9LUX | pdb_00009lux

Single-chain Fv antibody of G2 fused with antigen peptide from chicken prion protein

PDB DOI: https://doi.org/10.2210/pdb9LUX/pdb

Classification: IMMUNE SYSTEM
Organism(s): Gallus gallus, Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-02-10 Released: 2025-06-11
Deposition Author(s): Hanazono, Y., Yabuno, S., Hayashi, T., Numoto, N., Ito, N., Oda, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.226 (Depositor), 0.226 (DCC)
R-Value Work:
0.194 (Depositor), 0.194 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structures reveal how the multispecific antibody G2 achieves binding to different peptides.

Hanazono, Y., Yabuno, S., Hayashi, T., Numoto, N., Kamatari, Y.O., Ito, N., Oda, M.

(2025) FEBS Lett

PubMed: 40527602 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.70095
Primary Citation of Related Structures:
9LUX, 9LUY

PubMed Abstract:
Monoclonal antibody G2, obtained via immunization with the chicken prion protein (ChPrP), has unique antigen-binding specificity. G2 specifically binds to the ChPrP-derived peptide (Pep18mer) as expected, but also to three other peptides. In this study, we determined the crystal structures of G2 single-chain Fv antibodies covalently linked to Pep18mer and another peptide, PepH4P6. Both bound peptides formed similar U-shaped structures that stuck into the G2 antigen-binding pocket. Their three-dimensional structures were stabilized by interactions within the peptides, and the structure of the bound Pep18mer was similar to that of the corresponding ChPrP region. G2 acquired the binding ability to both Pep18mer and PepH4P6 via deletion of the 95th residue of the light chain during affinity maturation, consistent with our structural analysis.

Organizational Affiliation

Medical Research Laboratory, Institute of Integrated Research, Institute of Science Tokyo, Japan.

Macromolecule Content

Total Structure Weight: 174.65 kDa
Atom Count: 12,729
Modeled Residue Count: 1,522
Deposited Residue Count: 1,626
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major prion protein homolog,Single-chain Fv antibody of G2 fused with antigen peptide from chicken prion protein	A, B, C, D, E A, B, C, D, E, F	271	Gallus gallus, Mus musculus This entity is chimeric	Mutation(s): 0 Gene Names: PRNP, PRN-P
UniProt
Find proteins for P27177 (Gallus gallus) Explore P27177 Go to UniProtKB: P27177
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P27177
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain X [auth E] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain Y [auth F] MOL2 format, chain X [auth E] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain Y [auth F] mmCIF format, chain X [auth E] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] L [auth B] G [auth A], H [auth A], I [auth A], J [auth A], L [auth B], M [auth B], O [auth C], P [auth C], Q [auth C], R [auth C], U [auth D], V [auth D], W [auth D], X [auth E], Y [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth E] Focus chain Y [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth E] Focus chain Y [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain N [auth B] SDF format, chain K [auth A] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A]	K [auth A], N [auth B], S [auth C], T [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain K [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C]