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- PDB-6wa0: De novo designed receptor transmembrane domains enhance CAR-T cyt... -

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Basic information

Entry
Database: PDB / ID: 6wa0
TitleDe novo designed receptor transmembrane domains enhance CAR-T cytotoxicity and attenuate cytokine release
ComponentsDe novo designed receptor transmembrane domain proMP C3.1
KeywordsBIOSYNTHETIC PROTEIN / Transmembrane domain / de novo design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.484 Å
AuthorsCall, M.J. / Call, M.E. / Chandler, N.J. / Nguyen, J.V. / Trenker, R.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1158249 Australia
CitationJournal: To Be Published
Title: De novo designed receptor transmembrane domains enhance CAR-T cytotoxicity and attenuate cytokine release
Authors: 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.
History
DepositionMar 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: De novo designed receptor transmembrane domain proMP C3.1
B: De novo designed receptor transmembrane domain proMP C3.1
C: De novo designed receptor transmembrane domain proMP C3.1
D: De novo designed receptor transmembrane domain proMP C3.1
E: De novo designed receptor transmembrane domain proMP C3.1
F: De novo designed receptor transmembrane domain proMP C3.1
G: De novo designed receptor transmembrane domain proMP C3.1
H: De novo designed receptor transmembrane domain proMP C3.1
I: De novo designed receptor transmembrane domain proMP C3.1


Theoretical massNumber of molelcules
Total (without water)31,2779
Polymers31,2779
Non-polymers00
Water0
1
A: De novo designed receptor transmembrane domain proMP C3.1
B: De novo designed receptor transmembrane domain proMP C3.1
C: De novo designed receptor transmembrane domain proMP C3.1


Theoretical massNumber of molelcules
Total (without water)10,4263
Polymers10,4263
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-45 kcal/mol
Surface area5760 Å2
MethodPISA
2
D: De novo designed receptor transmembrane domain proMP C3.1
E: De novo designed receptor transmembrane domain proMP C3.1
F: De novo designed receptor transmembrane domain proMP C3.1


Theoretical massNumber of molelcules
Total (without water)10,4263
Polymers10,4263
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-43 kcal/mol
Surface area5710 Å2
MethodPISA
3
G: De novo designed receptor transmembrane domain proMP C3.1
H: De novo designed receptor transmembrane domain proMP C3.1
I: De novo designed receptor transmembrane domain proMP C3.1


Theoretical massNumber of molelcules
Total (without water)10,4263
Polymers10,4263
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-43 kcal/mol
Surface area6010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.159, 96.159, 79.299
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein/peptide
De novo designed receptor transmembrane domain proMP C3.1


Mass: 3475.213 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pMM-TrpLE Fusion / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.32 % / Description: Small ellipsoid crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10 mg/ml peptide in 30mM C8E4 65 v/v 2-methyl-2,4-pentanediol 0.1 M tris chloride pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.3→48.08 Å / Num. obs: 6676 / % possible obs: 100 % / Redundancy: 10.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.054 / Rrim(I) all: 0.172 / Net I/σ(I): 10.7 / Num. measured all: 67364
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.3-3.5610.42.0441414313540.5440.6562.1481.3100
8.72-48.088.80.03935684040.9990.0140.04140.599.5

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSMar 15, 2019 BUILT=20190315data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EH6

5eh6


Resolution: 3.484→41.638 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 24.27
RfactorNum. reflection% reflection
Rfree0.259 565 9.98 %
Rwork0.2201 --
obs0.2238 5660 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 210.24 Å2 / Biso mean: 110.7016 Å2 / Biso min: 56.49 Å2
Refinement stepCycle: final / Resolution: 3.484→41.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2097 0 0 0 2097
Num. residues----268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.484-3.83410.2791410.24511243
3.8341-4.38840.25461400.20231265
4.3884-5.52690.28811400.22961253
5.5269-41.6380.23811440.21571334
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5192-0.87180.5531.4487-0.90550.48950.22320.2176-0.69720.0231-0.29230.04610.3711-0.1097-00.7568-0.0469-0.0040.88620.01770.8007-39.18930.048416.8824
20.6233-0.3281-0.81510.82240.03431.2313-0.05990.2057-0.0127-0.4416-0.3741-0.25780.62540.1424-0.00010.8131-0.08340.00750.80890.05150.8007-37.921916.495530.1914
30.3771-0.39610.3320.81870.0130.6292-0.006-0.31040.36920.0031-0.09950.1042-0.2679-0.1493-00.7614-0.025-0.02990.80480.01210.864-34.639247.336219.4283
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A or chain B or chain CA - a0
2X-RAY DIFFRACTION2chain E or chain F or chain DE - e0
3X-RAY DIFFRACTION3chain G or chain H or chain IG - g0

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