9VX2 | pdb_00009vx2

Crystal structure of the apo form of HisMab-1 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 
    0.288 (Depositor), 0.288 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Functional and Structural Characterization of a Novel Anti-His-tag Antibody, HisMab-1.

Hitomi, N.Hoshi, S.Kaneko, M.K.Kato, R.Iwasaki, K.Takagi, J.Kato, Y.Harada-Hikita, A.Arimori, T.

(2025) J Mol Biology 438: 169574-169574

  • DOI: https://doi.org/10.1016/j.jmb.2025.169574
  • Primary Citation of Related Structures:  
    9VX2, 9VX3

  • PubMed Abstract: 

    The polyhistidine tag (His-tag) is one of the most widely used peptide tags for the purification of recombinant proteins, owing to its compatibility with immobilized metal affinity chromatography. While numerous anti-His-tag antibodies are commercially available, their quantitative affinity data and structural insights are limited. Here, we present a detailed physicochemical and structural characterization of a novel anti-His-tag antibody, HisMab-1. Isothermal titration calorimetry showed that the Fab fragment of HisMab-1 binds to a hexahistidine peptide in an enthalpy-driven manner, with a dissociation constant (K D ) of ∼30 nM at a neutral pH. The crystal structure of the HisMab-1-hexahistidine peptide complex at 2.39-Å resolution revealed that HisMab-1 primarily recognizes the first, second, fourth, and fifth histidine residues of the peptide through multiple interactions, including hydrogen bonding and π-π stacking, which collectively contribute to the high specificity of the antibody. Notably, HisMab-1 also binds to a His-tag embedded within a conformationally constrained β-hairpin loop without reducing affinity, highlighting its structural adaptability. These findings establish HisMab-1 as a high-affinity, high-specificity, structurally validated anti-His-tag antibody with broad potential in diverse protein engineering and structural biology applications.


  • Organizational Affiliation
    • Laboratory for Protein Synthesis and Expression, Institute for Protein Research, The University of Osaka, 3-2, Yamadaoka, Suita, Osaka 565-0871, Japan.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HisMab-1 immunoglobulin heavy chain variable region
A, C
226Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HisMab-1 immunoglobulin light chain variable region
B, D
220Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free:  0.288 (Depositor), 0.288 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.719α = 90
b = 191.099β = 90
c = 177.383γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP21H02416
Japan Society for the Promotion of Science (JSPS)JapanJP25K02215
Japan Agency for Medical Research and Development (AMED)JapanJP24am0521010
Japan Agency for Medical Research and Development (AMED)JapanJP23ama121001
Japan Agency for Medical Research and Development (AMED)JapanJP19am0101083

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release
  • Version 1.1: 2025-12-24
    Changes: Database references