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- PDB-7jo8: Crystal structure of a Chimeric Antigen Receptor (CAR) scFv domai... -

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Basic information

Entry
Database: PDB / ID: 7jo8
TitleCrystal structure of a Chimeric Antigen Receptor (CAR) scFv domain rearrangement forming a VL-VL dimer
Components47G4-CD828Z
KeywordsIMMUNE SYSTEM / Chimeric Antigen Receptor (CAR) antibody scfv rearrangement VL-VL complex
Function / homologyMALONATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.399 Å
AuthorsCheung, J. / Hendrickson, W.A. / Kochenderfer, J.N. / Youkharibache, P.
CitationJournal: Crystals / Year: 2023
Title: Crystal Structure of a Chimeric Antigen Receptor (CAR) scFv Domain Rearrangement Forming a VL-VL Dimer
Authors: Cheung, J. / Wazir, S. / Bell, D.R. / Kochenderfer, J.N. / Hendrickson, W.A. / Youkharibache, P.
History
DepositionAug 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 47G4-CD828Z
B: 47G4-CD828Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1495
Polymers23,6142
Non-polymers5353
Water3,873215
1
A: 47G4-CD828Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1473
Polymers11,8071
Non-polymers3402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 47G4-CD828Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0012
Polymers11,8071
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.322, 79.221, 40.616
Angle α, β, γ (deg.)90.000, 109.560, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 6 or resid 9...
21(chain B and (resid 2 through 6 or resid 9...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 6 or resid 9...A2 - 6
121(chain A and (resid 2 through 6 or resid 9...A9
131(chain A and (resid 2 through 6 or resid 9...A11 - 21
141(chain A and (resid 2 through 6 or resid 9...A24 - 27
151(chain A and (resid 2 through 6 or resid 9...A354
161(chain A and (resid 2 through 6 or resid 9...A2 - 108
171(chain A and (resid 2 through 6 or resid 9...A556 - 63
181(chain A and (resid 2 through 6 or resid 9...A65
191(chain A and (resid 2 through 6 or resid 9...A67 - 72
1101(chain A and (resid 2 through 6 or resid 9...A83 - 88
1111(chain A and (resid 2 through 6 or resid 9...A90 - 108
211(chain B and (resid 2 through 6 or resid 9...B2 - 6
221(chain B and (resid 2 through 6 or resid 9...B9
231(chain B and (resid 2 through 6 or resid 9...B11 - 21
241(chain B and (resid 2 through 6 or resid 9...B24 - 27
251(chain B and (resid 2 through 6 or resid 9...B354
261(chain B and (resid 2 through 6 or resid 9...B1 - 110
271(chain B and (resid 2 through 6 or resid 9...B556 - 63
281(chain B and (resid 2 through 6 or resid 9...B65
291(chain B and (resid 2 through 6 or resid 9...B67 - 72
2101(chain B and (resid 2 through 6 or resid 9...B83 - 88
2111(chain B and (resid 2 through 6 or resid 9...B90 - 108

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Components

#1: Antibody 47G4-CD828Z


Mass: 11807.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: ammonium sulfate, PEG 400, magnesium sulfate, Tris pH 85.

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC HF-4M / Detector: PIXEL / Date: May 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.399→200 Å / Num. obs: 46445 / % possible obs: 99.8 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.022 / Rrim(I) all: 0.074 / Χ2: 0.975 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.429.31.36122270.5490.461.440.54597.5
1.42-1.4510.21.19123370.6520.3811.2530.56699.2
1.45-1.4811.21.03623050.7490.3141.0850.58599.8
1.48-1.5110.90.8723240.8070.2690.9120.61999.9
1.51-1.5411.50.74622810.8260.2240.780.637100
1.54-1.5811.30.62723190.890.1920.6570.66100
1.58-1.6211.50.52323550.9260.1570.5470.691100
1.62-1.6610.90.43922800.9430.1370.460.728100
1.66-1.7110.50.35523390.9610.1140.3730.769100
1.71-1.7610.90.26923240.980.0840.2820.847100
1.76-1.8311.50.20923200.9880.0640.2190.942100
1.83-1.912.10.16323360.9930.0480.171.101100
1.9-1.9911.80.12523080.9960.0370.131.17699.9
1.99-2.0911.50.123340.9960.030.1041.307100
2.09-2.2211.70.08723160.9970.0260.0911.371100
2.22-2.3910.60.07523450.9980.0240.0791.378100
2.39-2.6311.50.06223330.9980.0190.0651.351100
2.63-3.0212.30.04523260.9990.0130.0471.289100
3.02-3.812.30.034235910.010.0351.303100
3.8-20011.30.03223770.9990.010.0331.343100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.9 Å19.77 Å
Translation1.9 Å19.77 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASER2.8.2phasing
PHENIX1.16-3549refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ejg, 4yjz, 3auv, 1ktr, 6i07, 1h8n, 5ogi, 6j71

6ejg

4yjz

3auv

1ktr

6i07

1h8n

5ogi

6j71


Resolution: 1.399→39.61 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1713 2259 4.86 %
Rwork0.1549 44183 -
obs0.1557 46442 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.03 Å2 / Biso mean: 25.0445 Å2 / Biso min: 9.76 Å2
Refinement stepCycle: final / Resolution: 1.399→39.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1643 0 36 215 1894
Biso mean--42.83 35.01 -
Num. residues----217
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A474X-RAY DIFFRACTION6.458TORSIONAL
12B474X-RAY DIFFRACTION6.458TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3991-1.42960.29721350.2818262696
1.4296-1.46280.25691400.2579275699
1.4628-1.49940.24931310.23272779100
1.4994-1.540.23591430.22142721100
1.54-1.58530.22951330.19832800100
1.5853-1.63640.20471370.1922740100
1.6364-1.69490.21181580.18052781100
1.6949-1.76280.19931460.16832737100
1.7628-1.8430.18021460.16432772100
1.843-1.94020.16331490.15342751100
1.9402-2.06170.15281400.14142772100
2.0617-2.22090.16411290.14592760100
2.2209-2.44440.18831630.16122766100
2.4444-2.7980.16661320.15642791100
2.798-3.52480.17181340.13762791100
3.5248-39.610.12611430.12612840100
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)
17.52843.02250.3192.83141.06981.905-0.0142-0.3028-0.120.0922-0.0664-0.16640.08350.03160.050.15840.0294-0.03120.12790.02730.172711.328216.866326.6758
24.1599-1.489-0.27663.4634-0.14513.8096-0.0622-0.17560.2410.06050.0619-0.2029-0.2542-0.13590.02880.1250.01570.00130.06870.00750.10584.815327.359426.5821
33.4875-2.1653-0.7745.19810.8562.8006-0.0971-0.2207-0.56180.32790.11520.37780.2506-0.0175-0.03220.16950.03360.00160.14420.04360.19011.249219.13131.1133
44.0562-1.36910.12364.2884-0.68212.8520.0307-0.09910.2461-0.2074-0.0691-0.1681-0.17190.00930.0410.09720.0097-0.01270.11490.01310.1069.039725.621723.4331
55.3911-5.0316-0.39717.75531.88521.9447-0.1563-0.0602-0.0050.41980.161-0.04350.05410.1521-0.03080.1025-0.0297-0.00510.12920.01130.14911.607143.299613.8138
69.8275-0.26190.91914.14940.29391.35910.10940.3092-0.11980.0853-0.1799-0.0227-0.00490.18170.04290.14630.00420.0120.14740.01510.118613.665539.72979.1924
73.8889-0.8072-2.18982.4250.82954.7762-0.08220.049-0.05910.17630.0288-0.04110.2773-0.02580.0860.1405-0.0081-0.00740.0790.01030.086.46832.079611.5893
83.26750.185-0.48863.5171.02552.21680.01140.2150.146-0.0889-0.05140.15880.0695-0.0410.04140.1137-0.0123-0.0140.15350.00650.09970.521636.61514.5224
98.2832-7.2506-5.44188.87735.77434.77560.02470.19010.0223-0.0906-0.13440.1648-0.0405-0.15060.11110.1424-0.0112-0.01460.16740.02280.18134.784143.52198.9237
102.7622-0.91041.22897.8431-1.89811.696-0.02330.0261-0.1084-0.12960.0786-0.3830.21050.1715-0.07650.13640.00560.02570.11090.00220.102910.32929.995414.5686
118.2373-5.16170.1063.24730.01132.0468-0.3341-0.59720.10921.17390.28450.4081-0.16350.01180.02420.2932-0.00410.03940.1871-0.01350.2046.463650.300519.8662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 25 )A2 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 49 )A26 - 49
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 84 )A50 - 84
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 108 )A85 - 108
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 18 )B1 - 18
6X-RAY DIFFRACTION6chain 'B' and (resid 19 through 25 )B19 - 25
7X-RAY DIFFRACTION7chain 'B' and (resid 26 through 49 )B26 - 49
8X-RAY DIFFRACTION8chain 'B' and (resid 50 through 68 )B50 - 68
9X-RAY DIFFRACTION9chain 'B' and (resid 69 through 84 )B69 - 84
10X-RAY DIFFRACTION10chain 'B' and (resid 85 through 102 )B85 - 102
11X-RAY DIFFRACTION11chain 'B' and (resid 103 through 110 )B103 - 110

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