PDB-4rwy: Crystal structure of VH1-46 germline-derived CD4-binding site-dir...

ID or keywords:

Entry

Database: PDB / ID: 4rwy

Title

Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 8ANC131 in complex with HIV-1 clade B YU2 gp120

Components

(Antibody 8ANC131 ...) x 2
HIV-1 YU2 gp120

Keywords

VIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 attachment protein / Broadly neutralizing antibody 8ANC131 / VIRAL PROTEIN-IMMUNE SYSTEM complex

Function / homology

Function and homology information

Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...
Similarity search - Function

Biological species

Human immunodeficiency virus 1

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.128 Å

Authors

Acharya, P. / Luongo, T.S. / Kwong, P.D.

Citation

Journal: Cell(Cambridge,Mass.) / Year: 2015
Title: Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors.
Authors: Zhou, T. / Lynch, R.M. / Chen, L. / Acharya, P. / Wu, X. / Doria-Rose, N.A. / Joyce, M.G. / Lingwood, D. / Soto, C. / Bailer, R.T. / Ernandes, M.J. / Kong, R. / Longo, N.S. / Louder, M.K. / ...

History

Deposition	Dec 8, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 1, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2	Oct 16, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4rwy.cif.gz	457.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4rwy.ent.gz	383 KB	Display	PDB format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rw/4rwy ftp://data.pdbj.org/pub/pdb/validation_reports/rw/4rwy	HTTPS FTP

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Related structure data

Related structure data	4rx4C 4ydiC 4ydjC 4ydkC 4ydlC 4ye4C 4yflC C: citing same article (ref.)
Similar structure data	5f9w-2 4rx4-2 4xnz-2 5cd5-d 5wi9-2 4ydl-2 6p8m-d 4xnz-1 4xny-d 4xvt-d 4xnz-3 5f9w-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&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) #169 - Jan 2014 HIV Envelope Glycoprotein similarity (7) #62 - Feb 2005 Major Histocompatibility Complex similarity (7) #170 - Feb 2014 Broadly Neutralizing Antibodies similarity (6) #252 - Dec 2020 Hepatitis C Virus Protease/Helicase similarity (1)

Deposited unit

A: HIV-1 YU2 gp120

H: Antibody 8ANC131 Heavy chain

L: Antibody 8ANC131 Light chain

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	66.250, 67.137, 214.101
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Antibody , 2 types, 2 molecules HL

#2: Antibody	Antibody 8ANC131 Heavy chain Mass: 24302.467 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): 293F / Production host: Homo sapiens (human)
#3: Antibody	Antibody 8ANC131 Light chain Mass: 23453.100 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): 293F / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 7 molecules A

#1: Protein

HIV-1 YU2 gp120

Mass: 41695.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Human immunodeficiency virus 1 / Strain: Clade B YU2 / Plasmid: pVRC8400 / Cell line (production host): 293F / Production host:

Homo sapiens (human) / References: UniProt: P35961*PLUS

#4: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 4 types, 238 molecules

#5: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#6: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#7: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.78 Å³/Da / Density % sol: 55.81 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 6% w/v PEG 3000, 0.1 M HEPES pH 7.5, 0.2M NaCl, 4% v/v 2,2,2 Trifluoroethanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 200 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 6, 2012

Radiation

Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.12→50 Å / Num. obs: 43335 / % possible obs: 72.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / R_merge(I) obs: 0.078 / R_sym value: 0.093 / Net I/σ(I): 17.3

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	R_sym value	Diffraction-ID	% possible all
2.12-2.16	2.8	0.427	1.74	0.477	1	17.3
2.16-2.2	2.9	0.404	2.19	0.436	1	27.1
2.2-2.24	3.3	0.388	2.09	0.434	1	33.9
2.24-2.28	3.6	0.352	2.53	0.383	1	38.5
2.28-2.33	3.9	0.33	2.9	0.355	1	43
2.33-2.39	4.3	0.315	3.02	0.373	1	48.6

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.9_1690)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.128→28.837 Å / SU ML: 0.29 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 34.48 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2535	2138	4.94 %	RANDOM
R_work	0.219	-	-	-
all	0.2207	54558	-	-
obs	0.2207	43292	79.35 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.128→28.837 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6006	0	120	231	6357

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6294
X-RAY DIFFRACTION	f_angle_d	0.745	8534
X-RAY DIFFRACTION	f_dihedral_angle_d	12.584	2300
X-RAY DIFFRACTION	f_chiral_restr	0.031	966
X-RAY DIFFRACTION	f_plane_restr	0.004	1100

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 (%)
2.128-2.1773	0.3463	54	0.3071	1056	X-RAY DIFFRACTION	31
2.1773-2.2317	0.3555	68	0.2992	1442	X-RAY DIFFRACTION	42
2.2317-2.2921	0.3408	90	0.2818	1621	X-RAY DIFFRACTION	48
2.2921-2.3595	0.2755	97	0.27	1851	X-RAY DIFFRACTION	54
2.3595-2.4356	0.323	104	0.279	2156	X-RAY DIFFRACTION	63
2.4356-2.5226	0.3484	134	0.2903	2483	X-RAY DIFFRACTION	73
2.5226-2.6235	0.3316	179	0.2852	2860	X-RAY DIFFRACTION	84
2.6235-2.7428	0.3022	155	0.2747	3165	X-RAY DIFFRACTION	92
2.7428-2.8873	0.3311	166	0.279	3445	X-RAY DIFFRACTION	100
2.8873-3.068	0.2831	162	0.2695	3459	X-RAY DIFFRACTION	100
3.068-3.3046	0.3072	161	0.2582	3470	X-RAY DIFFRACTION	100
3.3046-3.6366	0.2959	177	0.2224	3464	X-RAY DIFFRACTION	100
3.6366-4.1615	0.2473	178	0.1943	3515	X-RAY DIFFRACTION	100
4.1615-5.2379	0.1785	212	0.1552	3482	X-RAY DIFFRACTION	100
5.2379-28.8397	0.2078	201	0.1876	3685	X-RAY DIFFRACTION	100

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	3.4238	-0.459	-0.2153	3.3661	-0.5982	3.4645	-0.187	0.0056	0.3069	0.09	0.0203	0.1884	-0.671	-0.3925	0.149	0.7732	0.0438	-0.0341	0.3889	-0.0702	0.3394	-12.5268	0.3185	51.2921
2	1.6316	-1.1419	0.468	2.9559	-0.5764	2.478	-0.1209	0.0392	0.1253	0.0935	0.0096	0.1627	-0.2643	-0.3945	0.0882	0.6251	-0.0301	0.0051	0.3922	-0.0537	0.2881	-12.4541	-7.6999	44.053
3	3.7015	-0.885	1.0436	3.5113	0.0856	4.2303	-0.0312	-0.1839	-0.1746	0.2129	-0.0781	0.5718	-0.3483	-0.6683	0.1527	0.3612	-0.0845	0.0604	0.3244	-0.1283	0.3894	-20.4979	-21.9874	44.1967
4	2.2741	-0.3882	0.5321	2.8617	-0.1287	2.4248	0.0004	-0.0016	-0.3941	0.1134	-0.1635	0.4291	0.2682	-0.3419	0.1106	0.5178	-0.0924	0.0593	0.419	-0.1016	0.3854	-16.2742	-25.7478	44.3271
5	-0.0065	-0.0018	-0.002	0.0014	0.0001	0.0048	-0.1483	-0.0715	-0.0626	0.0194	-0.0495	-0.012	0.0851	0.0306	-0	0.556	-0.0209	-0.0102	0.5247	0.0314	0.3645	12.5529	-35.2179	28.7711
6	0.3766	0.1029	0.1252	0.4032	-0.0858	0.7792	-0.1356	0.0236	-0.3175	0.0083	-0.1878	-0.0467	0.0329	0.0686	-0.3372	0.4736	-0.0246	0.0089	0.1185	-0.0567	-0.1559	4.9597	-31.0723	26.5723
7	7.3694	1.1613	-3.1872	7.5022	-1.8361	2.1227	0.3815	1.1346	0.7285	-1.1126	0.3397	-0.097	-0.5426	0.1564	-0.7318	0.5733	-0.0567	0.1032	0.6616	-0.0102	0.413	27.743	-43.2268	-6.5268
8	4.3117	-0.5127	-0.7211	2.9049	-0.6817	4.3641	0.0382	0.0643	0.0211	0.0742	-0.1188	-0.2535	-0.2312	0.6789	0.0977	0.5202	0.0035	0.0042	0.4601	0.0222	0.2938	30.2856	-42.0689	2.7374
9	2.9294	-0.8064	-0.65	2.1626	-0.0794	4.2834	0.0743	0.626	-0.0171	-0.7448	-0.2252	0.1583	-0.4021	-0.752	0.0359	0.9526	0.174	-0.1116	0.5475	-0.0472	0.3402	-1.3041	-20.5064	6.7108
10	2.0111	1.976	0.0653	3.5757	-2.293	5.1406	0.3071	0.0095	0.5101	-0.3637	-0.3073	-0.1555	-1.239	-0.1527	-0.0195	0.8506	0.0345	0.0038	0.354	-0.0225	0.3694	6.9718	-14.5336	15.1932
11	0.9637	-0.1575	-0.6254	0.7542	1.2337	2.2966	0.1144	0.1997	-0.0059	-0.375	-0.1067	0.0135	-0.4786	-0.097	-0.0009	0.6839	0.0648	0.0031	0.4117	0.0321	0.2863	11.356	-34.4813	-0.1259
12	4.8522	-2.8057	0.0643	9.2156	-0.1683	5.4331	0.4216	0.6456	-0.1362	-0.9736	-0.5076	-0.1768	-0.1011	0.3119	0.1353	0.4805	0.0337	0.0616	0.5446	-0.0685	0.2183	15.3251	-46.3456	-14.7319

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 44 through 82 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 83 through 258 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 259 through 327 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 328 through 492 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 1 through 17 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 18 through 124 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 125 through 145 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 146 through 216 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 1 through 38 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 39 through 61 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 62 through 188 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 189 through 214 )

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