5VF6 | pdb_00005vf6

Crystal structure of single chain variable fragment (scFv45).

• PDB DOI: https://doi.org/10.2210/pdb5VF6/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Gallus gallus
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2017-04-06 Released: 2018-01-31 
• Deposition Author(s): Shrestha, O.K., Tocilj, A., Joshua-Tor, L., Tonks, N.K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.196 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Harnessing insulin- and leptin-induced oxidation of PTP1B for therapeutic development.

Krishnan, N., Bonham, C.A., Rus, I.A., Shrestha, O.K., Gauss, C.M., Haque, A., Tocilj, A., Joshua-Tor, L., Tonks, N.K.

(2018) Nat Commun 9: 283-283

• PubMed: 29348454 
• DOI: https://doi.org/10.1038/s41467-017-02252-2
• Primary Citation Related Structures: 
  5VF6


• PubMed Abstract: 
  

  The protein tyrosine phosphatase PTP1B is a major regulator of glucose homeostasis and energy metabolism, and a validated target for therapeutic intervention in diabetes and obesity. Nevertheless, it is a challenging target for inhibitor development. Previously, we generated a recombinant antibody (scFv45) that recognizes selectively the oxidized, inactive conformation of PTP1B. Here, we provide a molecular basis for its interaction with reversibly oxidized PTP1B. Furthermore, we have identified a small molecule inhibitor that mimics the effects of scFv45. Our data provide proof-of-concept that stabilization of PTP1B in an inactive, oxidized conformation by small molecules can promote insulin and leptin signaling. This work illustrates a novel paradigm for inhibiting the signaling function of PTP1B that may be exploited for therapeutic intervention in diabetes and obesity.

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Organizational Affiliation: 
• Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
Graduate Program in Genetics and Medical Scientist Training Program, Stony Brook University, 100 Nicolls Road, Stony Brook, NY, 11794, USA.
W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 25.56 kDa 
• Atom Count: 1,993 
• Modeled Residue Count: 226 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
single chain variable fragment	A	250	Gallus gallus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.196 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.232	α = 90
b = 97.232	β = 90
c = 61.26	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-01-31 
Deposition Author(s): Shrestha, O.K., Tocilj, A., Joshua-Tor, L., Tonks, N.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM55989

Revision History  

• Version 1.0: 2018-01-31
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary