8UJI | pdb_00008uji

anti-Phosphohistidine Fab hSC44.ck with 3pTza peptide

• PDB DOI: https://doi.org/10.2210/pdb8UJI/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Oryctolagus cuniculus, synthetic construct
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-10-11 Released: 2025-03-19 
• Deposition Author(s): Kalagiri, R., Stanfield, R.L., Hunter, T., Wilson, I.A.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.260 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Using phage display for rational engineering of a higher-affinity humanized 3' phosphohistidine-specific antibody.

Martyn, G.D., Kalagiri, R., Veggiani, G., Stanfield, R.L., Choudhuri, I., Sala, M., Meisenhelder, J., Chen, C., Biswas, A., Levy, R.M., Lyumkis, D., Wilson, I.A., Hunter, T., Sidhu, S.S.

(2025) Commun Chem 8: 381-381

• PubMed: 41310398 
• DOI: https://doi.org/10.1038/s42004-025-01768-9
• Primary Citation Related Structures: 
  8UHH, 8UHJ, 8UHN, 8UHP, 8UHS, 8UHT, 8UIG, 8UIH, 8UIO, 8UIT, 8UJI


• PubMed Abstract: 
  

  Histidine phosphorylation is a non-canonical post-translational modification (PTM), with 1-phosphohistidine (1-pHis) and 3-phosphohistidine (3-pHis) isoforms, that is understudied due to a lack of robust reagents, including high-affinity pHis-specific antibodies. Engineering pHis antibodies is challenging due to the labile nature of its phosphoramidate (P-N) bond. We developed a strategy for in vitro engineering of antibodies for the detection of native 3-pHis targets, in which the rabbit SC44-8 anti-3-pTza mAb is humanized into a scaffold (hSC44) that is suitable for phage display. Six unique Fab phage-displayed hSC44 scaffold libraries were screened for antibodies that bound 3-pHis with higher affinity and had specificity for 3-pHis versus 3-pTza. hSC44.20N32F ^L , the best engineered antibody, has ~10-fold higher affinity for 3-pHis than parental hSC44. Eleven new Fab structures, including the first antibody-pHis peptide structures, together with structural and quantum mechanical calculations, provided molecular insights into 3-pHis and 3-pTza discrimination by hSC44.20N32F ^L and the increased affinity obtained through engineering. We demonstrated the utility of these high-affinity 3-pHis-specific antibodies for the recognition of pHis proteins in mammalian cells by immunoblotting and immunofluorescence staining. Our work describes a general method for engineering labile PTM-specific antibodies and provides novel antibodies for investigating the role of 3-pHis in cell biology.

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Organizational Affiliation: 
• School of Pharmacy, University of Waterloo, Kitchener, ON, Canada.
Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
Division of Biotechnology and Molecular Medicine, Louisiana State University, Baton Rouge, LA, USA.
Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA, USA.
Department of Physics, University of California San Diego, La Jolla, CA, USA.
Center for Biophysics and Computational Biology, and Department of Chemistry, Temple University, Philadelphia, PA, USA.
The Skaggs Institute for Chemical Biology, The Scripps Research Institute, San Diego, CA, USA.
Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA. [e-mail].
School of Pharmacy, University of Waterloo, Kitchener, ON, Canada. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 96.32 kDa 
• Atom Count: 6,835 
• Modeled Residue Count: 880 
• Deposited Residue Count: 904 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hSC44.CK Fab heavy chain	A [auth H], C [auth A]	225	Oryctolagus cuniculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
hSC44.CK Fab light chain	B [auth L], D [auth B]	218	Oryctolagus cuniculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
3-pTza peptide	E [auth C], F [auth D]	9	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	G [auth H]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.260 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.498	α = 90
b = 139.615	β = 90
c = 73.616	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Kalagiri, R., Stanfield, R.L., Hunter, T., Wilson, I.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA242443

Revision History  

• Version 1.0: 2025-03-19
  Type: Initial release
  
• Version 1.1: 2026-07-15
  Changes: Database references