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- PDB-6w9y: De novo designed receptor transmembrane domains enhance CAR-T cyt... -

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Basic information

Entry
Database: PDB / ID: 6w9y
TitleDe novo designed receptor transmembrane domains enhance CAR-T cytotoxicity and attenuate cytokine release
ComponentsDe novo designed receptor transmembrane domain proMP 1.2
KeywordsBIOSYNTHETIC PROTEIN / Transmembrane domain / de novo design
Function / homology(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 1.2
B: De novo designed receptor transmembrane domain proMP 1.2
C: De novo designed receptor transmembrane domain proMP 1.2
D: De novo designed receptor transmembrane domain proMP 1.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5175
Polymers13,1604
Non-polymers3571
Water00
1
A: De novo designed receptor transmembrane domain proMP 1.2
B: De novo designed receptor transmembrane domain proMP 1.2
C: De novo designed receptor transmembrane domain proMP 1.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2274
Polymers9,8703
Non-polymers3571
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-28 kcal/mol
Surface area6690 Å2
2
D: De novo designed receptor transmembrane domain proMP 1.2


Theoretical massNumber of molelcules
Total (without water)3,2901
Polymers3,2901
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2460 Å2
Unit cell
Length a, b, c (Å)41.489, 64.975, 85.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein/peptide
De novo designed receptor transmembrane domain proMP 1.2


Mass: 3290.124 Da / Num. of mol.: 4
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)
#2: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
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: 2.21 Å3/Da / Density % sol: 44.38 % / Description: hexagonal discs
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 35 mg/ml peptide in LCP 25% w/v poly(ethylene glycol) 1500 10% v/v succinate-phosphate-glycine pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryo Stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953737 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953737 Å / Relative weight: 1
ReflectionResolution: 2.55→32.35 Å / Num. obs: 3956 / % possible obs: 98.94 % / Redundancy: 4.9 % / Biso Wilson estimate: 60.27 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.06635 / Rpim(I) all: 0.0338 / Rrim(I) all: 0.07495 / Net I/σ(I): 12.72
Reflection shellResolution: 2.55→2.641 Å / Redundancy: 5 % / Rmerge(I) obs: 0.5728 / Mean I/σ(I) obs: 2.41 / Num. unique obs: 381 / CC1/2: 0.936 / CC star: 0.983 / Rpim(I) all: 0.2793 / Rrim(I) all: 0.6397 / % possible all: 97.14

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Processing

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

5eh6


Resolution: 2.55→32.35 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 41.41
RfactorNum. reflection% reflection
Rfree0.3259 395 10.04 %
Rwork0.2773 --
obs-3956 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 171.98 Å2 / Biso mean: 86.13 Å2 / Biso min: 41.72 Å2
Refinement stepCycle: final / Resolution: 2.55→32.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms815 0 25 0 840
Biso mean--88.42 --
Num. residues----108
LS refinement shellResolution: 2.55→2.641 Å
RfactorNum. reflection% reflection
Rfree0.2793 37 10 %
Rwork0.3131 381 -
obs--97.14 %
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)
18.2973-2.29421.75832.4077-0.3132.33850.0016-0.04220.2964-0.17150.07340.2664-0.3509-1.7547-0.3180.421-0.13740.03060.87570.0210.5771-3.230213.4433-5.8795
25.3966-0.54181.57088.05936.10149.888-0.07120.7479-0.4375-0.40680.3431-0.6538-0.18391.2677-0.45250.3-0.02140.05230.62070.14980.46035.21714.5074-4.5679
38.2631.7551-1.7419.2366-0.34822.2997-0.1791-0.8868-0.29560.0984-0.0444-0.8027-1.28290.0850.53630.58910.0350.05580.6135-0.00330.4908-0.352419.9087-2.313
46.07012.08782.34588.01054.97653.2949-0.0426-0.12070.684-1.6622-0.1478-0.7556-0.4239-0.53920.34260.98210.0890.15081.03130.01740.7429-6.379226.6499-1.1003
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 29 )A2 - 29
2X-RAY DIFFRACTION2chain 'B' and (resid 2 through 29 )B2 - 29
3X-RAY DIFFRACTION3chain 'C' and (resid 2 through 29 )C2 - 29
4X-RAY DIFFRACTION4chain 'D' and (resid 3 through 26 )D3 - 26

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