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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.171 (Depositor), 0.172 (DCC)
R-Value Work:
0.155 (Depositor), 0.156 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

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

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

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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	3D Interactions
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.171 (Depositor), 0.172 (DCC)
R-Value Work: 0.155 (Depositor), 0.156 (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

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Entry History

Deposition Data

Released Date: 2021-02-10

Deposition Author(s):

Hendrickson, W.A.

Kochenderfer, J.N.

Youkharibache, P.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.