8IPC

The recombinant NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA14 tag inserted between the residues 181 and 184


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Recombinant production of antibody antigen-binding fragments with an N-terminal human growth hormone tag in mammalian cells.

Adachi, Y.Kaneko, M.K.Kato, Y.Nogi, T.

(2023) Protein Expr Purif 208-209: 106289-106289

  • DOI: https://doi.org/10.1016/j.pep.2023.106289
  • Primary Citation of Related Structures:  
    8IPC

  • PubMed Abstract: 

    Antigen-binding fragments (Fabs) of antibodies are both key biopharmaceuticals and valuable tools for basic life science. To streamline the production of diverse Fabs by capitalizing on standard and highly optimized protein production protocols, we here explore a method to prepare recombinant Fabs as secreted fusion proteins with an N-terminal human growth hormone domain and an octa-histidine tag. These tagged Fabs can be purified with standard immobilized metal chelate affinity chromatography. We first demonstrated Fab overproduction using the rat monoclonal antibody NZ-1. Optimization of linker residues enabled the complete removal of the tags by TEV protease, leaving only two additional residues at the N-terminus of the heavy chain. We purified NZ-1 Fab at ∼4 μg/mL of culture supernatant and further confirmed that the NZ-1 Fab from the fusion protein maintained its native fold and binding affinity for target cell-surface antigens. We also showed that several other Fabs of mouse IgG 1 s, the major subclass in mice, could be produced with the same procedure. Our preparation method can provide greater flexibility in functional and structural modifications of target Fabs because specialized purification techniques are not necessary.


  • Organizational Affiliation

    Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
The recombinantly-expressed heavy chain of the monoclonal antibody NZ-1A [auth H]221Rattus norvegicusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
The recombinantly-expressed light chain of the monoclonal antibody NZ-1B [auth L]214Rattus norvegicusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Putative zinc metalloprotease aq_1964C [auth A]192Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: aq_1964
EC: 3.4.24
UniProt
Find proteins for O67776 (Aquifex aeolicus (strain VF5))
Explore O67776 
Go to UniProtKB:  O67776
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67776
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
B [auth L]L-PEPTIDE LINKINGC5 H7 N O3GLN
SNN
Query on SNN
C [auth A]L-PEPTIDE LINKINGC4 H6 N2 O2ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.935α = 90
b = 75.086β = 90
c = 173.522γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan22H02561

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-31
    Type: Initial release