7JO8 | pdb_00007jo8

Crystal structure of a Chimeric Antigen Receptor (CAR) scFv domain rearrangement forming a VL-VL dimer

• PDB DOI: https://doi.org/10.2210/pdb7JO8/pdb

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


• Deposited: 2020-08-06 Released: 2021-02-10 
• Deposition Author(s): Cheung, J., Hendrickson, W.A., Kochenderfer, J.N., Youkharibache, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Models: experimental

Literature

Crystal Structure of a Chimeric Antigen Receptor (CAR) scFv Domain Rearrangement Forming a VL-VL Dimer

Cheung, J., Wazir, S., Bell, D.R., Kochenderfer, J.N., Hendrickson, W.A., Youkharibache, P.

(2023) Crystals (Basel) 13

• DOI: https://doi.org/10.3390/cryst13040710

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 24.15 kDa 
• Atom Count: 2,021 
• Modeled Residue Count: 217 
• Deposited Residue Count: 220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
47G4-CD828Z	A, B	110	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	C [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PG4	E [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
MLI	D [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.322	α = 90
b = 79.221	β = 109.56
c = 40.616	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Cheung, J., Hendrickson, W.A., Kochenderfer, J.N., Youkharibache, P.

Revision History  

• Version 1.0: 2021-02-10
  Type: Initial release
  
• Version 1.1: 2023-05-03
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary