Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA. [e-mail].
Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA. [e-mail].
PhD Programs in Biochemistry, Biology, & Chemistry, CUNY Graduate Center, New York, NY, 10016, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 32.71 kDa 
• Atom Count: 2,423 
• Modeled Residue Count: 282 
• Deposited Residue Count: 282 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 5	A	282	Homo sapiens	Mutation(s): 0  Gene Names: PTPN5 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P54829 (Homo sapiens) Explore P54829  Go to UniProtKB:  P54829
PHAROS:  P54829 GTEx:  ENSG00000110786

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.206 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M38SLT

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.976	α = 90
b = 64.492	β = 90
c = 137.21	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
DIMPLE	data reduction
DIMPLE	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-06-21 
Deposition Author(s): Ebrahim, A., Guerrero, L., Riley, B.T., Kim, M., Huang, Q., Finke, A.D., Keedy, D.A.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM133769

Revision History  

• 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, Author supporting evidence, Data collection, Database references, Refinement description, Structure summary
• Version 2.1: 2026-02-04
  Changes: Database references, Structure summary