PDB-4rnr: Crystal structure of broadly neutralizing anti-HIV antibody PGT130

ID or keywords:

Entry

Database: PDB / ID: 4rnr

Title

Crystal structure of broadly neutralizing anti-HIV antibody PGT130

Components

PGT130 Heavy Chain
PGT130 Light Chain

Keywords

IMMUNE SYSTEM / PGT130 / PGT 130 / Immunoglobulin Fold / Broadly Neutralizing Antibody / HIV-1 gp120 binding / N-linked glycan

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: 2.758 Å

Authors

Kong, L. / Wilson, I.A.

Citation

Journal: J.Virol. / Year: 2015
Title: Two Classes of Broadly Neutralizing Antibodies within a Single Lineage Directed to the High-Mannose Patch of HIV Envelope.
Authors: Doores, K.J. / Kong, L. / Krumm, S.A. / Le, K.M. / Sok, D. / Laserson, U. / Garces, F. / Poignard, P. / Wilson, I.A. / Burton, D.R.

History

Deposition	Oct 24, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 19, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jan 28, 2015	Group: Database references
Revision 1.2	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_ptnr1_PDB_ins_code / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	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

-
Download

PDBx/mmCIF format	4rnr.cif.gz	342.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4rnr.ent.gz	283.9 KB	Display	PDB format
PDBx/mmJSON format	4rnr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Similar structure data	6nb5-1 6l98-d 4uom-d 4qhk-1 4qhk-3 4m5y-1 4ktd-d 3tnn-1 4odu-2 6y1m-d 5f6h-3 1mcq-d 7kqy-2 5kg9-2 1emt-d 5tf1-d 4yx2-2 4wht-6 5tqa-2 4qhk-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

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#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

A: PGT130 Heavy Chain

B: PGT130 Light Chain

C: PGT130 Heavy Chain

D: PGT130 Light Chain

hetero molecules

97.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PGT130 Heavy Chain

B: PGT130 Light Chain

hetero molecules

defined by author&software
48.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: PGT130 Heavy Chain

D: PGT130 Light Chain

hetero molecules

defined by author&software
48.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	67.021, 69.052, 272.236
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody

PGT130 Heavy Chain

Mass: 25235.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Cell line (production host): 293 Freestyle / Production host:

Homo sapiens (human)

#2: Antibody

PGT130 Light Chain

Mass: 22863.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Cell line (production host): 293 Freestyle / Production host:

Homo sapiens (human)

#3: 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.: 4
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

Has protein modification

Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.27 Å³/Da / Density % sol: 62.43 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 40% PEG 400, 0.2 M NaCl, 0.1 M Na/K phosphate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: Sep 23, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 2.75→50 Å / Num. obs: 30636 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell	Resolution: 2.75→2.8 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.7 / R_sym value: 0.67 / % possible all: 85.3

-
Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
HKL-2000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.758→47.754 Å / SU ML: 0.47 / σ(F): 1.34 / Phase error: 32.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2694	1544	5.05 %
R_work	0.2436	-	-
obs	0.2449	30568	91.09 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.758→47.754 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6450	0	56	0	6506

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6688
X-RAY DIFFRACTION	f_angle_d	1.103	9120
X-RAY DIFFRACTION	f_dihedral_angle_d	14.35	2344
X-RAY DIFFRACTION	f_chiral_restr	0.046	1043
X-RAY DIFFRACTION	f_plane_restr	0.013	1151

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 (%)
2.7576-2.8466	0.386	141	0.3565	2302	X-RAY DIFFRACTION	82
2.8466-2.9483	0.3883	131	0.3401	2457	X-RAY DIFFRACTION	86
2.9483-3.0663	0.3985	126	0.3265	2484	X-RAY DIFFRACTION	87
3.0663-3.2059	0.4022	136	0.3294	2479	X-RAY DIFFRACTION	86
3.2059-3.3748	0.3434	135	0.3059	2515	X-RAY DIFFRACTION	89
3.3748-3.5862	0.3211	128	0.2857	2615	X-RAY DIFFRACTION	90
3.5862-3.863	0.3146	133	0.2749	2726	X-RAY DIFFRACTION	94
3.863-4.2515	0.2634	146	0.2369	2770	X-RAY DIFFRACTION	96
4.2515-4.8662	0.1947	144	0.1916	2852	X-RAY DIFFRACTION	98
4.8662-6.1289	0.2384	168	0.2071	2861	X-RAY DIFFRACTION	97
6.1289-47.7609	0.2336	156	0.2202	2963	X-RAY DIFFRACTION	95

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	2.624	2.7023	-0.0948	2.8022	0.4883	4.9355	-0.5193	-0.123	0.6651	0.3973	-0.0904	0.1073	-2.4682	0.5184	0.466	2.1082	-0.3137	-0.4536	0.3359	-0.1148	0.7407	7.7685	13.7345	46.1189
2	3.6971	2.1868	3.8556	5.08	1.1846	4.3605	-0.567	0.0032	-0.0182	0.1565	-0.1218	-1.8588	-0.5003	2.4191	-0.2172	2.0838	-1.4201	-0.5212	1.4267	-0.1069	0.8795	22.0076	11.6421	38.2673
3	4.3607	-1.8368	0.5718	4.7148	-0.7786	8.1128	-0.7596	1.2668	0.5168	-0.7402	-0.1879	-0.0092	-2.0102	1.1571	0.8758	1.5825	-0.725	-0.217	1.0908	0.0362	0.6917	11.0049	9.2029	33.2457
4	0.9721	0.378	0.4332	0.6927	0.0483	2.0124	-0.6847	0.6412	0.8446	0.4777	0.0367	-0.1682	-2.9748	0.997	0.5633	1.8957	-0.6101	-0.393	0.7635	0.0819	0.9445	10.0082	14.8522	38.085
5	3.3726	0.9973	-0.1856	1.831	0.0725	6.2819	-0.3045	0.1094	0.1341	-0.0089	0.0046	0.0928	-1.583	0.2307	0.2686	0.9032	-0.0296	-0.1516	0.3639	-0.045	0.5921	5.8577	2.054	55.017
6	6.0999	-0.8771	1.4928	5.8489	-2.3288	5.9063	0.1042	-0.2475	-0.3251	-0.3399	-0.3387	-0.2153	-0.2089	0.1564	0.1787	0.8898	0.1133	0.0241	0.4323	-0.0065	0.483	6.1781	0.5862	66.552
7	4.6422	0.3182	-0.1648	4.7636	-0.9474	8.9534	-0.3116	0.6803	-0.1797	-0.6166	-0.145	-0.0563	-0.4949	1.0171	0.4624	0.4257	-0.0539	-0.1322	0.9379	-0.1543	0.6767	7.9898	-11.7572	28.1483
8	5.4767	1.8566	-0.3868	3.8727	0.3951	7.1963	0.0771	0.3161	-0.2706	-0.0704	-0.0826	-0.4497	-0.2842	2.1808	0.0563	0.4381	-0.0839	-0.0257	0.9995	-0.1072	0.5784	13.2608	-9.1601	33.9498
9	7.1804	-1.6502	-2.4642	9.4383	0.2871	3.9545	0.1474	0.1628	-0.595	0.1427	-0.1279	-0.3764	1.0755	0.6161	0.0423	1.0181	0.0619	-0.1211	0.5342	0.1029	0.453	1.4334	-19.2426	59.5052
10	7.205	1.1025	-1.5194	4.1463	0.6669	8.1489	0.1661	-0.7149	0.3725	0.323	-0.1407	0.3366	-0.2782	-0.6472	-0.0436	0.7182	0.0844	-0.0892	0.4685	-0.0534	0.4283	-8.1272	-10.2309	65.6853
11	5.8042	-0.6314	0.9197	0.535	1.5277	8.8267	0.0234	-0.568	-0.9929	0.1238	-0.1385	0.9024	3.7803	-1.8433	-0.0977	0.377	-0.8653	-0.338	1.3808	0.0586	0.8074	-29.4183	-35.0346	25.8434
12	9.2754	-6.155	0.4083	4.3513	1.1215	6.5201	0.267	-0.6055	0.0802	1.0084	-0.408	0.1274	0.7167	-1.3859	0.2201	0.9436	-0.611	-0.1574	1.1159	0.2608	0.6577	-23.6107	-29.9323	33.1099
13	7.4167	1.3301	1.7634	3.1487	2.0834	6.5638	0.4182	-1.3791	-0.9468	0.4748	-0.3234	0.307	1.524	-2.9473	-0.0354	0.9034	-0.5268	-0.0165	1.8984	0.2827	0.9944	-32.6766	-32.4835	37.727
14	1.4931	0.0082	1.9188	2.3273	1.0245	6.2167	0.3457	-0.2285	-0.2721	0.3995	-0.1791	0.0209	0.9848	-1.3868	-0.1599	0.3884	-0.1882	-0.0543	0.7986	0.0419	0.6533	-23.4186	-26.6993	18.5903
15	4.2818	-1.3714	-0.9198	4.4887	1.797	5.3567	-0.1186	-0.2135	0.1388	0.0369	0.2775	-0.0638	0.2905	0.1045	-0.147	0.2676	0.0136	0.0469	0.7881	0.0351	0.637	-19.3358	-24.0149	2.0596
16	8.7096	-0.029	-6.4357	4.2421	-1.7354	6.0076	0.0673	-0.7756	-0.8661	0.3164	-0.2807	0.3021	0.5815	0.8155	0.185	0.8221	-0.0115	-0.2704	0.6689	-0.1247	0.7908	-4.9913	-26.2116	39.8485
17	5.2732	1.2077	1.0611	5.3685	-0.7012	7.4988	0.5805	-0.2211	-0.8653	0.291	0.1103	-0.8646	2.3513	0.6861	-0.6526	1.0138	0.1385	-0.2656	0.5711	-0.0743	0.7318	-5.539	-32.7874	32.6094
18	3.1879	0.6706	0.4367	2.1617	-2.2933	9.6659	0.0928	-0.2161	0.2006	0.0258	-0.012	-0.0533	0.5342	-0.0791	-0.0925	0.3642	0.1536	-0.0833	0.3641	-0.1887	0.5677	-11.666	-19.2957	16.6369
19	4.1877	-2.091	2.1931	5.8028	-2.9916	5.7268	-0.0532	-0.1982	0.2841	-0.0048	-0.0138	-0.0342	-0.2741	-0.1349	0.0637	0.2549	-0.0056	0.0088	0.5771	-0.0664	0.4721	-7.535	-9.0728	4.0224

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 17 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 18 through 35 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 35A through 62 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 63 through 94 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 95 through 145 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 146 through 215 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 3 through 32 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 33 through 106 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 106A through 118 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 119 through 210 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 2 through 34 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 35 through 52 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 53 through 72 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 73 through 143 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 144 through 214 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 3 through 32 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 33 through 91 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 92 through 129 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 130 through 210 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi