9PVL | pdb_00009pvl

Crystal Structure of Fluorophore-binding Protein JF657-bp

  • Classification: DE NOVO PROTEIN
  • Organism(s): synthetic construct
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2025-08-01 Released: 2026-07-15 
  • Deposition Author(s): Bera, A.K., Tran, L., An, L., Baker, D.
  • Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 
    0.245 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9PVL

This is version 1.2 of the entry. See complete history

Literature

De novo design of orthogonal far-red, orange, and green fluorophore-binding proteins for multiplexed imaging.

Tran, L.Klein, S.Juergens, D.Sharma, S.Decarreau, J.Lee, G.R.Wang, Y.Chen, W.Bera, A.K.Kang, A.Woods, J.Joyce, E.Vafeados, D.K.Roullier, N.Li, X.Liu, B.Bo, Y.Muratspahic, E.Brown, T.A.Grimm, J.B.Patel, R.Lavis, L.D.Mahamid, J.An, L.Baker, D.

(2026) Science : eaeb0822-eaeb0822

  • DOI: https://doi.org/10.1126/science.aeb0822
  • Primary Citation Related Structures: 
    11MQ, 9PVL

  • PubMed Abstract: 

    Fluorescent proteins and small-molecule dyes offer complementary advantages for biological imaging: proteins are amenable to genetic tagging, whereas dyes provide superior brightness and photostability. To combine these strengths, we used de novo protein design to generate small, nanomolar-affinity, high-selectivity binders (NovoTags) for three cell-permeable dyes spanning the visible spectrum. We show that the NovoTag fluorescent lifetimes can be tuned and demonstrate their application in lifetime and wavelength-based multiplexed fluorescence imaging. We further design a two-chain NovoTag that functions as a chemically induced dimerization system with fluorescent readout in living cells, or as a minimally perturbing proximity probe in fixed cells. Our approach combines the advantages of fluorescent proteins and small-molecule dyes, expanding the toolkit for cellular imaging.


  • Organizational Affiliation
    • Department of Chemical Engineering, University of Washington, Seattle, WA, USA.

Macromolecule Content 

  • Total Structure Weight: 63.89 kDa 
  • Atom Count: 4,915 
  • Modeled Residue Count: 544 
  • Deposited Residue Count: 544 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
JF657-bpA,
B [auth C],
C [auth D],
D [auth B]
136synthetic constructMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE4

Query on PE4



Download:Ideal Coordinates CCD File
E [auth A]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
H [auth C],
J [auth D],
K [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
I [auth C]
L [auth B]
M [auth B]
F [auth A],
G [auth A],
I [auth C],
L [auth B],
M [auth B],
N [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free:  0.245 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.358α = 90
b = 123.987β = 92.278
c = 56.639γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--
Bill & Melinda Gates FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-15
    Type: Initial release
  • Version 1.1: 2026-07-22
    Changes: Database references
  • Version 1.2: 2026-07-29
    Changes: Database references