PDB-6a0x: Crystal structure of broadly neutralizing antibody 13D4

ID or keywords:

Entry

Database: PDB / ID: 6a0x

Title

Crystal structure of broadly neutralizing antibody 13D4

Components

Antibody 13D4, Fab Heavy Chain
Antibody 13D4, Fab Light Chain

Keywords

IMMUNE SYSTEM /

Antibody

Function / homology

Immunoglobulins /

Immunoglobulin-like /

Sandwich / Mainly Beta

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Li, S. / Li, T.

Funding support

China, 2items

Citation

Journal: J. Virol. / Year: 2018
Title: Structural Basis for the Broad, Antibody-Mediated Neutralization of H5N1 Influenza Virus.
Authors: Lin, Q. / Li, T. / Chen, Y. / Lau, S.Y. / Wei, M. / Zhang, Y. / Zhang, Z. / Yao, Q. / Li, J. / Li, Z. / Wang, D. / Zheng, Q. / Yu, H. / Gu, Y. / Zhang, J. / Chen, H. / Li, S. / Xia, N.

History

Deposition	Jun 6, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 20, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jul 4, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Sep 19, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 2.0	Nov 22, 2023	Group: Data collection / Database references ...Data collection / Database references / Polymer sequence / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6a0x.cif.gz	674.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6a0x.ent.gz	564.1 KB	Display	PDB format
PDBx/mmJSON format	6a0x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a0/6a0x ftp://data.pdbj.org/pub/pdb/validation_reports/a0/6a0x	HTTPS FTP

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Related structure data

Related structure data	6a0zC 3cleS 4ki5S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5waw-d 4h20-d 1ggi-2 2aj3-3 5ibu-2 6p9i-1 1cgs-d 1dbj-d 1b4j-d 3r06-2 4kmt-d 1ggc-d 2w65-1 3nab-d 1kem-d 3ejy-3 3cmo-1 6vl9-1 5ibu-1 1jgu-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

6a0zC

3cleS

4ki5S

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: Antibody 13D4, Fab Heavy Chain

B: Antibody 13D4, Fab Light Chain

C: Antibody 13D4, Fab Heavy Chain

D: Antibody 13D4, Fab Light Chain

E: Antibody 13D4, Fab Heavy Chain

F: Antibody 13D4, Fab Light Chain

G: Antibody 13D4, Fab Heavy Chain

H: Antibody 13D4, Fab Light Chain

190 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Antibody 13D4, Fab Heavy Chain

B: Antibody 13D4, Fab Light Chain

defined by author&software
Evidence: gel filtration
47.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Antibody 13D4, Fab Heavy Chain

D: Antibody 13D4, Fab Light Chain

defined by author&software
47.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Antibody 13D4, Fab Heavy Chain

F: Antibody 13D4, Fab Light Chain

defined by author&software
47.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Antibody 13D4, Fab Heavy Chain

H: Antibody 13D4, Fab Light Chain

defined by author&software
47.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	81.382, 108.957, 108.184
Angle α, β, γ (deg.)	90.00, 90.08, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	Antibody 13D4, Fab Heavy Chain Mass: 23888.648 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody	Antibody 13D4, Fab Light Chain Mass: 23630.027 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.52 Å³/Da / Density % sol: 51.26 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 12.5% (w/v) PEG 3350, 150 mM potassium acetate

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Data collection

Diffraction	Mean temperature: 277.15 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97946 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 2.3→50 Å / Num. obs: 83892 / % possible obs: 99.7 % / Redundancy: 7.3 % / R_pim(I) all: 0.051 / R_sym value: 0.119 / Net I/σ(I): 18.7
Reflection shell	Resolution: 2.3→2.34 Å / Num. unique obs: 4144 / R_pim(I) all: 0.478 / R_sym value: 0.999

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Processing

Software

Name	Version	Classification
HKL-2000	V706E	data collection
PHASER		phasing
Coot		model building
PHENIX	1.11.1_2575	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3CLE, 4KI5

3cle

4ki5

Resolution: 2.3→48.657 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.85

	R_factor	Num. reflection	% reflection
R_free	0.2428	4063	4.85 %
R_work	0.2053	-	-
obs	0.2071	83838	99.27 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.3→48.657 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13360	0	0	391	13751

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	13716
X-RAY DIFFRACTION	f_angle_d	0.694	18700
X-RAY DIFFRACTION	f_dihedral_angle_d	11.263	8120
X-RAY DIFFRACTION	f_chiral_restr	0.046	2084
X-RAY DIFFRACTION	f_plane_restr	0.004	2388

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 (%)
2.2947-2.3217	0.3384	113	0.2867	2440	X-RAY DIFFRACTION	88
2.3217-2.35	0.3216	132	0.2822	2734	X-RAY DIFFRACTION	99
2.35-2.3797	0.3702	119	0.2874	2789	X-RAY DIFFRACTION	99
2.3797-2.411	0.3702	149	0.2804	2727	X-RAY DIFFRACTION	99
2.411-2.4441	0.3147	163	0.2788	2706	X-RAY DIFFRACTION	100
2.4441-2.479	0.2983	157	0.2663	2754	X-RAY DIFFRACTION	99
2.479-2.516	0.2983	122	0.2606	2761	X-RAY DIFFRACTION	99
2.516-2.5553	0.3669	157	0.2558	2713	X-RAY DIFFRACTION	100
2.5553-2.5972	0.2913	140	0.2629	2737	X-RAY DIFFRACTION	100
2.5972-2.642	0.2924	148	0.2648	2741	X-RAY DIFFRACTION	99
2.642-2.69	0.3167	116	0.2566	2743	X-RAY DIFFRACTION	100
2.69-2.7417	0.3197	171	0.2486	2722	X-RAY DIFFRACTION	100
2.7417-2.7977	0.2601	136	0.2411	2796	X-RAY DIFFRACTION	100
2.7977-2.8585	0.2759	108	0.2464	2769	X-RAY DIFFRACTION	100
2.8585-2.925	0.3118	190	0.2325	2717	X-RAY DIFFRACTION	100
2.925-2.9981	0.2343	156	0.232	2757	X-RAY DIFFRACTION	100
2.9981-3.0792	0.2768	136	0.2197	2767	X-RAY DIFFRACTION	100
3.0792-3.1698	0.2175	151	0.2048	2744	X-RAY DIFFRACTION	100
3.1698-3.2721	0.2343	177	0.2075	2744	X-RAY DIFFRACTION	100
3.2721-3.389	0.2008	140	0.1987	2775	X-RAY DIFFRACTION	100
3.389-3.5246	0.2272	117	0.2076	2758	X-RAY DIFFRACTION	100
3.5246-3.685	0.2144	138	0.1892	2795	X-RAY DIFFRACTION	100
3.685-3.8792	0.2094	89	0.1906	2846	X-RAY DIFFRACTION	100
3.8792-4.1221	0.2078	137	0.1823	2778	X-RAY DIFFRACTION	100
4.1221-4.4402	0.2641	119	0.1729	2757	X-RAY DIFFRACTION	100
4.4402-4.8867	0.1996	128	0.149	2792	X-RAY DIFFRACTION	99
4.8867-5.5929	0.1967	152	0.1673	2776	X-RAY DIFFRACTION	100
5.5929-7.0431	0.2525	175	0.214	2774	X-RAY DIFFRACTION	100
7.0431-48.6682	0.2002	127	0.1921	2863	X-RAY DIFFRACTION	99

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	1.128	-0.9963	0.1876	2.4566	-0.0762	1.5175	0.0304	-0.0502	-0.0889	0.4803	-0.0604	0.1632	0.4801	-0.1528	0.0001	0.6634	-0.0368	0.0742	0.4698	-0.0389	0.452	-54.2963	104.1985	206.0467
2	0.3495	0.3493	-0.0458	1.5608	-0.1516	0.7302	0.0235	-0.0475	0.1106	-0.2099	-0.1825	0.1706	0.022	-0.0631	0	0.3094	0.0269	-0.0307	0.3906	-0.0437	0.4205	-48.1535	118.7273	237.6154
3	0.9207	0.2242	1.7858	2.72	1.1794	2.4478	0.1068	0.1361	0.1238	0.2717	-0.2225	-0.0264	0.2535	-0.2397	0	0.3773	-0.006	0.073	0.3892	0.0137	0.3296	-54.8508	125.238	201.3803
4	0.6494	-0.3041	1.2285	0.0091	0.1408	1.8401	0.0564	-0.0871	-0.0692	-0.3117	0.0025	-0.0814	0.0236	-0.0097	-0	0.398	0.0203	-0.0079	0.3732	0.0133	0.4631	-41.8182	130.3128	230.5136
5	0.5566	0.621	0.0731	0.9381	0.3681	1.142	-0.1044	-0.026	0.217	-0.0938	-0.0153	-0.2246	-0.2175	0.2362	0.0004	0.3323	-0.006	0.0024	0.4082	-0.0273	0.4807	-34.0205	131.4016	240.0328
6	0.9392	-1.0049	-0.4985	2.5145	-0.306	1.659	-0.0247	-0.0163	0.0913	0.5428	-0.028	-0.2229	-0.4459	0.1646	0.0007	0.701	-0.0307	-0.0528	0.4871	0.0151	0.4987	-68.2524	162.1689	151.9707
7	0.6056	0.6902	-0.3443	1.6368	0.4687	0.8639	0.0383	-0.0091	-0.1669	-0.2325	-0.1747	-0.1239	0.049	0.0757	-0.0033	0.29	0.0352	0.0149	0.3656	0.0223	0.4188	-74.4717	147.6397	183.5088
8	1.0449	0.3754	-1.8628	2.3913	-1.4482	2.513	0.1541	0.1259	-0.1537	0.1944	-0.2323	0.1113	-0.2134	0.26	-0.0004	0.4007	-0.0034	-0.059	0.4197	-0.0098	0.3307	-67.6911	141.1525	147.3114
9	0.2259	-0.1354	-0.8703	0.3564	-0.2495	1.7171	0.0347	-0.0832	0.0307	-0.3053	0.0066	0.0731	-0.002	-0.0284	0.0003	0.3613	0.0086	0.008	0.3705	-0.0261	0.4253	-80.8272	136.0367	176.4027
10	0.7316	0.6943	-0.2735	0.8611	-0.2583	1.1575	-0.1601	-0.0491	-0.2731	0.0248	-0.0035	0.2372	0.2645	-0.082	0	0.334	-0.0112	-0.0089	0.4122	0.0416	0.4886	-88.6318	134.9537	185.9128
11	0.7921	-0.6178	-0.076	0.7753	-0.2227	1.2231	0.0345	-0.0395	-0.1018	-0.0043	-0.0259	-0.2137	0.0801	0.0939	0.007	0.4774	-0.1487	-0.1184	0.4498	0.1045	0.4365	-27.7083	165.598	155.6391
12	0.4075	0.1472	-0.2518	1.1638	0.5217	2.2892	0.1792	-0.1238	0.0547	-0.0903	0.0433	-0.2363	-0.1882	0.0733	0.0442	0.4909	-0.0776	-0.1016	0.5309	0.1014	0.4359	-28.6868	165.6718	151.091
13	0.8177	0.2324	0.5386	-0.0543	-0.1567	-0.1092	0.1135	-0.2062	-0.3137	-0.1779	-0.0021	0.2	0.1004	0.0064	0.0007	0.2935	0.0409	-0.0028	0.384	0.0286	0.447	-36.8069	149.6916	186.9729
14	0.4444	0.0714	-0.0477	1.723	-0.3373	0.9725	0.098	-0.0499	0.044	-0.1205	-0.1438	-0.3287	0.0654	0.0113	-0	0.2905	0.0167	0.0212	0.3777	0.044	0.3965	-30.8843	152.016	185.5202
15	1.094	-0.1662	0.0403	2.389	-1.8062	1.043	-0.322	0.2088	-0.1375	-0.1718	0.0221	0.0279	0.5198	0.3083	-0.0356	0.851	-0.03	0.0895	0.4571	0.0038	0.3755	-23.5257	143.5955	149.6857
16	0.7991	0.6582	-0.9918	1.0157	-1.5023	1.7394	-0.1021	-0.1128	0.055	-0.4629	0.2429	0.1859	0.6671	-0.117	0.1915	0.456	-0.029	-0.0128	0.3043	0.0105	0.2997	-36.9622	141.1264	173.487
17	1.3205	-0.0514	0.0817	2.1691	-1.1236	1.316	0.0921	-0.2432	-0.1155	-0.5008	0.2131	0.1706	0.2483	-0.2613	0.2226	0.4001	-0.0252	-0.0646	0.3719	0.051	0.3972	-41.786	138.2972	182.3737
18	0.628	0.0077	0.6991	0.5131	0.1024	2.4362	0.0836	0.0417	0.0134	0.0967	-0.0053	-0.1819	0.0682	0.0248	0.0003	0.4664	0.1066	0.1056	0.462	0.0971	0.4251	-69.0615	155.2054	225.5915
19	0.3814	0.079	-0.5836	-0.1197	0.0579	0.1548	0.0704	0.1499	0.2475	0.2495	0.0629	0.1538	-0.1993	0.0036	0.0002	0.265	-0.0207	-0.0333	0.3793	0.0321	0.4319	-77.4559	171.1215	191.6373
20	0.716	-0.2507	0.0886	1.5141	0.0553	0.7514	0.0445	-0.0162	-0.0645	0.0437	-0.0737	-0.3412	-0.0108	0.0177	-0	0.2725	-0.0307	-0.0284	0.3547	0.0363	0.3773	-71.595	168.8246	193.1106
21	0.7936	-0.0524	0.2558	2.2952	-1.6913	1.1861	-0.3085	-0.1597	0.1761	0.2139	0.1207	-0.0182	-0.428	0.2066	-0.0008	0.8499	0.0354	-0.0654	0.4952	-0.0182	0.4022	-64.3158	177.2559	228.9654
22	0.9097	-0.7018	0.8764	0.9557	-1.3051	1.5886	-0.0656	0.1281	-0.0947	0.4959	0.2335	0.1677	-0.6571	-0.1048	0.2804	0.5178	0.0051	0.0041	0.3322	-0.0015	0.3725	-76.9476	179.7649	205.1935
23	0.9976	-0.234	0.3746	0.7413	-0.9922	0.9488	0.0525	0.1926	0.0117	0.3494	0.2375	0.2365	-0.0411	-0.3587	0.0797	0.3265	0.03	0.0632	0.4149	0.1104	0.4612	-86.2584	183.8169	191.9979

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 111 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 112 through 214 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 1 through 101 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 102 through 174 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 175 through 214 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 2 through 111 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 112 through 214 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 1 through 101 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 102 through 174 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 175 through 214 )
11	X-RAY DIFFRACTION	11	chain 'E' and (resid 2 through 52 )
12	X-RAY DIFFRACTION	12	chain 'E' and (resid 52a through 111 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 112 through 145 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 146 through 214 )
15	X-RAY DIFFRACTION	15	chain 'F' and (resid 1 through 90 )
16	X-RAY DIFFRACTION	16	chain 'F' and (resid 91 through 155 )
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 156 through 214 )
18	X-RAY DIFFRACTION	18	chain 'G' and (resid 2 through 111 )
19	X-RAY DIFFRACTION	19	chain 'G' and (resid 112 through 145 )
20	X-RAY DIFFRACTION	20	chain 'G' and (resid 146 through 214 )
21	X-RAY DIFFRACTION	21	chain 'H' and (resid 1 through 90 )
22	X-RAY DIFFRACTION	22	chain 'H' and (resid 91 through 174 )
23	X-RAY DIFFRACTION	23	chain 'H' and (resid 175 through 214 )

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