PDB-4tuj: Crystal structure of monoclonal antibody against neuroblastoma as...

ID or keywords:

Entry

Database: PDB / ID: 4tuj

Title

Crystal structure of monoclonal antibody against neuroblastoma associated antigen.

Components

Heavy chain of monoclonal antibody against neuroblastoma associated antigen
Light chain of monoclonal antibody against neuroblastoma associated antigen
peptide1

Keywords

IMMUNE SYSTEM / antibody / neuroblastoma

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Mus musculus (house mouse)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.89 Å

Authors

Grudnik, P. / Golik, P. / Horwacik, I. / Zdzalik, M. / Rokita, H. / Dubin, G.

Citation

Journal: Mol.Cell Proteomics / Year: 2015
Title: Structural Basis of GD2 Ganglioside and Mimetic Peptide Recognition by 14G2a Antibody.
Authors: Horwacik, I. / Golik, P. / Grudnik, P. / Kolinski, M. / Zdzalik, M. / Rokita, H. / Dubin, G.

History

Deposition	Jun 24, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jul 15, 2015	Provider: repository / Type: Initial release
Revision 1.1	Oct 14, 2015	Group: Database references
Revision 1.2	Dec 20, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4tuj.cif.gz	343.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4tuj.ent.gz	279.9 KB	Display	PDB format
PDBx/mmJSON format	4tuj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4tuj_validation.pdf.gz	462.9 KB	Display	wwPDB validaton report
Full document	4tuj_full_validation.pdf.gz	466.3 KB	Display
Data in XML	4tuj_validation.xml.gz	35.3 KB	Display
Data in CIF	4tuj_validation.cif.gz	51.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tu/4tuj ftp://data.pdbj.org/pub/pdb/validation_reports/tu/4tuj	HTTPS FTP

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Related structure data

Related structure data	4trpC 4tukC 4tulC 4tuoC 1f8tS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6y54-1 3u0t-2 4wht-8 3dgg-2 4ncc-2 4kkl-2 2aj3-1 5ye4-2 4mhh-3 6d9g-2 6pxg-3 2v7h-2 2a1w-2 4jfz-d 2g2r-2 4hk3-d 3nz8-2 5tdo-2 5wtg-1 4kjq-2 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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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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: Heavy chain of monoclonal antibody against neuroblastoma associated antigen

B: Light chain of monoclonal antibody against neuroblastoma associated antigen

E: peptide1

C: Heavy chain of monoclonal antibody against neuroblastoma associated antigen

D: Light chain of monoclonal antibody against neuroblastoma associated antigen

F: peptide1

97.9 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Heavy chain of monoclonal antibody against neuroblastoma associated antigen

B: Light chain of monoclonal antibody against neuroblastoma associated antigen

E: peptide1

defined by software
48.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Heavy chain of monoclonal antibody against neuroblastoma associated antigen

D: Light chain of monoclonal antibody against neuroblastoma associated antigen

F: peptide1

defined by software
48.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	43.380, 69.820, 78.000
Angle α, β, γ (deg.)	111.45, 101.14, 90.35
Int Tables number	1
Space group name H-M	P1

#1: Antibody	Heavy chain of monoclonal antibody against neuroblastoma associated antigen Mass: 22748.438 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody	Light chain of monoclonal antibody against neuroblastoma associated antigen Mass: 24251.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Protein/peptide	peptide1 Mass: 1948.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 433 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 43.99 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Bis-Tris containing PEG 5000

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Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 17, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.89→40.84 Å / Num. obs: 60908 / % possible obs: 90.92 % / Redundancy: 3.9 % / R_merge(I) obs: 0.069 / Net I/σ(I): 9.66
Reflection shell	Resolution: 1.89→1.99 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.548 / Mean I/σ(I) obs: 1.85 / % possible all: 84.54

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1F8T

1f8t

Resolution: 1.89→24.777 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.56 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2324	3069	5.05 %
R_work	0.1789	-	-
obs	0.1816	60776	90.75 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.89→24.777 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6305	0	0	433	6738

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	6480
X-RAY DIFFRACTION	f_angle_d	1.388	8838
X-RAY DIFFRACTION	f_dihedral_angle_d	11.395	2198
X-RAY DIFFRACTION	f_chiral_restr	0.083	1003
X-RAY DIFFRACTION	f_plane_restr	0.007	1138

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.887-1.9165	0.3932	120	0.2867	2261	X-RAY DIFFRACTION	80
1.9165-1.9479	0.3171	137	0.2613	2599	X-RAY DIFFRACTION	88
1.9479-1.9815	0.2864	132	0.219	2566	X-RAY DIFFRACTION	88
1.9815-2.0175	0.2394	142	0.2094	2526	X-RAY DIFFRACTION	89
2.0175-2.0563	0.2713	149	0.2107	2614	X-RAY DIFFRACTION	89
2.0563-2.0982	0.2661	129	0.2137	2532	X-RAY DIFFRACTION	89
2.0982-2.1438	0.2712	148	0.2005	2596	X-RAY DIFFRACTION	90
2.1438-2.1937	0.2838	155	0.1918	2571	X-RAY DIFFRACTION	90
2.1937-2.2485	0.2802	123	0.1839	2608	X-RAY DIFFRACTION	90
2.2485-2.3092	0.2224	126	0.1842	2652	X-RAY DIFFRACTION	91
2.3092-2.3771	0.2352	131	0.1829	2623	X-RAY DIFFRACTION	91
2.3771-2.4538	0.272	149	0.1958	2634	X-RAY DIFFRACTION	91
2.4538-2.5414	0.2499	128	0.1933	2687	X-RAY DIFFRACTION	92
2.5414-2.6431	0.2767	133	0.1948	2638	X-RAY DIFFRACTION	91
2.6431-2.7632	0.2658	158	0.1939	2630	X-RAY DIFFRACTION	92
2.7632-2.9087	0.2404	148	0.197	2700	X-RAY DIFFRACTION	92
2.9087-3.0906	0.2979	141	0.1962	2655	X-RAY DIFFRACTION	93
3.0906-3.3287	0.231	155	0.185	2687	X-RAY DIFFRACTION	93
3.3287-3.6627	0.2103	149	0.1675	2690	X-RAY DIFFRACTION	93
3.6627-4.1905	0.202	132	0.1537	2723	X-RAY DIFFRACTION	94
4.1905-5.2712	0.1756	143	0.1392	2759	X-RAY DIFFRACTION	95
5.2712-24.7792	0.2032	141	0.1768	2756	X-RAY DIFFRACTION	95

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	3.7702	0.1185	-2.418	1.9111	1.0895	2.581	0	-0.1344	-0.0841	0.0669	-0.1393	-0.1422	0.116	0.1937	0.0965	0.164	-0.0054	-0.0199	0.2048	0.0352	0.2343	30.7913	-31.0262	-37.4581
2	2.9567	-1.8899	1.0808	5.3635	0.8111	1.4147	-0.1374	0.5634	0.1662	-0.6416	-0.1632	-0.507	-0.2881	0.2908	0.3705	0.2013	-0.0499	-0.0164	0.3383	0.0619	0.279	36.9416	-21.9363	-44.632
3	0.7049	-0.0471	1.2205	2.6982	-0.7964	4.3789	-0.1062	-0.113	0.0395	0.1392	0.0347	0.0488	-0.3288	-0.1542	0.0772	0.2051	0.035	0.0063	0.1904	-0.0113	0.2121	29.1701	-21.2426	-37.7799
4	1.2317	0.1465	-0.8437	1.6434	-1.182	0.9667	0.2239	-0.318	-0.6329	-0.0422	-0.4249	0.2774	0.0794	-0.1189	0.2371	0.2032	0.0479	0.0205	0.252	-0.0411	0.3913	13.5434	-47.7672	-37.6967
5	3.8334	0.2979	1.4537	2.6195	-1.4535	1.2697	0.2813	0.4543	-0.6275	-0.3664	-0.3942	0.1092	0.0915	0.2622	0.0345	0.2613	0.0972	-0.0005	0.3355	-0.1356	0.3563	12.7522	-48.5225	-44.0147
6	2.6048	2.8017	4.1992	4.1588	4.3477	9.1406	0.0312	0.4268	-0.2752	-0.4274	-0.3701	0.4124	0.3975	-0.2505	0.3286	0.3349	0.1098	-0.0534	0.4915	-0.2302	0.4809	7.0483	-51.8992	-49.1199
7	2.0652	1.1249	0.8938	1.5577	0.0564	1.8176	0.6659	0.5286	-0.8503	-0.5707	-0.8734	0.1367	0.7327	0.4936	0.0943	0.4513	0.3111	-0.0805	0.1861	-0.3482	0.8872	13.4877	-58.9607	-45.1483
8	1.3482	0.0867	0.2166	2.3994	-0.3753	2.3662	-0.3816	-0.3465	0.381	0.1642	0.1348	0.1517	-0.6535	-0.8442	0.1938	0.3861	0.191	-0.0612	0.3763	-0.0204	0.3843	12.52	-11.4838	-50.6417
9	4.0497	0.5475	0.4571	7.3466	-2.8231	3.7513	-0.2129	0.0171	-0.5122	-0.0023	0.302	0.1723	0.0679	-0.1688	-0.0547	0.1848	0.0002	0.008	0.2071	0.0216	0.2922	20.6773	-20.6438	-53.0137
10	2.8381	1.1213	0.7813	2.0143	-0.3367	4.239	-0.4512	0.3217	0.218	-0.2138	0.2107	0.0866	-0.4977	-0.3835	0.219	0.2712	0.0401	-0.0246	0.2656	0.0443	0.2751	16.9818	-14.947	-58.1912
11	2.3975	0.54	1.3375	1.4858	0.1668	0.9245	-0.2985	0.0118	0.3707	-0.0298	0.1759	0.0223	-0.2917	-0.1042	0.1232	0.2182	0.0641	0.028	0.2554	-0.045	0.2212	10.9955	-21.3641	-49.74
12	2.6707	-0.571	0.4299	2.5547	-0.9561	1.9237	0.0967	-0.1215	-0.7278	-0.0504	0.0447	0.1257	0.2434	-0.009	-0.1335	0.1621	-0.013	-0.0125	0.1571	-0.0023	0.3704	-1.7607	-46.4837	-40.635
13	3.3837	-0.9231	1.5383	3.0428	-1.9447	2.8669	0.1162	-0.1144	-0.7178	-0.0147	0.1521	0.2345	0.1507	-0.084	-0.2119	0.1696	-0.0006	0.0225	0.1655	-0.0364	0.3257	-2.7469	-44.3183	-41.5936
14	1.9644	0.0912	0.3686	2.1802	-0.3787	0.1392	0.0096	-0.2022	0.434	0.9319	-0.2273	-0.3651	-0.875	0.2207	0.158	0.631	-0.1083	-0.171	0.2776	0.0653	0.4561	32.0015	-6.419	-45.8516
15	2.3421	0.9969	1.0728	2.2173	-0.6709	4.3378	-0.1546	0.0618	0.0813	-0.0961	0.1135	-0.1087	-0.4395	0.344	0.0173	0.2875	-0.0484	-0.0081	0.282	-0.0157	0.1559	16.4234	-61.3788	-90.6224
16	1.7349	0.1513	1.4342	3.1005	0.6134	4.1487	-0.5312	0.6904	-0.0602	-1.0314	0.7468	-0.6965	-0.0333	0.7156	-0.2097	0.7579	-0.333	0.1544	0.8339	-0.1829	0.4637	40.061	-36.8983	-84.8953
17	6.7268	1.1059	1.7013	2.1669	0.8365	2.7152	0.0591	-0.1623	0.1088	0.3275	0.0284	-0.0738	-0.3658	-0.4434	-0.1245	0.4754	0.0952	0.0032	0.4027	-0.0186	0.2764	20.694	-57.1764	-64.0772
18	2.6167	0.3515	1.3215	2.5567	-0.1936	3.9699	0.0418	-0.3659	-0.2357	0.2066	0.0549	-0.06	0.2489	-0.3868	-0.0903	0.3301	-0.0191	-0.0479	0.3197	0.0477	0.2778	18.6179	-68.1351	-67.9158
19	3.7654	1.2427	1.5562	2.3269	0.166	2.9454	0.1642	-0.1722	-0.1732	0.194	0.0754	-0.0434	0.1001	-0.4509	-0.2197	0.3103	0.0139	0.0152	0.3416	0.0456	0.2347	19.0042	-63.0812	-71.3134
20	3.371	4.7743	1.1314	6.7092	1.6846	0.3362	0.1074	0.0559	-0.4484	-0.2051	0.1927	-0.0385	0.2949	0.0904	-0.2862	0.4536	0.0298	-0.1091	0.3205	-0.0868	0.3877	32.0527	-47.9952	-63.3682
21	1.3853	-0.5681	1.8995	1.4585	-1.0128	3.6472	-0.521	0.4548	0.4914	-0.3306	0.5648	0.0647	-0.6423	-0.0742	-0.0297	0.5574	-0.18	-0.0723	0.4506	0.1198	0.3724	31.6552	-29.115	-76.6111
22	3.4469	0.5818	1.1437	0.8737	-1.5274	6.0171	-0.3603	0.4067	0.4009	-0.2124	0.4766	0.4479	-0.456	-0.2777	-0.1486	0.4794	-0.0915	-0.0451	0.3742	0.0343	0.3153	30.5492	-30.8289	-73.4766
23	6.0832	3.4335	-1.7173	5.6665	3.4689	5.6522	0.1944	0.4544	-0.1988	-0.6348	0.3332	0.6849	-0.217	-0.7366	-0.3987	0.5675	-0.0645	-0.1156	0.4035	0.152	0.4621	11.0049	-77.1321	-79.9348

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 17 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 18 through 33 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 34 through 106 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 107 through 134 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 135 through 174 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 175 through 187 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 188 through 212 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 37 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 38 through 53 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 54 through 95 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 96 through 119 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 120 through 161 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 162 through 217 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 1 through 14 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 2 through 119 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 120 through 212 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1 through 18 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 19 through 80 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 81 through 107 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 108 through 119 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 120 through 161 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 162 through 217 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 1 through 13 )

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Jul 12, 2017. Major update of PDB

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Yorodumi