8UBS | pdb_00008ubs

Crystal structure of NrdJ-1 split intein fusion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.221 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Programmable protein ligation on cell surfaces.

Kofoed, C.Erkalo, G.Tay, N.E.S.Ye, X.Lin, Y.Muir, T.W.

(2025) Nature 645: 793-800

  • DOI: https://doi.org/10.1038/s41586-025-09287-2
  • Primary Citation of Related Structures:  
    8UBS

  • PubMed Abstract: 

    The surface landscapes of cells differ as a function of cell type and are frequently altered in disease contexts 1-3 . Exploiting such differences is key to many therapeutic strategies and is the basis for developing diagnostic and basic-science tools. State-of-the-art strategies typically target single surface antigens, but each individual receptor rarely defines the specific cell type 4,5 . The development of programmable molecular systems that integrate multiple cell-surface features to convert on-target inputs to user-defined outputs is therefore highly desirable. Here we describe an autonomous decision-making device driven by proximity-gated protein trans-splicing that allows local generation of an active protein from two otherwise inactive polypeptide fragments. We show that this protein-actuator platform can perform convergent protein ligation on designated cell surfaces, allowing highly selective generation of active proteins, which can either remain physically associated with the cell surface on which they were manufactured or be released into the surrounding milieu. Because of its intrinsic modularity and tunability, we demonstrate that the technology is compatible with different types of input, targeting modality and functional output, allowing for the localized interrogation or manipulation of cellular systems.


  • Organizational Affiliation
    • Department of Chemistry, Princeton University, Princeton, NJ, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NrdJ-1
A, B, C, D
151marine metagenomeMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMT (Subject of Investigation/LOI)
Query on FMT

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
P [auth C],
Q [auth C],
R [auth D],
S [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.221 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.793α = 90
b = 84.383β = 90
c = 174.709γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States2R01GM086868-25
European Molecular Biology Organization (EMBO)European UnionEMBO ALTF 1189-2020

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release
  • Version 1.1: 2025-07-30
    Changes: Database references
  • Version 1.2: 2025-08-13
    Changes: Database references
  • Version 1.3: 2025-10-01
    Changes: Database references