PDB-4npy: Crystal structure of germline Fab PGT121, a putative precursor of...

ID or keywords:

Entry

Database: PDB / ID: 4npy

Title

Crystal structure of germline Fab PGT121, a putative precursor of the broadly reactive and potent HIV-1 neutralizing antibody

Components

germline PGT121 heavy chain
germline PGT121 light chain

Keywords

IMMUNE SYSTEM / IgG-fold / anti-HIV antibody precursor / HIV Env gp120

Function / homology

Function and homology information

immunoglobulin complex /

plasma membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / PHASER / Resolution: 1.796 Å

Authors

Julien, J.-P. / Diwanji, D.C. / Wilson, I.A.

Citation

Journal: Plos Pathog. / Year: 2013
Title: The Effects of Somatic Hypermutation on Neutralization and Binding in the PGT121 Family of Broadly Neutralizing HIV Antibodies.
Authors: Sok, D. / Laserson, U. / Laserson, J. / Liu, Y. / Vigneault, F. / Julien, J.P. / Briney, B. / Ramos, A. / Saye, K.F. / Le, K. / Mahan, A. / Wang, S. / Kardar, M. / Yaari, G. / Walker, L.M. / ...

History

Deposition	Nov 22, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 11, 2013	Provider: repository / Type: Initial release
Revision 2.0	Dec 25, 2019	Group: Derived calculations / Polymer sequence Category: entity_poly / pdbx_struct_mod_residue / struct_conn Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4npy.cif.gz	353.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4npy.ent.gz	289.1 KB	Display	PDB format
PDBx/mmJSON format	4npy.json.gz		Tree view	PDBx/mmJSON format
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Validation report

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

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Related structure data

Related structure data	4jy6S 4fq1 4fqc 4fqq 4jy4 4jy5 4nco S: Starting model for refinement
Similar structure data	3mug-2 4fq1-d 4r26-d 6e8v-5 4fqq-2 4fqq-4 4fqq-1 4org-2 6umh-1 3mug-4 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 - 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)

Deposited unit

L: germline PGT121 light chain

H: germline PGT121 heavy chain

A: germline PGT121 light chain

B: germline PGT121 heavy chain

hetero molecules

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

1

L: germline PGT121 light chain

H: germline PGT121 heavy chain

hetero molecules

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

2

A: germline PGT121 light chain

B: germline PGT121 heavy chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	53.720, 54.900, 320.730
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	germline PGT121 light chain Mass: 22889.266 Da / Num. of mol.: 2 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: Q6GMX6*PLUS
#2: Antibody	germline PGT121 heavy chain Mass: 25333.508 Da / Num. of mol.: 2 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: Q6GMX6*PLUS
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 610 / 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: 2.45 Å³/Da / Density % sol: 49.83 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M magnesium acetate, 20% w/v PEG8000, 0.1 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 10, 2011 / Details: Adjustable focusing mirrors in K-B geometry
Radiation	Monochromator: double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 1.796→50 Å / Num. all: 86588 / Num. obs: 89562 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / B_iso Wilson estimate: 32.9 Å² / R_merge(I) obs: 0.074 / Net I/σ(I): 9.3
Reflection shell	Resolution: 1.796→1.9 Å / Redundancy: 2.4 % / R_merge(I) obs: 0.503 / Mean I/σ(I) obs: 1.3 / % possible all: 93.1

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure: PHASER
Starting model: PDB ENTRY 4JY6

4jy6

Resolution: 1.796→48.837 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 23.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2199	4251	5.02 %
R_work	0.1818	-	-
obs	0.1838	84738	94.1 %
all	-	84738	-

Solvent computation

Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.796→48.837 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6674	0	18	610	7302

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6879
X-RAY DIFFRACTION	f_angle_d	1.162	9394
X-RAY DIFFRACTION	f_dihedral_angle_d	13.75	2424
X-RAY DIFFRACTION	f_chiral_restr	0.078	1063
X-RAY DIFFRACTION	f_plane_restr	0.005	1186

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 (%)
1.7958-1.8162	0.4495	47	0.3898	1316	X-RAY DIFFRACTION	47
1.8162-1.8376	0.4227	120	0.3627	2469	X-RAY DIFFRACTION	87
1.8376-1.86	0.3247	150	0.3326	2534	X-RAY DIFFRACTION	91
1.86-1.8835	0.3263	141	0.3119	2623	X-RAY DIFFRACTION	93
1.8835-1.9083	0.348	132	0.2857	2618	X-RAY DIFFRACTION	93
1.9083-1.9345	0.3299	157	0.2768	2590	X-RAY DIFFRACTION	94
1.9345-1.9621	0.2685	148	0.258	2723	X-RAY DIFFRACTION	95
1.9621-1.9914	0.2763	151	0.2488	2689	X-RAY DIFFRACTION	96
1.9914-2.0225	0.336	145	0.2358	2702	X-RAY DIFFRACTION	96
2.0225-2.0557	0.3193	126	0.2203	2735	X-RAY DIFFRACTION	97
2.0557-2.0911	0.2436	145	0.2086	2733	X-RAY DIFFRACTION	97
2.0911-2.1291	0.2518	148	0.2012	2754	X-RAY DIFFRACTION	97
2.1291-2.1701	0.2357	137	0.2008	2744	X-RAY DIFFRACTION	97
2.1701-2.2144	0.2283	153	0.1962	2759	X-RAY DIFFRACTION	97
2.2144-2.2625	0.2332	143	0.1966	2766	X-RAY DIFFRACTION	98
2.2625-2.3152	0.2503	149	0.1869	2776	X-RAY DIFFRACTION	98
2.3152-2.3731	0.2521	133	0.194	2770	X-RAY DIFFRACTION	98
2.3731-2.4372	0.2308	144	0.1909	2795	X-RAY DIFFRACTION	98
2.4372-2.5089	0.2515	159	0.1983	2760	X-RAY DIFFRACTION	98
2.5089-2.5899	0.2281	137	0.1952	2793	X-RAY DIFFRACTION	98
2.5899-2.6825	0.2751	140	0.1996	2797	X-RAY DIFFRACTION	98
2.6825-2.7899	0.2689	142	0.1836	2791	X-RAY DIFFRACTION	98
2.7899-2.9168	0.2218	146	0.1736	2769	X-RAY DIFFRACTION	97
2.9168-3.0706	0.2008	159	0.1744	2767	X-RAY DIFFRACTION	96
3.0706-3.2629	0.2067	146	0.1658	2741	X-RAY DIFFRACTION	96
3.2629-3.5148	0.1821	160	0.1553	2733	X-RAY DIFFRACTION	95
3.5148-3.8684	0.1636	153	0.1435	2771	X-RAY DIFFRACTION	95
3.8684-4.4278	0.1657	150	0.1288	2755	X-RAY DIFFRACTION	95
4.4278-5.5773	0.1473	135	0.1308	2818	X-RAY DIFFRACTION	94
5.5773-48.8552	0.2045	155	0.1734	2896	X-RAY DIFFRACTION	92

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	1.6741	-0.2637	0.1064	3.7187	0.4994	3.5553	-0.0141	-0.0066	0.1794	-0.1051	0.0196	-0.2644	-0.0851	0.1323	-0.0089	0.141	0.0015	0.0025	0.2176	-0.0247	0.1617	62.4255	55.5589	4.4619
2	2.6844	-1.2178	0.0563	3.2758	-1.0693	3.9135	-0.0256	-0.1299	0.1971	0.1033	0.0141	-0.1857	-0.0141	0.0854	0.0061	0.1049	-0.0018	-0.0144	0.1247	-0.0325	0.1947	57.8607	60.9113	43.322
3	2.5901	-0.3894	0.8634	2.0528	0.2453	2.982	-0.0187	0.0934	-0.0503	-0.1508	0.0068	0.0369	0.0427	-0.046	0.0097	0.1302	-0.0098	0.0197	0.184	-0.0229	0.1362	74.5252	39.6348	9.4736
4	2.1072	-0.4642	-0.4474	0.5254	-0.1266	1.022	-0.0638	0.0224	-0.1185	0.0482	0.0123	0.09	0.063	-0.0292	0.0582	0.1746	-0.0007	0.0023	0.1567	-0.0276	0.2503	60.5377	45.3333	37.4885
5	2.4061	-0.0506	0.5021	2.4774	-0.0932	3.3263	0.0768	0.0606	-0.0817	-0.0972	-0.0952	0.1866	0.0264	-0.1699	0.0263	0.1771	0.0042	-0.0084	0.1283	-0.0405	0.1352	69.5658	73.3252	70.105
6	3.2666	-1.1444	-0.9399	2.0535	0.3754	2.9487	0.0917	0.2879	0.0316	-0.1525	-0.04	0.072	-0.0384	-0.1579	-0.043	0.1755	0.0085	-0.0258	0.1523	0.0178	0.1908	77.6295	74.5256	32.048
7	1.0464	-0.4414	-0.6929	2.709	0.9949	3.0871	0.0133	-0.0652	0.0366	0.0575	0.0085	-0.1329	-0.0464	0.0471	-0.0067	0.1437	0.0029	-0.0292	0.1006	0.015	0.133	85.961	60.7532	71.5153
8	1.0993	0.128	-0.5591	0.7698	0.6287	1.5373	-0.0378	0.161	0.157	-0.0543	0.0661	-0.0361	-0.2164	-0.2438	0.0268	0.1778	0.0272	-0.0171	0.1463	0.0048	0.1854	88.6788	71.8034	42.2937
9	1.541	0.2845	-0.2024	4.7842	-1.1087	1.1989	-0.0381	-0.0025	0.2319	0.0413	0.031	-0.0533	-0.148	0.0435	0.0224	0.1357	-0.0022	0.0006	0.1261	-0.0212	0.1424	92.2291	74.0532	41.9322

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'L' and (resseq 2:109)
2	X-RAY DIFFRACTION	2	chain 'L' and (resseq 110:209)
3	X-RAY DIFFRACTION	3	chain 'H' and (resseq 2:101)
4	X-RAY DIFFRACTION	4	chain 'H' and (resseq 102:213)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 1:109)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 110:208)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 2:101)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 102:141)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 142:213)

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