6W9Y | pdb_00006w9y

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

PDB DOI: https://doi.org/10.2210/pdb6W9Y/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free:
0.326 (Depositor), 0.327 (DCC)
R-Value Work:
0.277 (Depositor), 0.279 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

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.

Macromolecule Content

Total Structure Weight: 13.52 kDa
Atom Count: 840
Modeled Residue Count: 108
Deposited Residue Count: 120
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo designed receptor transmembrane domain proMP 1.2	A, B, C, D	30	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OLB Query on OLB Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-QJRAZLAKSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.326 (Depositor), 0.327 (DCC)
R-Value Work: 0.277 (Depositor), 0.279 (DCC)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.489	α = 90
b = 64.975	β = 90
c = 85.16	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-03-31

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2021-03-31
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

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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.