PDB-5jxa: Crystal structure of ligand-free VRC03 antigen-binding fragment.

ID or keywords:

Entry

Database: PDB / ID: 5jxa

Title

Crystal structure of ligand-free VRC03 antigen-binding fragment.

Components

VRC03 Heavy chain
VRC03 Light chain

Keywords

IMMUNE SYSTEM / HIV-1 / CD4 binding site / neutralizing / antibody development

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / COPPER (II) ION / PHOSPHATE ION

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Zhou, T. / Moquin, S. / Joyce, M.G. / Mascola, J.R. / Kwong, P.D.

Citation

Journal: Structure / Year: 2016
Title: Somatic Hypermutation-Induced Changes in the Structure and Dynamics of HIV-1 Broadly Neutralizing Antibodies.
Authors: Davenport, T.M. / Gorman, J. / Joyce, M.G. / Zhou, T. / Soto, C. / Guttman, M. / Moquin, S. / Yang, Y. / Zhang, B. / Doria-Rose, N.A. / Hu, S.L. / Mascola, J.R. / Kwong, P.D. / Lee, K.K.

History

Deposition	May 12, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 27, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 17, 2016	Group: Database references
Revision 1.2	Oct 18, 2017	Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _citation.journal_id_ISSN ..._citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Sep 27, 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 / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5jxa.cif.gz	274 KB	Display	PDBx/mmCIF format
PDB format	pdb5jxa.ent.gz	222.9 KB	Display	PDB format
PDBx/mmJSON format	5jxa.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5jxa_validation.pdf.gz	460.7 KB	Display	wwPDB validaton report
Full document	5jxa_full_validation.pdf.gz	464.4 KB	Display
Data in XML	5jxa_validation.xml.gz	24.9 KB	Display
Data in CIF	5jxa_validation.cif.gz	38.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jx/5jxa ftp://data.pdbj.org/pub/pdb/validation_reports/jx/5jxa	HTTPS FTP

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Related structure data

Related structure data	5jofC 3se8S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4hkb-3 3piq-3 3ghb-1 4jy6-2 4jy6-1 1him-1 2h32-d 4evn-3 4c83-1 3piq-6 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) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

H: VRC03 Heavy chain

L: VRC03 Light chain

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	162.185, 50.804, 71.757
Angle α, β, γ (deg.)	90.00, 108.15, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	L-687- HOH
2	1	L-708- HOH

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Antibody , 2 types, 2 molecules HL

#1: Antibody	VRC03 Heavy chain Mass: 25450.602 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	VRC03 Light chain Mass: 23146.795 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 635 molecules

#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#5: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 626 / 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: 57.44 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES pH 7.5, 13% PEG 4,000, 10 mM CuCl2, 350 mM NaCl

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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: Aug 22, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.6→50 Å / Num. obs: 65283 / % possible obs: 88.9 % / Redundancy: 3.6 % / Net I/σ(I): 22.12

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
PDB_EXTRACT	3.2	data extraction
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3se8

3se8

Resolution: 1.6→22.954 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.43 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1796	3242	4.97 %
R_work	0.1596	-	-
obs	0.1606	65282	88.88 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6→22.954 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3391	0	30	626	4047

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3524
X-RAY DIFFRACTION	f_angle_d	0.866	4795
X-RAY DIFFRACTION	f_dihedral_angle_d	12.682	2092
X-RAY DIFFRACTION	f_chiral_restr	0.056	521
X-RAY DIFFRACTION	f_plane_restr	0.006	614

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 (%)
1.6004-1.6242	0.2753	73	0.2467	1164	X-RAY DIFFRACTION	39
1.6242-1.6496	0.3255	77	0.2473	1433	X-RAY DIFFRACTION	48
1.6496-1.6767	0.2828	76	0.2334	1735	X-RAY DIFFRACTION	57
1.6767-1.7056	0.2585	100	0.2299	2037	X-RAY DIFFRACTION	66
1.7056-1.7366	0.2859	100	0.2198	2222	X-RAY DIFFRACTION	73
1.7366-1.7699	0.2578	117	0.2233	2453	X-RAY DIFFRACTION	81
1.7699-1.8061	0.2642	154	0.213	2643	X-RAY DIFFRACTION	88
1.8061-1.8453	0.2398	142	0.1935	2817	X-RAY DIFFRACTION	94
1.8453-1.8882	0.2015	154	0.1831	2973	X-RAY DIFFRACTION	98
1.8882-1.9354	0.1946	138	0.1745	3010	X-RAY DIFFRACTION	99
1.9354-1.9877	0.1775	147	0.1631	3000	X-RAY DIFFRACTION	100
1.9877-2.0462	0.162	168	0.1587	3033	X-RAY DIFFRACTION	100
2.0462-2.1122	0.1774	176	0.1599	3020	X-RAY DIFFRACTION	100
2.1122-2.1876	0.1844	158	0.1551	3001	X-RAY DIFFRACTION	100
2.1876-2.2751	0.199	167	0.1508	3015	X-RAY DIFFRACTION	100
2.2751-2.3786	0.1729	169	0.1494	3027	X-RAY DIFFRACTION	100
2.3786-2.5038	0.1699	161	0.1459	3027	X-RAY DIFFRACTION	100
2.5038-2.6605	0.1498	156	0.1534	3066	X-RAY DIFFRACTION	100
2.6605-2.8656	0.1688	153	0.1581	3025	X-RAY DIFFRACTION	100
2.8656-3.1533	0.1531	182	0.1606	3032	X-RAY DIFFRACTION	100
3.1533-3.608	0.1782	165	0.1479	3067	X-RAY DIFFRACTION	100
3.608-4.54	0.1619	156	0.1369	3071	X-RAY DIFFRACTION	100
4.54-22.9567	0.1718	153	0.1588	3169	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	1.1396	-0.1794	-0.5771	1.3358	0.7934	2.1322	-0.1109	-0.2675	0.1141	0.1008	0.1763	-0.034	-0.148	0.2948	0.1277	0.1562	0.016	-0.0228	0.1966	-0.0391	0.1154	-5.3944	20.6411	-13.8486
2	2.1134	0.0184	2.3014	2.2187	1.3668	5.341	-0.0169	0.1181	0.0808	-0.0106	0.1837	-0.0438	-0.3886	0.4031	-0.0301	0.2137	-0.0053	-0.0146	0.1344	-0.0136	0.1717	-7.7088	28.0242	-17.2719
3	0.1873	0.0599	-0.1293	1.2884	0.6049	1.4586	-0.0181	-0.0449	0.1086	0.0761	0.0291	-0.0553	-0.0996	0.134	-0.0201	0.1497	0.0148	-0.0181	0.147	-0.0089	0.1102	-3.2686	18.7462	-13.5783
4	2.6125	0.0603	0.1391	2.76	0.5333	1.139	0.1968	-0.7321	0.0651	0.3163	-0.1527	0.0955	0.1568	-0.1638	-0.0228	0.2281	-0.0819	0.0111	0.4015	-0.047	0.1652	-31.4892	-2.3812	-9.3027
5	1.8342	-1.1852	-0.1229	4.0338	0.0203	1.9197	0.0394	-0.8053	-0.1786	0.628	-0.0272	0.1409	0.3517	-0.1429	-0.0997	0.3175	-0.0877	0.0096	0.5254	0.0456	0.2005	-31.5131	-8.8764	-5.4897
6	0.8308	-1.5215	-0.6636	4.0777	0.0204	1.6442	0.0372	-0.6236	-0.0339	0.2363	0.0368	0.8187	0.0223	-0.7335	-0.0127	0.5255	-0.2114	0.061	1.0068	0.0609	0.3978	-40.0235	-8.212	-2.706
7	1.7593	0.2476	-0.1249	1.9229	0.0129	1.6537	-0.0649	0.0539	-0.1067	-0.0572	0.0209	-0.0249	0.0769	0.0461	0.0266	0.1407	-0.0021	0.0104	0.1162	-0.011	0.1463	-3.4272	3.1358	-31.8434
8	2.0271	0.3328	-0.7844	1.7249	0.2435	1.7709	-0.0438	-0.1648	-0.1927	0.1352	0.0205	-0.0892	0.2005	0.1829	0.0338	0.1702	0.0266	-0.0084	0.1667	0.0248	0.1741	3.0221	2.0683	-25.2577
9	1.484	1.1093	0.0234	1.0251	-0.2075	0.2434	0.0809	-0.0926	-0.2122	0.1331	-0.124	-0.0917	0.0662	0.0284	0.0161	0.1583	0.0027	-0.0002	0.0812	0.0021	0.1346	-7.4928	-2.2497	-25.8984
10	1.5598	-0.2617	-1.2932	3.4111	1.0904	2.6845	-0.0256	-0.8346	0.3128	0.7076	0.0381	0.1264	0.2521	-0.4061	0.0378	0.2287	-0.0619	0.0216	0.5204	-0.1009	0.2259	-42.5829	-6.0774	-13.6487
11	5.3557	-1.0782	0.908	0.7169	0.0773	0.6618	0.0407	-0.1829	0.1284	0.0205	-0.0301	-0.0583	0.0418	-0.0659	-0.0069	0.1863	-0.0189	-0.006	0.1201	0.0036	0.1721	-29.9522	-7.0093	-23.6514
12	5.6334	-0.4993	0.4519	1.4456	0.2918	1.3214	0.1294	-0.0447	0.1873	-0.0386	-0.1057	0.1115	0.0341	-0.28	0.0069	0.1757	-0.0129	-0.0213	0.1946	0.0041	0.1535	-40.5074	-6.6892	-25.1141
13	7.4076	-1.6554	-1.2636	3.3495	1.1027	3.7427	-0.0628	-0.5869	-0.5799	0.3749	0.004	0.1403	0.369	-0.6126	0.0337	0.2409	-0.0767	-0.03	0.3292	0.057	0.2192	-46.1541	-13.2289	-21.6407

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 59 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 60 through 73 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 74 through 111 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 112 through 175 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 176 through 203 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 204 through 217 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 1 through 38 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 39 through 75 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 76 through 113 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 114 through 128 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 129 through 174 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 175 through 204 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 205 through 214 )

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