8JOW

Crystal structure of rabbit antibody with phosphorylated peptide bound

• PDB DOI: https://doi.org/10.2210/pdb8JOW/pdb

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


• Deposited: 2023-06-08 Released: 2024-06-12 
• Deposition Author(s): Caaveiro, J.M.M., Kawade, R., Tsumoto, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED), Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.199 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 

Literature

Origin of high binding affinity and selectivity of phosphorylated epitope-specific rabbit antibodies

Kawade, R., Nakakido, M., Matsunaga, R., Akiba, H., Entzminger, K., Maruyama, T., Okamura, S., Caaveiro, J.M.M., Kuroda, D., Tsumoto, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 53.59 kDa 
• Atom Count: 4,072 
• Modelled Residue Count: 476 
• Deposited Residue Count: 516 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody (scFv)	A, C	246	Oryctolagus cuniculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ARG-PRO-HIS-PHE-PRO-GLN-PHE-SEP-TYR-SER-ALA-SER	B, D	12	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P31749 (Homo sapiens) Explore P31749  Go to UniProtKB:  P31749
GTEx:  ENSG00000142208

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	B, D	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.199 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.52	α = 71.31
b = 43.56	β = 84.39
c = 63.52	γ = 87.57

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-12 
Deposition Author(s): Caaveiro, J.M.M., Kawade, R., Tsumoto, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H04202
Japan Society for the Promotion of Science (JSPS)	Japan	JP16H02420
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H05766
Japan Society for the Promotion of Science (JSPS)	Japan	JP20H02531
Japan Agency for Medical Research and Development (AMED)	Japan	JP20wm0325002s
Japan Agency for Medical Research and Development (AMED)	Japan	JP19ak0101117h
Japan Agency for Medical Research and Development (AMED)	Japan	JP20ak0101139h
Japan Agency for Medical Research and Development (AMED)	Japan	JP18ak0101100h
Japan Agency for Medical Research and Development (AMED)	Japan	JP18am0101094j
Japan Agency for Medical Research and Development (AMED)	Japan	JP18dm0107064h
Japan Agency for Medical Research and Development (AMED)	Japan	JP18mk0101081h
Japan Agency for Medical Research and Development (AMED)	Japan	JP18fm0208030h
Japan Agency for Medical Research and Development (AMED)	Japan	JP18fk0108073h
Japan Agency for Medical Research and Development (AMED)	Japan	JP18ak0101100h
Japan Science and Technology	Japan	JPMJCR20H8

Revision History  

• Version 1.0: 2024-06-12
  Type: Initial release