7TA8 | pdb_00007ta8

NMR structure of crosslinked cyclophilin A


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 7TA8

This is version 1.4 of the entry. See complete history

Literature

The Magic of Linking Rings: Discovery of a Unique Photoinduced Fluorescent Protein Crosslink.

Lu, M.Toptygin, D.Xiang, Y.Shi, Y.Schwieters, C.D.Lipinski, E.C.Ahn, J.Byeon, I.L.Gronenborn, A.M.

(2022) J Am Chem Soc 144: 10809-10816

  • DOI: https://doi.org/10.1021/jacs.2c02054
  • Primary Citation Related Structures: 
    7TA8

  • PubMed Abstract: 

    Fluorosubstituted tryptophans serve as valuable probes for fluorescence and nuclear magnetic resonance (NMR) studies of proteins. Here, we describe an unusual photoreactivity introduced by replacing the single tryptophan in cyclophilin A with 7-fluoro-tryptophan. UV exposure at 282 nm defluorinates 7-fluoro-tryptophan and crosslinks it to a nearby phenylalanine, generating a bright fluorophore. The crosslink-containing fluorescent protein possesses a large quantum yield of ∼0.40 with a fluorescence lifetime of 2.38 ns. The chemical nature of the crosslink and the three-dimensional protein structure were determined by mass spectrometry and NMR spectroscopy. To the best of our knowledge, this is the first report of a Phe-Trp crosslink in a protein. Our finding may break new ground for developing novel fluorescence probes and for devising new strategies to exploit aromatic crosslinks in proteins.


  • Organizational Affiliation
    • Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, United States.

Macromolecule Content 

  • Total Structure Weight: 18.07 kDa 
  • Atom Count: 1,268 
  • Modeled Residue Count: 165 
  • Deposited Residue Count: 165 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase A165Homo sapiensMutation(s): 0 
Gene Names: PPIACYPA
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62937 (Homo sapiens)
Explore P62937 
Go to UniProtKB:  P62937
PHAROS:  P62937
GTEx:  ENSG00000196262 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62937
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP50AI150481
National Science Foundation (NSF, United States)United StatesCHE-1708773

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-01
    Type: Initial release
  • Version 1.1: 2022-06-29
    Changes: Database references
  • Version 1.2: 2023-04-12
    Changes: Advisory, Derived calculations
  • Version 1.3: 2023-06-14
    Changes: Other
  • Version 1.4: 2024-10-30
    Changes: Data collection, Database references, Structure summary