6W9Z

De novo designed receptor transmembrane domains enhance CAR-T cytotoxicity and attenuate cytokine release

• PDB DOI: https://doi.org/10.2210/pdb6W9Z/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-03-24 Released: 2021-03-31 
• Deposition Author(s): Call, M.J., Call, M.E., Chandler, N.J., Nguyen, J.V., Trenker, R.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.276 
• R-Value Work: 0.219 
• R-Value Observed: 0.224 

Starting Model: experimental

Literature

De novo designed receptor transmembrane domains enhance CAR-T cytotoxicity and attenuate cytokine release

Elazar, A., Chandler, N.J., Davey, A.S., Weinstein, J.Y., Nguyen, J.V., Trenker, R., Jenkins, M., Call, M.J., Call, M.E., Fleishman, S.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: assay for oligomerization, native gel electrophoresis

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 21.81 kDa 
• Atom Count: 1,479 
• Modelled Residue Count: 173 
• Deposited Residue Count: 180 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo designed receptor transmembrane domain ProMP C2.1	A, B, C, D, E, F	30	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLB	G [auth B], H [auth D]	(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-QJRAZLAKSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SCH	A, B, C, D, E, F	L-PEPTIDE LINKING	C4 H9 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.276 
• R-Value Work: 0.219 
• R-Value Observed: 0.224 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.1	α = 90
b = 56.205	β = 90
c = 91.637	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-31 
Deposition Author(s): Call, M.J., Call, M.E., Chandler, N.J., Nguyen, J.V., Trenker, R.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1158249

Revision History  

• Version 1.0: 2021-03-31
  Type: Initial release
  
• Version 2.0: 2021-06-16
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description