PDB-5ty6: Crystal structure of the broadly neutralizing Influenza A antibod...

ID or keywords:

Entry

Database: PDB / ID: 5ty6

Title

Crystal structure of the broadly neutralizing Influenza A antibody VRC 315 13-1b02 Fab.

Components

VRC 315 13-1b02 Fab Heavy chain
VRC 315 13-1b02 Fab Light chain

Keywords

IMMUNE SYSTEM /

antibody /

influenza /

human vaccine trial

Function / homology

Immunoglobulins /

Immunoglobulin-like /

Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.361 Å

Authors

Joyce, M.G. / Andrews, S.F. / Mascola, J.R. / McDermott, A.B. / Kwong, P.D.

Citation

Journal: Sci Immunol / Year: 2017
Title: Preferential induction of cross-group influenza A hemagglutinin stem-specific memory B cells after H7N9 immunization in humans.
Authors: Andrews, S.F. / Joyce, M.G. / Chambers, M.J. / Gillespie, R.A. / Kanekiyo, M. / Leung, K. / Yang, E.S. / Tsybovsky, Y. / Wheatley, A.K. / Crank, M.C. / Boyington, J.C. / Prabhakaran, M.S. / ...

History

Deposition	Nov 18, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 25, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 28, 2018	Group: Data collection / Database references / Category: citation / citation_author 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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Oct 4, 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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PDBx/mmCIF format	5ty6.cif.gz	257.4 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ty/5ty6 ftp://data.pdbj.org/pub/pdb/validation_reports/ty/5ty6	HTTPS FTP

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Related structure data

Related structure data	5u4rC 5wcaC 5wccC 5wcdC 5k9jS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6oed-1 4yxl-2 1plg-d 3piq-2 1dee-5 2fjf-10 4why-4 3g5x-1 1dqq-1 6ghg-2 4wht-9 4py7-2 6cnr-d 3qg6-2 3qeg-d 2fjf-5 1kcu-d 4jdv-2 4wht-6 5jor-3 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

H: VRC 315 13-1b02 Fab Heavy chain

L: VRC 315 13-1b02 Fab Light chain

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	64.942, 79.055, 107.723
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	VRC 315 13-1b02 Fab Heavy chain Mass: 24608.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody	VRC 315 13-1b02 Fab Light chain Mass: 23176.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 553 / 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: 2.89 Å³/Da / Density % sol: 57.49 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.5 M Lithium sulfate, 20% PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 29, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.36→32.219 Å / Num. obs: 106372 / % possible obs: 89.8 % / Redundancy: 3.4 % / R_merge(I) obs: 0.108 / Net I/σ(I): 8.26
Reflection shell	Resolution: 1.36→1.42 Å / Redundancy: 2.4 % / R_merge(I) obs: 0.811 / Mean I/σ(I) obs: 1.16 / % possible all: 89.3

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000		data collection
PDB_EXTRACT	3.2	data extraction
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing
HKL		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5K9J

5k9j

Resolution: 1.361→32.219 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.18 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1726	5302	4.99 %
R_work	0.1594	-	-
obs	0.16	106303	89.28 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.361→32.219 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3313	0	18	553	3884

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3411
X-RAY DIFFRACTION	f_angle_d	1.051	4636
X-RAY DIFFRACTION	f_dihedral_angle_d	19.527	1230
X-RAY DIFFRACTION	f_chiral_restr	0.086	522
X-RAY DIFFRACTION	f_plane_restr	0.006	592

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 (%)
1.3614-1.3768	0.3071	138	0.2996	2535	X-RAY DIFFRACTION	69
1.3768-1.393	0.2621	178	0.2904	3328	X-RAY DIFFRACTION	90
1.393-1.41	0.291	206	0.2778	3431	X-RAY DIFFRACTION	92
1.41-1.4279	0.2886	170	0.2663	3472	X-RAY DIFFRACTION	93
1.4279-1.4467	0.264	189	0.2603	3490	X-RAY DIFFRACTION	93
1.4467-1.4665	0.2462	180	0.2502	3467	X-RAY DIFFRACTION	93
1.4665-1.4874	0.2686	190	0.2361	3469	X-RAY DIFFRACTION	93
1.4874-1.5096	0.2159	184	0.2228	3449	X-RAY DIFFRACTION	93
1.5096-1.5332	0.2329	214	0.2126	3468	X-RAY DIFFRACTION	93
1.5332-1.5584	0.2179	169	0.1996	3445	X-RAY DIFFRACTION	93
1.5584-1.5852	0.2141	159	0.1905	3505	X-RAY DIFFRACTION	93
1.5852-1.6141	0.2066	179	0.1836	3500	X-RAY DIFFRACTION	93
1.6141-1.6451	0.189	199	0.1751	3422	X-RAY DIFFRACTION	92
1.6451-1.6787	0.179	192	0.1679	3469	X-RAY DIFFRACTION	92
1.6787-1.7152	0.1949	190	0.165	3394	X-RAY DIFFRACTION	92
1.7152-1.7551	0.1973	187	0.1615	3431	X-RAY DIFFRACTION	91
1.7551-1.799	0.189	167	0.1586	3447	X-RAY DIFFRACTION	91
1.799-1.8476	0.1852	192	0.1568	3406	X-RAY DIFFRACTION	91
1.8476-1.902	0.17	199	0.1544	3384	X-RAY DIFFRACTION	91
1.902-1.9633	0.1536	182	0.1434	3395	X-RAY DIFFRACTION	90
1.9633-2.0335	0.1645	149	0.1397	3406	X-RAY DIFFRACTION	90
2.0335-2.1149	0.1537	163	0.1407	3370	X-RAY DIFFRACTION	89
2.1149-2.2111	0.1716	187	0.1409	3342	X-RAY DIFFRACTION	89
2.2111-2.3277	0.1654	161	0.1464	3365	X-RAY DIFFRACTION	88
2.3277-2.4735	0.1494	160	0.1453	3326	X-RAY DIFFRACTION	88
2.4735-2.6644	0.1564	165	0.1495	3308	X-RAY DIFFRACTION	87
2.6644-2.9323	0.1595	176	0.1519	3279	X-RAY DIFFRACTION	86
2.9323-3.3563	0.1504	146	0.1515	3283	X-RAY DIFFRACTION	85
3.3563-4.227	0.1592	178	0.1427	3222	X-RAY DIFFRACTION	83
4.227-32.2283	0.1637	153	0.1617	3193	X-RAY DIFFRACTION	79

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	1.705	-0.187	0.6444	1.4635	0.5073	3.8458	-0.0704	0.0037	0.0467	-0.0748	-0.0221	0.3303	-0.5661	-0.3121	0.1428	0.2234	-0.0104	-0.0528	0.202	-0.0063	0.3158	-14.7059	1.9047	25.1433
2	1.2583	0.0774	0.3264	1.7592	-0.0505	0.7935	-0.0035	-0.0206	0.0234	-0.0688	0.0034	0.0816	-0.0347	-0.019	0.0006	0.1752	0.0043	-0.017	0.1677	-0.0148	0.1636	-4.6486	2.378	29.7469
3	1.6457	0.7801	0.4041	1.9389	-0.0911	2.2931	-0.1367	0.1088	0.1354	-0.3676	0.1979	0.0286	-0.1542	0.0955	-0.0935	0.2397	-0.006	-0.0318	0.2022	0.0073	0.2138	-7.9584	3.5898	20.7103
4	1.0521	0.1966	0.87	0.6986	0.3348	0.976	-0.0271	-0.0956	0.0765	0.0883	-0.0164	0.0664	0.0121	-0.0572	0.0611	0.1886	-0.0043	-0.0049	0.1714	-0.0088	0.1882	-7.4605	-3.8979	32.0757
5	2.1743	1.1778	0.2231	2.8176	-0.7883	2.2574	-0.0725	-0.0254	-0.1408	-0.3079	0	0.0745	0.1138	-0.0852	-0.0113	0.1769	-0.0034	-0.0154	0.1763	0.0218	0.2111	-29.1957	-22.0304	4.5479
6	1.7503	-0.0625	0.104	1.0419	-0.0701	1.042	-0.0605	-0.1363	-0.0903	0.114	0.0866	0.0245	-0.0166	-0.1094	0.01	0.1769	-0.0023	-0.0202	0.1979	0.0261	0.1788	-28.0112	-19.4389	11.6816
7	2.4167	0.8471	0.0118	4.6506	0.0113	1.606	0.0701	-0.2163	-0.0082	0.2842	-0.0817	0.2374	0.1106	-0.151	0.0252	0.1621	-0.0041	-0.0096	0.2128	0.0281	0.2192	-36.9209	-18.7907	9.6327
8	3.4846	1.3684	0.6163	6.9724	-0.0156	1.5141	0.0582	0.031	-0.0641	-0.245	-0.0271	-0.0366	0.06	-0.1457	0.0097	0.1775	0.006	-0.0119	0.2445	0.0397	0.2355	-37.0836	-18.1959	4.357
9	3.7836	1.8901	-0.5825	2.554	-0.2138	1.7031	0.0417	0.0186	0.0831	-0.0235	0.0653	-0.0023	-0.024	-0.0195	-0.1125	0.2147	0.0245	-0.0047	0.1824	0.0019	0.2008	-2.4316	-24.8596	29.7769
10	1.3506	0.726	0.2298	2.0517	0.0551	1.2923	0.0592	-0.102	-0.0625	0.1928	-0.0578	-0.0789	0.0674	0.0182	0.0196	0.2173	-0.007	-0.0186	0.1628	-0.007	0.1785	-0.661	-18.1826	37.767
11	1.1438	1.0804	0.7069	2.2036	0.7702	0.7199	-0.0256	-0.0705	0.1186	0.0592	0.0309	0.1286	0.0283	-0.0221	0.0011	0.183	0.0123	0.0006	0.1809	0.0082	0.1895	-7.2857	-22.0352	30.364
12	0.8311	-0.455	0.0742	4.1238	-2.5578	3.0963	0.0895	0.0699	-0.0225	-0.0631	0.0703	0.2786	-0.0363	-0.201	-0.1491	0.1868	-0.0186	-0.0438	0.2199	0.0209	0.2003	-26.4851	-23.8235	-2.0826
13	0.6708	-0.1617	0.0978	0.8797	-1.3449	3.1806	0.0481	0.0566	0.0077	-0.0108	0.0177	0.0615	0.0222	0.0761	-0.0183	0.1788	-0.0149	-0.0251	0.1792	0.018	0.1855	-16.2089	-28.9643	7.9332
14	0.6904	-0.2045	-0.3905	1.1383	-0.5467	2.9021	-0.0126	-0.0376	-0.0443	0.0831	0.0124	0.0194	-0.0255	-0.004	-0.0643	0.1336	-0.0153	-0.0287	0.1693	0.0134	0.1795	-16.4706	-26.5576	11.3274
15	0.82	-0.0444	-0.0552	1.5142	-0.5989	4.8047	0.0195	0.1413	0.0719	-0.178	-0.0786	-0.0189	-0.1101	0.0721	-0.0585	0.1691	0.0022	-0.0175	0.2074	0.0341	0.1707	-18.7151	-21.9527	-5.2771
16	0.697	-0.6925	0.7757	1.1112	-1.355	3.1518	0.122	0.1285	-0.0507	-0.1748	-0.0743	0.0298	0.4853	0.1676	-0.0632	0.2222	-0.0055	-0.0335	0.1779	0.0128	0.184	-15.9225	-34.7665	0.9603

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 17 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 18 through 75 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 76 through 87 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 88 through 119 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 120 through 145 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 146 through 188 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 189 through 203 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 204 through 214 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 1 through 18 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 19 through 75 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 76 through 113 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 114 through 128 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 129 through 150 )
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 151 through 174 )
15	X-RAY DIFFRACTION	15	chain 'L' and (resid 175 through 188 )
16	X-RAY DIFFRACTION	16	chain 'L' and (resid 190 through 211 )

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