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- PDB-6w9z: De novo designed receptor transmembrane domains enhance CAR-T cyt... -

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Basic information

Entry
Database: PDB / ID: 6w9z
TitleDe novo designed receptor transmembrane domains enhance CAR-T cytotoxicity and attenuate cytokine release
ComponentsDe novo designed receptor transmembrane domain ProMP C2.1
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: 2.7 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 2.0Jun 16, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_asym / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.occupancy / _atom_site.type_symbol / _entity.pdbx_number_of_molecules / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _struct_site_gen.label_asym_id
Revision 2.1Oct 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 C2.1
B: De novo designed receptor transmembrane domain ProMP C2.1
C: De novo designed receptor transmembrane domain ProMP C2.1
D: De novo designed receptor transmembrane domain ProMP C2.1
E: De novo designed receptor transmembrane domain ProMP C2.1
F: De novo designed receptor transmembrane domain ProMP C2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8058
Polymers21,0926
Non-polymers7132
Water362
1
A: De novo designed receptor transmembrane domain ProMP C2.1
B: De novo designed receptor transmembrane domain ProMP C2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3873
Polymers7,0312
Non-polymers3571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-14 kcal/mol
Surface area5340 Å2
MethodPISA
2
C: De novo designed receptor transmembrane domain ProMP C2.1
D: De novo designed receptor transmembrane domain ProMP C2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3873
Polymers7,0312
Non-polymers3571
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-15 kcal/mol
Surface area5330 Å2
MethodPISA
3
E: De novo designed receptor transmembrane domain ProMP C2.1
F: De novo designed receptor transmembrane domain ProMP C2.1


Theoretical massNumber of molelcules
Total (without water)7,0312
Polymers7,0312
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-13 kcal/mol
Surface area5070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.100, 56.205, 91.637
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein/peptide
De novo designed receptor transmembrane domain ProMP C2.1


Mass: 3515.323 Da / Num. of mol.: 6
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.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
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: 2.8 Å3/Da / Density % sol: 56.2 % / Description: Rhomboid Plates
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.7
Details: 40 mg/ml peptide in LCP 8 v/v 2-methyl-2,4-pentanediol 0.1 M ADA pH 6.7 0.4 M potassium nitrate 0.1 M tripotassium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95366 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95366 Å / Relative weight: 1
ReflectionResolution: 2.7→39.74 Å / Num. obs: 6655 / % possible obs: 96.14 % / Redundancy: 4.4 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07022 / Rpim(I) all: 0.03716 / Rrim(I) all: 0.0798 / Net I/σ(I): 13.26
Reflection shellResolution: 2.7→2.796 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.8554 / Mean I/σ(I) obs: 1.86 / Num. unique obs: 444 / CC1/2: 0.615 / CC star: 0.4492 / Rpim(I) all: 0.4492 / Rrim(I) all: 0.9694 / % possible all: 68.62

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSJan 26, 2018 BUILT=20180319data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EH6

5eh6


Resolution: 2.7→39.738 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 28.78
RfactorNum. reflection% reflection
Rfree0.2755 642 10.02 %
Rwork0.2189 --
obs0.2244 6409 96.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 102.32 Å2 / Biso mean: 38.0009 Å2 / Biso min: 9.38 Å2
Refinement stepCycle: final / Resolution: 2.7→39.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1427 0 50 2 1479
Biso mean--44.66 38.1 -
Num. residues----173
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.90840.30461100.199897083
2.9084-3.2010.28651260.20751156100
3.201-3.66390.25521320.20461183100
3.6639-4.6150.29551330.21691197100
4.615-39.7380.25591410.2414126199

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