PDB-6fy1: Crystal structure of a V2p-reactive RV144 vaccine-like antibody, ...

ID or keywords:

Entry

Database: PDB / ID: 6fy1

Title

Crystal structure of a V2p-reactive RV144 vaccine-like antibody, CAP228-16H, in complex with a scaffolded autologous V1V2

Components

CAP228 Autologous Scaffolded V1V2
CAP228-16H Heavy Chain
CAP228-16H Light Chain

Keywords

IMMUNE SYSTEM / Fab / HIV-1 Envelope V1V2

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.132 Å

Authors

Wibmer, C.K. / Moore, P.L. / Morris, L.

Citation

Journal: Nat Commun / Year: 2018
Title: Common helical V1V2 conformations of HIV-1 Envelope expose the alpha 4 beta 7 binding site on intact virions.
Authors: Wibmer, C.K. / Richardson, S.I. / Yolitz, J. / Cicala, C. / Arthos, J. / Moore, P.L. / Morris, L.

History

Deposition	Mar 10, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 17, 2018	Provider: repository / Type: Initial release
Revision 1.1	Nov 7, 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	May 1, 2024	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
Revision 1.3	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6fy1.cif.gz	563 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6fy1_validation.pdf.gz	461.2 KB	Display	wwPDB validaton report
Full document	6fy1_full_validation.pdf.gz	475 KB	Display
Data in XML	6fy1_validation.xml.gz	35.5 KB	Display
Data in CIF	6fy1_validation.cif.gz	48.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fy/6fy1 ftp://data.pdbj.org/pub/pdb/validation_reports/fy/6fy1	HTTPS FTP

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Related structure data

Related structure data	6fy2C 6fy3C C: citing same article (ref.)
Similar structure data	6pag-d 3k2o-d 2e9b-1 4hwb-d 7khh-d 6pe9-1 1w59-d 1it3-d 4nxv-5 2e8y-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

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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

Y: CAP228-16H Heavy Chain

X: CAP228 Autologous Scaffolded V1V2

Z: CAP228-16H Light Chain

H: CAP228-16H Heavy Chain

G: CAP228 Autologous Scaffolded V1V2

L: CAP228-16H Light Chain

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

1

H: CAP228-16H Heavy Chain

G: CAP228 Autologous Scaffolded V1V2

L: CAP228-16H Light Chain

defined by author&software
Evidence: Chains H and L were isolated from the same B cell and assemble into an antibody specific for chain G.
61.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

Y: CAP228-16H Heavy Chain

X: CAP228 Autologous Scaffolded V1V2

Z: CAP228-16H Light Chain

defined by software
Evidence: Chains H and L were isolated from the same B cell and assemble into an antibody specific for chain G.
61.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	81.991, 73.987, 191.034
Angle α, β, γ (deg.)	90.00, 91.98, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Antibody	CAP228-16H Heavy Chain Mass: 25145.332 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Donor CAP228 / Source: (gene. exp.) Homo sapiens (human) / Cell: Memory B cell / Gene: IGHV5-51 / Cell line (production host): FreeStyle 293-F Cells / Production host: Homo sapiens (human)
#2: Protein	CAP228 Autologous Scaffolded V1V2 Mass: 13280.855 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Donor's autologous, minority founder variant / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: Envelope / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / Variant (production host): GnTI-
#3: Antibody	CAP228-16H Light Chain Mass: 22647.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Donor CAP228 / Source: (gene. exp.) Homo sapiens (human) / Cell: Memory B cell / Gene: IGLV3-21 / Cell line (production host): FreeStyle 293-F / Production host: Homo sapiens (human)
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.11 % / Description: Plates
Crystal grow	Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris HCl (pH8.5), 5% PEG4000, 2 M sodium chloride, 10% butanol, and cryoprotected in 25% 2,3-Butanediol

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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 15, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.21→50 Å / Num. obs: 19842 / % possible obs: 89.7 % / Redundancy: 3.2 % / CC_1/2: 0.936 / R_merge(I) obs: 0.156 / R_pim(I) all: 0.098 / Net I/σ(I): 6.8
Reflection shell	Resolution: 3.21→3.27 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.791 / Mean I/σ(I) obs: 2 / CC_1/2: 0.812 / R_pim(I) all: 0.5 / % possible all: 89.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing
Coot	0.8.9	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: D_1200009079

Resolution: 3.132→40.971 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2707	1804	10.15 %
R_work	0.2207	-	-
obs	0.2259	17782	87.28 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.132→40.971 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7653	0	0	0	7653

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	7834
X-RAY DIFFRACTION	f_angle_d	0.681	10671
X-RAY DIFFRACTION	f_dihedral_angle_d	11.172	4657
X-RAY DIFFRACTION	f_chiral_restr	0.047	1222
X-RAY DIFFRACTION	f_plane_restr	0.005	1346

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 (%)
3.1316-3.2163	0.3943	96	0.2966	843	X-RAY DIFFRACTION	60
3.2163-3.3109	0.3202	136	0.3139	1249	X-RAY DIFFRACTION	92
3.3109-3.4177	0.3513	153	0.306	1275	X-RAY DIFFRACTION	90
3.4177-3.5398	0.3249	139	0.2934	1239	X-RAY DIFFRACTION	90
3.5398-3.6814	0.3305	135	0.2587	1280	X-RAY DIFFRACTION	89
3.6814-3.8488	0.2712	141	0.2671	1242	X-RAY DIFFRACTION	91
3.8488-4.0516	0.279	143	0.2512	1235	X-RAY DIFFRACTION	89
4.0516-4.3052	0.2842	139	0.2212	1237	X-RAY DIFFRACTION	87
4.3052-4.6372	0.2478	141	0.1835	1222	X-RAY DIFFRACTION	87
4.6372-5.103	0.255	141	0.1864	1227	X-RAY DIFFRACTION	88
5.103-5.8396	0.2828	135	0.2022	1231	X-RAY DIFFRACTION	87
5.8396-7.3504	0.2878	136	0.2214	1262	X-RAY DIFFRACTION	88
7.3504-40.9745	0.2141	169	0.1777	1436	X-RAY DIFFRACTION	98

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	4.4794	-0.17	0.1952	2.9917	0.3665	5.9123	-0.0715	-0.1387	0.12	0.2203	0.196	-0.4214	0.7979	0.436	-0.0001	0.754	0.0353	0.0438	0.8702	-0.1513	0.5836	28.813	-12.1495	71.7336
2	0.7645	0.0218	-0.5318	1.8388	-0.0704	0.3002	0.0443	-1.0283	-0.4091	0.2634	0.8138	-0.4142	-0.1192	1.4086	0.0058	1.0354	0.1711	-0.1328	1.7254	-0.5394	0.8532	21.5949	18.9018	94.328
3	0.2624	-0.0783	-0.0515	1.3123	0.1472	0.0216	0.2195	0.6184	-0.375	-1.1962	0.041	-0.9064	-0.3393	0.2182	0.0346	0.9619	-0.2083	0.0274	1.0361	0.2377	0.7576	-2.6995	-22.874	32.9609
4	0.3613	0.3391	-0.3066	0.7425	-0.0466	0.2958	0.2486	0.5733	0.1446	-0.6117	0.2378	0.9422	-0.8189	-0.3091	0.0044	0.7749	0.066	-0.2385	1.0105	0.1676	0.9018	13.3121	-17.5186	50.0326
5	1.9963	0.386	0.3762	0.2459	0.0797	0.0874	0.231	-1.3872	-1.3406	0.517	-0.4162	-0.1608	0.4361	-0.4835	-0.0098	0.9521	0.3148	-0.0371	1.2133	0.0932	0.6806	19.8641	-30.4892	55.9324
6	1.1191	-0.2814	-0.1143	1.0718	0.8748	0.9698	0.0707	0.0866	0.0419	-0.0407	-0.5203	0.2522	0.2208	0.0485	0.0002	0.928	0.088	0.0196	0.7924	0.0474	0.9645	2.6454	-22.081	31.7893
7	2.0257	-0.7266	1.5151	5.0319	0.142	2.4207	-0.1713	-0.168	0.8246	-0.5719	-0.2358	0.5423	-0.5915	-0.5158	-0.0004	0.7135	0.0617	-0.0905	1.0108	-0.1873	0.6612	10.8089	-3.6052	62.9422
8	1.2984	-1.6826	0.0384	3.4131	0.5182	1.1593	-0.2712	-0.187	0.7002	-1.0591	0.4658	1.0465	-1.5992	0.1797	0.0086	1.274	-0.0013	0.0943	1.4174	-0.2272	0.7891	16.9454	19.3498	80.4115
9	1.8196	1.1243	-0.3896	4.8378	0.8208	3.9309	0.04	-0.2572	-0.1767	0.5126	0.1366	-0.0905	0.5027	0.187	-0.0002	0.5635	0.0594	-0.0096	0.558	0.0285	0.528	33.3801	-34.7763	38.4439
10	0.8842	-0.2601	0.5844	4.2342	0.0916	2.5431	0.1682	0.1999	-0.0249	-0.2924	0.0159	-0.0516	-0.1796	0.0861	0.0001	0.5222	0.0076	0.0314	0.4153	-0.0091	0.607	23.9096	-43.2385	-1.0899
11	1.3823	0.1657	-0.3797	0.9835	-1.0941	1.081	-0.2016	0.7798	-1.0597	-1.6688	0.3998	0.6547	-0.3998	0.6806	-0.0364	1.4172	-0.3866	0.134	1.0475	0.136	1.262	44.265	2.6049	41.9065
12	1.5583	-0.3743	-1.3273	0.188	0.0853	1.233	-0.0682	-0.2866	0.7316	-0.3634	0.0097	-0.4208	-0.8025	0.5743	0.0008	1.1055	-0.1311	-0.1075	0.7013	-0.0318	0.8544	38.5217	-13.1197	48.865
13	0.5052	-0.3317	-0.3746	0.1801	0.079	0.3269	0.1392	1.3856	0.713	-0.0768	-0.4996	0.7998	-0.3931	-0.8774	0.0003	1.1821	-0.076	0.2433	1.2203	0.2225	1.2979	29.5585	12.681	50.4438
14	0.86	-0.2	0.144	3.0128	-0.3837	5.6911	0.0476	-0.1118	0.0704	-0.3088	-0.1364	-0.0695	-0.7016	-0.2245	0.0003	0.4279	-0.0659	0.0093	0.4723	-0.0284	0.5618	34.8289	-16.2227	27.1625
15	4.6562	1.5055	2.4854	4.4509	0.5886	3.169	-0.0667	0.2173	-0.0764	-0.0735	0.1209	0.0799	-0.3141	-0.023	-0.0005	0.3787	0.013	0.0264	0.4578	0.0082	0.4433	18.209	-30.4524	5.9928

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'Y' and (resid 2 through 121 )
2	X-RAY DIFFRACTION	2	chain 'Y' and (resid 122 through 211 )
3	X-RAY DIFFRACTION	3	chain 'X' and (resid 118 through 131 )
4	X-RAY DIFFRACTION	4	chain 'X' and (resid 157 through 176 )
5	X-RAY DIFFRACTION	5	chain 'X' and (resid 177 through 192 )
6	X-RAY DIFFRACTION	6	chain 'X' and (resid 193 through 245 )
7	X-RAY DIFFRACTION	7	chain 'Z' and (resid 2 through 106 )
8	X-RAY DIFFRACTION	8	chain 'Z' and (resid 108 through 201 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 1 through 121 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 122 through 226 )
11	X-RAY DIFFRACTION	11	chain 'G' and (resid 131 through 162 )
12	X-RAY DIFFRACTION	12	chain 'G' and (resid 163 through 192 )
13	X-RAY DIFFRACTION	13	chain 'G' and (resid 193 through 240 )
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 3 through 106 )
15	X-RAY DIFFRACTION	15	chain 'L' and (resid 107 through 211 )

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