PDB-5te6: Crystal Structure of Broadly Neutralizing VRC01-class Antibody N6...

ID or keywords:

Entry

Database: PDB / ID: 5te6

Title

Crystal Structure of Broadly Neutralizing VRC01-class Antibody N6 in Complex with HIV-1 Clade AE Strain 93TH057 gp120 Core

Components

Heavy chain of N6
Light chain of N6
clade A/E 93TH057 HIV-1 gp120 core

Keywords

IMMUNE SYSTEM /

HIV-1 / VRC01-class Antibody / N6 / CD4-binding site /

gp120

Function / homology

Function and homology information

viral envelope
Similarity search - Function

Biological species

Human immunodeficiency virus 1

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Zhou, T. / Kwong, P.D.

Citation

Journal: Immunity / Year: 2016
Title: Identification of a CD4-Binding-Site Antibody to HIV that Evolved Near-Pan Neutralization Breadth.
Authors: Huang, J. / Kang, B.H. / Ishida, E. / Zhou, T. / Griesman, T. / Sheng, Z. / Wu, F. / Doria-Rose, N.A. / Zhang, B. / McKee, K. / O'Dell, S. / Chuang, G.Y. / Druz, A. / Georgiev, I.S. / ...

History

Deposition	Sep 20, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 16, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 23, 2016	Group: Database references / Structure summary
Revision 1.2	Nov 30, 2016	Group: Database references
Revision 1.3	Jul 29, 2020	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / citation ...chem_comp / citation / 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 / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5te6.cif.gz	451 KB	Display	PDBx/mmCIF format
PDB format	pdb5te6.ent.gz	382.9 KB	Display	PDB format
PDBx/mmJSON format	5te6.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/te/5te6 ftp://data.pdbj.org/pub/pdb/validation_reports/te/5te6	HTTPS FTP

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Related structure data

Related structure data	5te4C 5te7C C: citing same article (ref.)
Similar structure data	4olz-d 4s1s-d 4lst-d 5te4-d 4jkp-d 4j6r-d 4om1-d 4xvt-d 3se9-d 4olw-d 4om0-d 4xmp-d 4ydl-2 4jdt-d 3u7y-d 6p8m-d 4xnz-2 4s1q-d 5te7-d 4olu-d 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	#163 - Jul 2013 HIV Capsid similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #169 - Jan 2014 HIV Envelope Glycoprotein similarity (3) #170 - Feb 2014 Broadly Neutralizing Antibodies similarity (3) #62 - Feb 2005 Major Histocompatibility Complex similarity (3)

Deposited unit

G: clade A/E 93TH057 HIV-1 gp120 core

H: Heavy chain of N6

L: Light chain of N6

hetero molecules

89.2 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)	64.692, 65.822, 238.012
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Antibody , 2 types, 2 molecules HL

#2: Antibody	Heavy chain of N6 Mass: 24188.283 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): HEK293 / Production host: Homo sapiens (human)
#3: Antibody	Light chain of N6 Mass: 23164.713 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): HEK293 / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 12 molecules G

#1: Protein

clade A/E 93TH057 HIV-1 gp120 core

Mass: 39211.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Human immunodeficiency virus 1 / Gene: HIV-1 Env / Plasmid: pVRC8400 / Cell line (production host): HEK293 / Production host:

Homo sapiens (human) / References: UniProt: A0A0M3KKW9

#4: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose /

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11
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 , 2 types, 92 molecules

#5: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.93 Å³/Da / Density % sol: 57.98 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 10 % w/v PEG 3350, 2 % (v/v) isopropanol, 0.1 M CaCl2, 0.1 M HEPES, pH 7.5

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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: Feb 18, 2015

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.4→50 Å / Num. obs: 41099 / % possible obs: 97 % / Redundancy: 4.6 % / B_iso Wilson estimate: 50.51 Å² / R_merge(I) obs: 0.124 / R_pim(I) all: 0.06 / R_rim(I) all: 0.138 / Χ²: 1.604 / Net I/av σ(I): 16.453 / Net I/σ(I): 8.8 / Num. measured all: 190962

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.4-2.44	3.6	0.794	1741	0.714	0.434	0.91	0.729	84.3
2.44-2.49	3.8	0.788	1854	0.722	0.428	0.901	0.738	90
2.49-2.53	3.9	0.68	1967	0.786	0.371	0.779	0.76	92.9
2.53-2.59	4.1	0.617	1984	0.832	0.333	0.704	0.783	95.8
2.59-2.64	4.2	0.566	2007	0.833	0.303	0.645	0.79	95.8
2.64-2.7	4.4	0.482	2014	0.875	0.254	0.546	0.85	98
2.7-2.77	4.4	0.421	2084	0.909	0.221	0.477	0.876	97.8
2.77-2.85	4.5	0.363	2054	0.926	0.19	0.411	0.96	98.7
2.85-2.93	4.6	0.312	2045	0.951	0.163	0.353	1.045	98.6
2.93-3.02	4.6	0.258	2112	0.964	0.134	0.291	1.175	99.1
3.02-3.13	4.7	0.213	2078	0.972	0.109	0.24	1.351	99.4
3.13-3.26	4.8	0.181	2063	0.978	0.091	0.203	1.5	99.5
3.26-3.41	4.9	0.154	2095	0.976	0.078	0.173	1.684	99.5
3.41-3.58	5	0.137	2117	0.982	0.067	0.153	2.038	99.4
3.58-3.81	5.1	0.129	2113	0.982	0.062	0.144	2.266	99.5
3.81-4.1	5.2	0.116	2129	0.988	0.055	0.129	2.479	99.2
4.1-4.52	5.3	0.096	2107	0.989	0.045	0.106	2.566	99.2
4.52-5.17	5.3	0.087	2142	0.992	0.04	0.096	2.184	98.6
5.17-6.51	5.3	0.086	2162	0.991	0.04	0.095	2.161	98.5
6.51-50	4.9	0.102	2231	0.985	0.05	0.114	2.866	95.7

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Processing

Software

Name	Version	Classification
PHENIX		refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing
PDB_EXTRACT	3.2	data extraction
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→44.14 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.78 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2782	1953	4.91 %
R_work	0.2269	37833	-
obs	0.2294	39786	97.62 %

Solvent computation

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

Displacement parameters

B_iso max: 210.88 Å² / B_iso mean: 79.2473 Å² / B_iso min: 29.73 Å²

Refinement step

Cycle: final / Resolution: 2.4→44.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5987	0	330	91	6408
B_iso mean	-	-	82.08	51.27	-
Num. residues	-	-	-	-	774

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6318
X-RAY DIFFRACTION	f_angle_d	0.543	8610
X-RAY DIFFRACTION	f_chiral_restr	0.045	987
X-RAY DIFFRACTION	f_plane_restr	0.003	1094
X-RAY DIFFRACTION	f_dihedral_angle_d	10.597	3752

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.4-2.46	0.3829	130	0.3446	2435	2565	90
2.46-2.5265	0.3408	134	0.3354	2569	2703	94
2.5265-2.6009	0.3744	125	0.3236	2616	2741	96
2.6009-2.6848	0.4017	132	0.3213	2665	2797	98
2.6848-2.7807	0.3914	147	0.3127	2681	2828	99
2.7807-2.8921	0.3678	138	0.2971	2700	2838	99
2.8921-3.0237	0.3652	134	0.2895	2700	2834	99
3.0237-3.183	0.3146	147	0.2819	2750	2897	99
3.183-3.3824	0.338	143	0.2638	2742	2885	100
3.3824-3.6434	0.2797	143	0.2321	2756	2899	99
3.6434-4.0099	0.2174	140	0.215	2756	2896	99
4.0099-4.5896	0.2358	146	0.1724	2783	2929	99
4.5896-5.7803	0.2194	146	0.1697	2797	2943	99
5.7803-44.1478	0.2425	148	0.1902	2883	3031	97

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	3.3402	0.3904	-0.6667	1.4181	0.9	3.6055	-0.0173	-0.1669	-0.3798	-0.1567	-0.1292	-0.0526	0.1	-0.3181	0.1751	0.6431	0.0531	-0.0279	0.2092	0.0279	0.5171	-13.971	-0.7576	-53.3856
2	4.312	4.3952	-0.3546	6.863	0.5715	0.6674	0.13	0.0025	-0.2791	0.2863	-0.1777	-0.5308	-0.1205	-0.1411	0.0566	0.9288	0.0528	0.0141	0.2498	-0.0627	0.5187	1.8294	14.1805	-62.9988
3	1.5308	0.8319	-0.4176	6.0502	-0.2204	2.4384	-0.0298	-0.4502	-0.2071	0.058	-0.2328	0.4592	0.5332	-0.6161	0.216	0.6288	-0.0729	0.0003	0.389	-0.0202	0.5782	-21.2302	1.1424	-48.0587
4	2.8948	-0.4894	0.2014	3.5879	1.5176	5.95	-0.1031	-0.1086	-0.4451	-0.0306	-0.1768	0.3813	0.3852	-0.6167	0.2679	0.4769	-0.0325	0.0039	0.366	-0.1063	0.5204	-22.9473	15.6898	-45.0843
5	2.8452	0.7462	-0.7952	1.0594	0.1258	3.598	-0.1559	0.1158	0.2776	-0.1505	-0.1047	0.3203	-0.451	-0.5524	0.2002	0.6836	0.1611	-0.0961	0.3304	-0.0885	0.6335	-18.5331	27.0051	-54.1177
6	4.6671	1.3423	0.9014	1.2276	1.1247	1.3645	-0.0278	-0.7036	1.0434	-0.3781	0.005	0.1658	-0.3009	-0.347	0.1358	0.8602	0.0868	-0.1849	0.3076	0.0583	0.7648	-16.7064	31.378	-56.8893
7	4.6915	0.0818	-1.3522	0.5502	-0.3525	4.2781	-0.1729	-0.4063	0.1522	-0.1979	-0.0974	0.015	-0.2614	-0.1056	0.1669	0.6455	0.0629	-0.0683	0.1326	-0.0812	0.5918	-12.2003	23.4432	-51.5311
8	7.7086	4.13	-0.4517	9.0051	0.6496	5.4878	-0.1872	-0.4944	0.2244	0.3008	0.0268	0.0695	-0.2569	-0.1142	0.1305	0.4985	0.0692	0.0508	0.3419	-0.0427	0.3584	-15.6193	4.441	-46.0283
9	4.7962	1.3396	0.3872	3.1178	0.1235	3.9978	-0.1188	-0.5507	-0.053	-0.1475	-0.179	-0.0274	0.0334	0.2377	0.2542	0.4856	0.1063	-0.0236	0.3772	0.019	0.3133	1.4896	27.1785	-31.7858
10	1.465	0.3887	0.3783	2.3028	2.6216	5.0484	0.0004	-0.5748	0.181	0.0267	-0.028	0.1062	-0.0587	0.2059	-0.0119	0.4104	0.0292	-0.0202	0.5377	-0.0261	0.3982	4.3318	32.2825	-23.7288
11	1.5649	0.245	2.1206	2.3197	-1.1847	3.835	0.0888	-0.4936	0.1177	0.1157	-0.1394	-0.0787	0.2849	0.977	0.1094	0.5949	0.0677	0.0006	1.7604	-0.2956	0.587	19.7668	41.072	-3.905
12	3.8366	0.9085	1.87	4.1804	0.0229	6.0784	0.0806	-1.0317	-0.2842	0.1948	-0.4484	-0.1789	0.2293	-0.4231	0.3407	0.5279	-0.0944	0.066	0.7969	0.153	0.5122	-5.7104	13.4945	-14.6618
13	4.9293	-3.4997	4.596	7.5328	-5.0727	4.981	-0.04	0.7202	-0.0118	0.4576	-0.8154	-0.2475	0.0673	0.9833	0.8967	0.6487	-0.0393	0.127	1.0704	0.0916	0.5218	-2.4054	17.4824	-14.0231
14	1.0066	0.0602	0.1328	1.885	0.9327	1.6586	-0.0542	-1.2595	-0.0241	0.1031	0.316	-0.1568	0.1529	-0.0127	-0.1358	0.6451	0.0174	-0.0467	2.0149	-0.1838	0.4735	6.9045	37.6906	4.4117
15	0.8003	-0.5922	0.0726	6.543	-1.7671	3.6421	-0.2208	-0.7975	0.3308	0.2714	0.3222	-0.2038	-0.6812	-0.4147	-0.0678	0.5779	0.0164	-0.0484	1.9105	-0.3745	0.6557	6.4831	47.8453	10.8081

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'G' and (resid 44 through 115 )	G	44 - 115
2	X-RAY DIFFRACTION	2	chain 'G' and (resid 116 through 215 )	G	116 - 215
3	X-RAY DIFFRACTION	3	chain 'G' and (resid 216 through 258 )	G	216 - 258
4	X-RAY DIFFRACTION	4	chain 'G' and (resid 259 through 291 )	G	259 - 291
5	X-RAY DIFFRACTION	5	chain 'G' and (resid 292 through 391 )	G	292 - 391
6	X-RAY DIFFRACTION	6	chain 'G' and (resid 392 through 425 )	G	392 - 425
7	X-RAY DIFFRACTION	7	chain 'G' and (resid 426 through 470 )	G	426 - 470
8	X-RAY DIFFRACTION	8	chain 'G' and (resid 471 through 492 )	G	471 - 492
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 1 through 59 )	H	1 - 59
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 60 through 137 )	H	60 - 137
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 138 through 215 )	H	138 - 215
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 1 through 75 )	L	1 - 75
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 76 through 102 )	L	76 - 102
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 103 through 174 )	L	103 - 174
15	X-RAY DIFFRACTION	15	chain 'L' and (resid 175 through 214 )	L	175 - 214

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