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

ID or keywords:

Entry

Database: PDB / ID: 7jo8

Title

Crystal structure of a Chimeric Antigen Receptor (CAR) scFv domain rearrangement forming a VL-VL dimer

Components

47G4-CD828Z

Keywords

IMMUNE SYSTEM / Chimeric Antigen Receptor (CAR) antibody scfv rearrangement VL-VL complex

Function / homology

MALONATE ION

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.399 Å

Authors

Cheung, J. / Hendrickson, W.A. / Kochenderfer, J.N. / Youkharibache, P.

Citation

Journal: 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

Deposition	Aug 6, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 10, 2021	Provider: repository / Type: Initial release
Revision 1.1	May 3, 2023	Group: 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 1.2	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7jo8.cif.gz	110.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7jo8.ent.gz	83.3 KB	Display	PDB format
PDBx/mmJSON format	7jo8.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7jo8_validation.pdf.gz	459.7 KB	Display	wwPDB validaton report
Full document	7jo8_full_validation.pdf.gz	461.7 KB	Display
Data in XML	7jo8_validation.xml.gz	13.7 KB	Display
Data in CIF	7jo8_validation.cif.gz	19.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jo/7jo8 ftp://data.pdbj.org/pub/pdb/validation_reports/jo/7jo8	HTTPS FTP

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Related structure data

Related structure data	1h8nS 1ktrS 3auvS 4yjzS 5ogiS 6ejgS 6i07S 6j71S S: Starting model for refinement
Similar structure data	1d7i-2 1pw3-1 5nml-4 5acm-2 2iqj-2 4hlb-d 5nml-7 5c9k-2 2jac-d 4s1z-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: 47G4-CD828Z

B: 47G4-CD828Z

hetero molecules

24.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 47G4-CD828Z

hetero molecules

defined by author
Evidence: gel filtration
12.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 47G4-CD828Z

hetero molecules

defined by author
12 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain A and (resid 2 through 6 or resid 9...
2	1	(chain B and (resid 2 through 6 or resid 9...

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	(chain A and (resid 2 through 6 or resid 9...	A	2 - 6
1	2	1	(chain A and (resid 2 through 6 or resid 9...	A	9
1	3	1	(chain A and (resid 2 through 6 or resid 9...	A	11 - 21
1	4	1	(chain A and (resid 2 through 6 or resid 9...	A	24 - 27
1	5	1	(chain A and (resid 2 through 6 or resid 9...	A	354
1	6	1	(chain A and (resid 2 through 6 or resid 9...	A	2 - 108
1	7	1	(chain A and (resid 2 through 6 or resid 9...	A	556 - 63
1	8	1	(chain A and (resid 2 through 6 or resid 9...	A	65
1	9	1	(chain A and (resid 2 through 6 or resid 9...	A	67 - 72
1	10	1	(chain A and (resid 2 through 6 or resid 9...	A	83 - 88
1	11	1	(chain A and (resid 2 through 6 or resid 9...	A	90 - 108
2	1	1	(chain B and (resid 2 through 6 or resid 9...	B	2 - 6
2	2	1	(chain B and (resid 2 through 6 or resid 9...	B	9
2	3	1	(chain B and (resid 2 through 6 or resid 9...	B	11 - 21
2	4	1	(chain B and (resid 2 through 6 or resid 9...	B	24 - 27
2	5	1	(chain B and (resid 2 through 6 or resid 9...	B	354
2	6	1	(chain B and (resid 2 through 6 or resid 9...	B	1 - 110
2	7	1	(chain B and (resid 2 through 6 or resid 9...	B	556 - 63
2	8	1	(chain B and (resid 2 through 6 or resid 9...	B	65
2	9	1	(chain B and (resid 2 through 6 or resid 9...	B	67 - 72
2	10	1	(chain B and (resid 2 through 6 or resid 9...	B	83 - 88
2	11	1	(chain B and (resid 2 through 6 or resid 9...	B	90 - 108

#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 interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.55 Å³/Da / Density % sol: 51.69 %
Crystal grow	Temperature: 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

Diffraction

Mean temperature: 110 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS-II

/ Beamline: 19-ID / Wavelength: 0.979 Å

Detector

Type: ADSC HF-4M / Detector: PIXEL / Date: May 23, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 1.399→200 Å / Num. obs: 46445 / % possible obs: 99.8 % / Redundancy: 11.2 % / R_merge(I) obs: 0.071 / R_pim(I) all: 0.022 / R_rim(I) all: 0.074 / Χ²: 0.975 / Net I/σ(I): 7.5

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.4-1.42	9.3	1.361	2227	0.549	0.46	1.44	0.545	97.5
1.42-1.45	10.2	1.191	2337	0.652	0.381	1.253	0.566	99.2
1.45-1.48	11.2	1.036	2305	0.749	0.314	1.085	0.585	99.8
1.48-1.51	10.9	0.87	2324	0.807	0.269	0.912	0.619	99.9
1.51-1.54	11.5	0.746	2281	0.826	0.224	0.78	0.637	100
1.54-1.58	11.3	0.627	2319	0.89	0.192	0.657	0.66	100
1.58-1.62	11.5	0.523	2355	0.926	0.157	0.547	0.691	100
1.62-1.66	10.9	0.439	2280	0.943	0.137	0.46	0.728	100
1.66-1.71	10.5	0.355	2339	0.961	0.114	0.373	0.769	100
1.71-1.76	10.9	0.269	2324	0.98	0.084	0.282	0.847	100
1.76-1.83	11.5	0.209	2320	0.988	0.064	0.219	0.942	100
1.83-1.9	12.1	0.163	2336	0.993	0.048	0.17	1.101	100
1.9-1.99	11.8	0.125	2308	0.996	0.037	0.13	1.176	99.9
1.99-2.09	11.5	0.1	2334	0.996	0.03	0.104	1.307	100
2.09-2.22	11.7	0.087	2316	0.997	0.026	0.091	1.371	100
2.22-2.39	10.6	0.075	2345	0.998	0.024	0.079	1.378	100
2.39-2.63	11.5	0.062	2333	0.998	0.019	0.065	1.351	100
2.63-3.02	12.3	0.045	2326	0.999	0.013	0.047	1.289	100
3.02-3.8	12.3	0.034	2359	1	0.01	0.035	1.303	100
3.8-200	11.3	0.032	2377	0.999	0.01	0.033	1.343	100

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	1.9 Å	19.77 Å
Translation	1.9 Å	19.77 Å

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Processing

Software

Name	Version	Classification
HKL-2000		data reduction
HKL-2000		data scaling
PHASER	2.8.2	phasing
PHENIX	1.16-3549	refinement
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 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

	R_factor	Num. reflection	% reflection
R_free	0.1713	2259	4.86 %
R_work	0.1549	44183	-
obs	0.1557	46442	99.67 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 93.03 Å² / B_iso mean: 25.0445 Å² / B_iso min: 9.76 Å²

Refinement step

Cycle: final / Resolution: 1.399→39.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1643	0	36	215	1894
B_iso mean	-	-	42.83	35.01	-
Num. residues	-	-	-	-	217

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	474	X-RAY DIFFRACTION	6.458	TORSIONAL
1	2	B	474	X-RAY DIFFRACTION	6.458	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.3991-1.4296	0.2972	135	0.2818	2626	96
1.4296-1.4628	0.2569	140	0.2579	2756	99
1.4628-1.4994	0.2493	131	0.2327	2779	100
1.4994-1.54	0.2359	143	0.2214	2721	100
1.54-1.5853	0.2295	133	0.1983	2800	100
1.5853-1.6364	0.2047	137	0.192	2740	100
1.6364-1.6949	0.2118	158	0.1805	2781	100
1.6949-1.7628	0.1993	146	0.1683	2737	100
1.7628-1.843	0.1802	146	0.1643	2772	100
1.843-1.9402	0.1633	149	0.1534	2751	100
1.9402-2.0617	0.1528	140	0.1414	2772	100
2.0617-2.2209	0.1641	129	0.1459	2760	100
2.2209-2.4444	0.1883	163	0.1612	2766	100
2.4444-2.798	0.1666	132	0.1564	2791	100
2.798-3.5248	0.1718	134	0.1376	2791	100
3.5248-39.61	0.1261	143	0.1261	2840	100

Refinement TLS params.

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

ID	L11 (°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)
1	7.5284	3.0225	0.319	2.8314	1.0698	1.905	-0.0142	-0.3028	-0.12	0.0922	-0.0664	-0.1664	0.0835	0.0316	0.05	0.1584	0.0294	-0.0312	0.1279	0.0273	0.1727	11.3282	16.8663	26.6758
2	4.1599	-1.489	-0.2766	3.4634	-0.1451	3.8096	-0.0622	-0.1756	0.241	0.0605	0.0619	-0.2029	-0.2542	-0.1359	0.0288	0.125	0.0157	0.0013	0.0687	0.0075	0.1058	4.8153	27.3594	26.5821
3	3.4875	-2.1653	-0.774	5.1981	0.856	2.8006	-0.0971	-0.2207	-0.5618	0.3279	0.1152	0.3778	0.2506	-0.0175	-0.0322	0.1695	0.0336	0.0016	0.1442	0.0436	0.1901	1.2492	19.131	31.1133
4	4.0562	-1.3691	0.1236	4.2884	-0.6821	2.852	0.0307	-0.0991	0.2461	-0.2074	-0.0691	-0.1681	-0.1719	0.0093	0.041	0.0972	0.0097	-0.0127	0.1149	0.0131	0.106	9.0397	25.6217	23.4331
5	5.3911	-5.0316	-0.3971	7.7553	1.8852	1.9447	-0.1563	-0.0602	-0.005	0.4198	0.161	-0.0435	0.0541	0.1521	-0.0308	0.1025	-0.0297	-0.0051	0.1292	0.0113	0.149	11.6071	43.2996	13.8138
6	9.8275	-0.2619	0.9191	4.1494	0.2939	1.3591	0.1094	0.3092	-0.1198	0.0853	-0.1799	-0.0227	-0.0049	0.1817	0.0429	0.1463	0.0042	0.012	0.1474	0.0151	0.1186	13.6655	39.7297	9.1924
7	3.8889	-0.8072	-2.1898	2.425	0.8295	4.7762	-0.0822	0.049	-0.0591	0.1763	0.0288	-0.0411	0.2773	-0.0258	0.086	0.1405	-0.0081	-0.0074	0.079	0.0103	0.08	6.468	32.0796	11.5893
8	3.2675	0.185	-0.4886	3.517	1.0255	2.2168	0.0114	0.215	0.146	-0.0889	-0.0514	0.1588	0.0695	-0.041	0.0414	0.1137	-0.0123	-0.014	0.1535	0.0065	0.0997	0.5216	36.6151	4.5224
9	8.2832	-7.2506	-5.4418	8.8773	5.7743	4.7756	0.0247	0.1901	0.0223	-0.0906	-0.1344	0.1648	-0.0405	-0.1506	0.1111	0.1424	-0.0112	-0.0146	0.1674	0.0228	0.1813	4.7841	43.5219	8.9237
10	2.7622	-0.9104	1.2289	7.8431	-1.8981	1.696	-0.0233	0.0261	-0.1084	-0.1296	0.0786	-0.383	0.2105	0.1715	-0.0765	0.1364	0.0056	0.0257	0.1109	0.0022	0.1029	10.329	29.9954	14.5686
11	8.2373	-5.1617	0.106	3.2473	0.0113	2.0468	-0.3341	-0.5972	0.1092	1.1739	0.2845	0.4081	-0.1635	0.0118	0.0242	0.2932	-0.0041	0.0394	0.1871	-0.0135	0.204	6.4636	50.3005	19.8662

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 25 )	A	2 - 25
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 26 through 49 )	A	26 - 49
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 50 through 84 )	A	50 - 84
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 85 through 108 )	A	85 - 108
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 18 )	B	1 - 18
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 19 through 25 )	B	19 - 25
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 26 through 49 )	B	26 - 49
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 50 through 68 )	B	50 - 68
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 69 through 84 )	B	69 - 84
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 85 through 102 )	B	85 - 102
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 103 through 110 )	B	103 - 110

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