PDB-5vvf: Crystal Structure of 354BG1 Fab

ID or keywords:

Entry

Database: PDB / ID: 5vvf

Title

Crystal Structure of 354BG1 Fab

Components

354BG1 Heavy Chain
354BG1 Light Chain

Keywords

IMMUNE SYSTEM /

HIV /

broadly neutralizing antibody

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: 2 Å

Authors

Scharf, L. / Gristick, H.B. / Bjorkman, P.J.

Funding support

United States, 1items

Citation

Journal: Elife / Year: 2017
Title: Asymmetric recognition of HIV-1 Envelope trimer by V1V2 loop-targeting antibodies.
Authors: Haoqing Wang / Harry B Gristick / Louise Scharf / Anthony P West / Rachel P Galimidi / Michael S Seaman / Natalia T Freund / Michel C Nussenzweig / Pamela J Bjorkman /

Abstract: The HIV-1 envelope (Env) glycoprotein binds to host cell receptors to mediate membrane fusion. The prefusion Env trimer is stabilized by V1V2 loops that interact at the trimer apex. Broadly ...

History

Deposition	May 19, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 6, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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	5vvf.cif.gz	187.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5vvf.ent.gz	148.2 KB	Display	PDB format
PDBx/mmJSON format	5vvf.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/vv/5vvf ftp://data.pdbj.org/pub/pdb/validation_reports/vv/5vvf	HTTPS FTP

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Related structure data

Related structure data	21204C 8693C 8695C 5viyC 5vj6C 3piqS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6c5i-d 5vh3-1 1wcb-2 4why-1 4xbg-1 6phh-2 6phh-1 6dg2-1 5d1z-5 3cfj-3 4yxh-2 5ig7-1 6srv-2 5tkj-4 7k8p-d 3ls5-d 8fab-2 4xbp-1 5chn-1 1rih-d 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	#163 - Jul 2013 HIV Capsid similarity (1) #170 - Feb 2014 Broadly Neutralizing Antibodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

H: 354BG1 Heavy Chain

L: 354BG1 Light Chain

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	95.630, 95.630, 103.951
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	L-418- HOH
2	1	L-511- HOH

#1: Antibody	354BG1 Heavy Chain Mass: 27111.328 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	354BG1 Light Chain Mass: 23527.102 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 242 / 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: 57.42 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.8 M ammonium sulfate, 0.1 M Bis-Tris pH 6.5, 2% v/v PEG 550 MME, 100 nM NDSB-256

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 10, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→82.82 Å / Num. obs: 37475 / % possible obs: 99.7 % / Redundancy: 5.5 % / Net I/σ(I): 7.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.11_2567: ???)	refinement
iMOSFLM	7.2.1	data processing
Aimless	7.0.038	data reduction
Aimless	7.0.038	data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2909 FAB (PDB CODE 3PIQ)

3piq

Resolution: 2→29.97 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.39

	R_factor	Num. reflection	% reflection
R_free	0.247	3724	9.97 %
R_work	0.21	-	-
obs	0.214	37356	99.4 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2→29.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3309	0	4	242	3555

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3401
X-RAY DIFFRACTION	f_angle_d	0.948	4635
X-RAY DIFFRACTION	f_dihedral_angle_d	15.148	2000
X-RAY DIFFRACTION	f_chiral_restr	0.057	510
X-RAY DIFFRACTION	f_plane_restr	0.006	602

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 (%)
2-2.0254	0.372	127	0.3222	1251	X-RAY DIFFRACTION	99
2.0254-2.052	0.3644	152	0.3268	1174	X-RAY DIFFRACTION	99
2.052-2.0801	0.3478	160	0.3257	1243	X-RAY DIFFRACTION	99
2.0801-2.1098	0.2901	143	0.3106	1208	X-RAY DIFFRACTION	99
2.1098-2.1413	0.2935	121	0.2934	1243	X-RAY DIFFRACTION	100
2.1413-2.1748	0.358	125	0.2779	1271	X-RAY DIFFRACTION	100
2.1748-2.2104	0.326	118	0.2735	1216	X-RAY DIFFRACTION	99
2.2104-2.2485	0.3123	123	0.2645	1254	X-RAY DIFFRACTION	100
2.2485-2.2894	0.2635	110	0.2608	1262	X-RAY DIFFRACTION	99
2.2894-2.3334	0.2993	126	0.2531	1257	X-RAY DIFFRACTION	99
2.3334-2.381	0.3229	129	0.2506	1219	X-RAY DIFFRACTION	99
2.381-2.4327	0.2973	149	0.2445	1229	X-RAY DIFFRACTION	99
2.4327-2.4893	0.2788	148	0.2473	1196	X-RAY DIFFRACTION	99
2.4893-2.5515	0.2522	139	0.2405	1236	X-RAY DIFFRACTION	99
2.5515-2.6205	0.2953	139	0.2436	1241	X-RAY DIFFRACTION	100
2.6205-2.6975	0.2602	141	0.2426	1244	X-RAY DIFFRACTION	100
2.6975-2.7846	0.2904	138	0.2309	1242	X-RAY DIFFRACTION	100
2.7846-2.884	0.2535	144	0.2367	1262	X-RAY DIFFRACTION	100
2.884-2.9994	0.2715	141	0.234	1247	X-RAY DIFFRACTION	100
2.9994-3.1357	0.2648	151	0.2173	1230	X-RAY DIFFRACTION	99
3.1357-3.3009	0.2571	150	0.2165	1241	X-RAY DIFFRACTION	99
3.3009-3.5074	0.2249	147	0.1976	1244	X-RAY DIFFRACTION	100
3.5074-3.7777	0.2149	130	0.1773	1258	X-RAY DIFFRACTION	100
3.7777-4.157	0.2195	120	0.1644	1317	X-RAY DIFFRACTION	100
4.157-4.7564	0.1795	139	0.1418	1245	X-RAY DIFFRACTION	98
4.7564-5.9848	0.2055	165	0.1662	1264	X-RAY DIFFRACTION	100
5.9848-29.9763	0.2141	149	0.1945	1338	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	2.9834	0.3545	-2.0082	1.0013	0.363	6.7693	0.2027	-0.4484	0.0452	0.1938	0.2641	-0.4838	-0.1496	1.1493	-0.3805	0.3616	-0.0478	-0.0871	0.4761	-0.0438	0.3318	62.76	-26.4903	11.3222
2	2.2983	-0.2089	-0.598	2.2672	1.0985	2.2974	0.1193	-0.7579	-0.1691	0.6616	0.0411	-0.1282	0.3089	0.4828	-0.2649	0.4818	-0.0348	-0.0843	0.5638	-0.0071	0.2356	54.63	-27.7792	21.8522
3	1.6072	-0.3947	-0.4694	1.6421	-0.2214	1.745	0.0355	-0.067	-0.0171	0.0218	0.0328	0.0449	0.3643	0.2095	-0.0304	0.3593	-0.0079	-0.0352	0.4175	-0.0228	0.2158	50.3487	-31.5486	12.0987
4	2.2788	0.07	-1.0876	2.4761	-0.309	4.699	0.0113	0.0071	-0.2238	-0.1543	-0.1029	-0.1544	0.7072	0.414	0.0219	0.4106	0.0534	-0.0119	0.5101	-0.0285	0.2939	59.0171	-32.3579	6.8553
5	2.0403	-0.501	-0.1975	2.0926	0.1914	2.8363	0.047	-0.5843	-0.0001	0.4974	-0.0091	0.1776	0.0484	-0.4838	-0.0044	0.3744	-0.044	0.0173	0.4887	-0.0339	0.1927	42.9948	-24.3251	19.1085
6	1.9522	0.8656	0.3937	1.6693	-0.361	1.1862	-0.1857	-0.348	0.2252	-0.0529	0.3166	-0.6739	0.0087	0.841	-0.1802	0.2772	0.0122	0.0394	0.564	-0.0678	0.44	68.1073	-22.4854	3.0542
7	2.706	-0.988	0.0491	1.9046	-0.3687	2.0426	-0.0684	-0.0591	0.6197	0.065	-0.1945	-0.7199	-0.2827	0.4944	0.2625	0.3205	-0.0758	0.0162	0.4756	0.0003	0.6423	73.0619	-4.5086	-4.9074
8	1.5672	1.8727	0.1567	6.1978	-0.0081	2.0611	-0.0939	0.2223	0.2218	-0.4402	0.2512	0.2038	0.197	-0.0975	-0.295	0.3358	-0.0401	0.0026	0.4116	0.0073	0.307	38.9314	-9.9685	0.7477
9	2.7437	1.5166	0.1116	3.3759	0.1621	1.2276	-0.1821	0.0244	-0.1808	-0.3083	0.1415	0.2948	0.1748	-0.4806	0.0285	0.2971	-0.0791	-0.0132	0.4263	-0.0547	0.2531	35.6128	-17.2845	6.4656
10	9.0865	-0.2799	-5.8781	2.6086	-1.3586	5.4313	0.1175	0.001	0.4178	0.2825	0.0064	-0.2952	-0.2204	0.2257	-0.0774	0.2644	-0.0831	-0.0075	0.3595	-0.081	0.2847	48.7679	-12.1414	11.276
11	1.0171	0.2437	-0.9703	1.4036	-0.5468	2.3786	0.1155	-0.0503	0.135	0.0341	-0.0374	-0.0202	-0.1678	-0.0647	-0.1083	0.2531	-0.0413	-0.0217	0.3321	-0.0333	0.2728	46.0917	-9.3809	2.9152
12	1.2068	-0.2855	-0.4405	2.005	0.9142	2.1592	0.0103	0.2987	0.0802	-0.4689	0.0183	-0.214	-0.2848	0.3794	-0.0197	0.4034	-0.0666	0.0659	0.3991	0.0122	0.3212	59.4295	-8.3388	-16.6451
13	2.8445	-0.1964	-0.2298	2.6151	-0.0811	2.2818	0.0122	0.5262	0.3114	-0.4522	-0.0039	-0.4292	-0.1488	0.1783	-0.0426	0.4047	-0.1	0.119	0.4166	0.0249	0.4069	62.2061	-5.2021	-18.0132

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN H AND RESID 1:17 )	H	1 - 17
2	X-RAY DIFFRACTION	2	( CHAIN H AND RESID 18:33 )	H	18 - 33
3	X-RAY DIFFRACTION	3	( CHAIN H AND RESID 34:75 )	H	34 - 75
4	X-RAY DIFFRACTION	4	( CHAIN H AND RESID 76:87 )	H	76 - 87
5	X-RAY DIFFRACTION	5	( CHAIN H AND RESID 88:103 )	H	88 - 103
6	X-RAY DIFFRACTION	6	( CHAIN H AND RESID 104:119 )	H	104 - 119
7	X-RAY DIFFRACTION	7	( CHAIN H AND RESID 120:213 )	H	120 - 213
8	X-RAY DIFFRACTION	8	( CHAIN L AND RESID 1:18 )	L	1 - 18
9	X-RAY DIFFRACTION	9	( CHAIN L AND RESID 19:38 )	L	19 - 38
10	X-RAY DIFFRACTION	10	( CHAIN L AND RESID 39:48 )	L	39 - 48
11	X-RAY DIFFRACTION	11	( CHAIN L AND RESID 49:128 )	L	49 - 128
12	X-RAY DIFFRACTION	12	( CHAIN L AND RESID 129:163 )	L	129 - 163
13	X-RAY DIFFRACTION	13	( CHAIN L AND RESID 164:213 )	L	164 - 213

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