PDB-3nz8: Crystal structure of the HIV-2 neutralizing Fab fragment 7C8

ID or keywords:

Entry

Database: PDB / ID: 3nz8

Title

Crystal structure of the HIV-2 neutralizing Fab fragment 7C8

Components

Mouse anti V3 antibody 7C8 Fab, heavy chain
Mouse anti V3 antibody 7C8 Fab, light chain

Keywords

IMMUNE SYSTEM / Antigen binding / Antibody / Fab / Immunological / HIV-2 / V3 / gp125

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Uchtenhagen, H. / Friemann, R. / Raszewski, G. / Spetz, A.-L. / Nilsson, L. / Achour, A.

Citation

Journal: Plos One / Year: 2011
Title: Crystal Structure of the HIV-2 Neutralizing Fab Fragment 7C8 with High Specificity to the V3 Region of gp125.
Authors: Uchtenhagen, H. / Friemann, R. / Raszewski, G. / Spetz, A.L. / Nilsson, L. / Achour, A.

History

Deposition	Jul 16, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 18, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Jan 24, 2018	Group: Advisory / Data collection / Structure summary Category: audit_author / diffrn_source / pdbx_unobs_or_zero_occ_atoms Item: _audit_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.3	Sep 6, 2023	Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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
Revision 1.4	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3nz8.cif.gz	347.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3nz8.ent.gz	289.2 KB	Display	PDB format
PDBx/mmJSON format	3nz8.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3nz8_validation.pdf.gz	456.7 KB	Display	wwPDB validaton report
Full document	3nz8_full_validation.pdf.gz	464.2 KB	Display
Data in XML	3nz8_validation.xml.gz	31.3 KB	Display
Data in CIF	3nz8_validation.cif.gz	43.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nz/3nz8 ftp://data.pdbj.org/pub/pdb/validation_reports/nz/3nz8	HTTPS FTP

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Related structure data

Related structure data	1i9jS S: Starting model for refinement
Similar structure data	5mx3-1 4k23-d 2eh7-d 1rul-d 5mvj-2 5eoq-d 3qnz-d 3dif-2 3bdy-1 5wuv-d 2f5a-d 6obz-1 1rua-d 1a3l-d 1kcs-d 3qo1-d 4odw-2 6pds-1 4jzo-2 5erw-d 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

Related structure data

1i9jS

S: Starting model for refinement

Similar structure data

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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

A: Mouse anti V3 antibody 7C8 Fab, heavy chain

B: Mouse anti V3 antibody 7C8 Fab, light chain

H: Mouse anti V3 antibody 7C8 Fab, heavy chain

L: Mouse anti V3 antibody 7C8 Fab, light chain

hetero molecules

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

1

A: Mouse anti V3 antibody 7C8 Fab, heavy chain

B: Mouse anti V3 antibody 7C8 Fab, light chain

hetero molecules

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

2

H: Mouse anti V3 antibody 7C8 Fab, heavy chain

L: Mouse anti V3 antibody 7C8 Fab, light chain

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

Unit cell

Length a, b, c (Å)	100.071, 100.071, 196.763
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Antibody	Mouse anti V3 antibody 7C8 Fab, heavy chain Mass: 23754.617 Da / Num. of mol.: 2 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): Hybridoma / Production host: Mus musculus (house mouse)
#2: Antibody	Mouse anti V3 antibody 7C8 Fab, light chain Mass: 24128.730 Da / Num. of mol.: 2 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): Hybridoma / Production host: Mus musculus (house mouse)
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H₂O
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: 2.97 Å³/Da / Density % sol: 58.58 %
Crystal grow	Temperature: 293 K / pH: 8.5 Details: 50 mM ammonium sulphate, 25% (w/v) PEG 8000 and 2.5% (v/v) PEG 400, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.97
Detector	Type: MAR CCD 130 mm / Detector: CCD / Date: Sep 14, 2003
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 2.7→44.6 Å / Num. obs: 32045 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / B_iso Wilson estimate: 0 Å² / R_merge(I) obs: 0.07 / R_sym value: 0.07 / Net I/σ(I): 21.1

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Processing

Software

Name	Version	Classification
MAR345dtb		data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1I9J

1i9j

Resolution: 2.7→42.8 Å / Cor.coef. F_o:F_c: 0.936 / Cor.coef. F_o:F_c free: 0.907 / SU B: 36.87 / SU ML: 0.326 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.877 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.273	1615	5 %	RANDOM
R_work	0.226	-	-	-
obs	0.229	30420	99.8 %	-
all	-	30420	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 88.34 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.39 Å²	2.19 Å²	0 Å²
2-	-	4.39 Å²	0 Å²
3-	-	-	-6.58 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→42.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6677	0	6	78	6761

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	6854
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.065	1.951	9340
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.806	5	863
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.132	24.436	266
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.43	15	1089
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.975	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	1047
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	5147
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.285	1.5	4327
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.536	2	7041
X-RAY DIFFRACTION	r_scbond_it	0.608	3	2527
X-RAY DIFFRACTION	r_scangle_it	1.05	4.5	2299
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.372	111	-
R_work	0.366	2193	-
obs	-	-	99.74 %

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	3.5124	2.3735	0.6078	6.0636	-0.864	3.7406	-0.0139	-0.0779	0.5115	-0.3149	-0.217	0.1968	-0.0072	-0.1229	0.231	0.2619	-0.0502	0.1109	0.2634	-0.0492	0.3896	35.065	-6.74	-14.557
2	1.2409	0.1451	0.637	0.9385	1.2274	5.9878	0.0869	-0.2018	0.2334	0.092	-0.2229	0.1465	-0.0263	-0.5928	0.1361	0.2097	-0.0706	0.0265	0.2816	0.0205	0.518	32.473	-8.376	-16.624
3	5.6302	0.5293	-2.3897	5.5644	-1.3994	9.7245	0.515	0.2717	0.2226	0.2033	-0.574	-0.5017	-0.6478	-0.1544	0.0591	0.1636	-0.1279	-0.0268	0.314	0.122	0.5397	34.442	-11.025	-42.314
4	6.6847	2.7761	-5.0879	7.7798	-3.4458	13.8597	0.2876	0.1631	-0.1147	-0.5862	-0.7457	-1.2875	0.0258	0.742	0.4581	0.1667	-0.0201	-0.0018	0.431	0.2114	0.7013	39.422	-15.048	-46.395
5	3.2643	0.547	0.029	3.5872	-2.8243	8.4774	-0.1026	-0.1518	0.7474	0.2342	0.0809	0.6842	-1.6269	-0.4569	0.0218	0.5039	0.121	-0.0115	0.1161	-0.0648	0.8656	29.789	13.649	-20.441
6	4.7076	0.3222	-0.7225	8.3008	-1.443	7.3018	-0.4609	0.1919	0.9584	-0.0852	0.387	-0.2192	-1.1743	1.1503	0.0739	0.5631	-0.186	-0.0726	0.2689	-0.0101	0.8111	40.287	14.798	-20.918
7	0.7137	0.6519	0.956	1.3833	2.0622	5.7249	-0.1201	0.1782	0.4058	-0.1379	0.1514	0.1081	-0.8004	-0.1181	-0.0313	0.2682	0.069	-0.0298	0.2655	0.0659	0.6758	30.318	2.816	-34.688
8	2.7417	3.3059	0.4991	10.6065	1.6064	3.8828	0.1357	0.0364	0.5326	0.1552	-0.2424	0.6871	-0.4418	-0.7214	0.1067	0.1619	0.023	-0.005	0.3985	0.0738	0.4856	23.178	-7.179	-53.367
9	1.3179	0.6512	-0.0157	5.4988	-2.2408	1.0878	0.1351	-0.0667	0.0083	-0.3331	0.018	0.2868	0.1455	-0.1898	-0.153	0.7218	-0.0864	0.0369	0.2675	-0.048	0.4197	64.33	16.412	-5.539
10	2.5555	1.1682	-0.1008	2.0901	-0.1102	6.8572	0.0085	-0.0433	-0.2543	-0.6692	0.0556	-0.3231	0.8973	0.1955	-0.0642	0.8311	0.0392	0.1454	0.0539	-0.0157	0.4405	74.408	13.881	-3.151
11	1.762	-0.5696	1.0009	1.8187	-2.4739	3.4026	0.1725	0.0475	-0.0953	-0.4408	-0.0964	0.0597	0.553	0.1434	-0.0761	0.8351	-0.1253	0.0986	0.1421	-0.1129	0.4159	65.453	19.954	-12.825
12	3.9186	-0.2008	2.1922	5.4301	2.6618	8.6116	-0.0489	0.7827	0.0342	-0.1642	-0.4646	0.7	0.7633	-0.7013	0.5134	0.4372	-0.2597	0.1333	0.3859	-0.124	0.4304	55.835	30.546	-37.485
13	10.4688	-3.5716	-2.7763	3.7043	-1.9076	4.6013	-0.2836	-0.3859	-0.16	-1.0779	0.9076	-0.0465	0.5874	-0.5281	-0.6239	2.6685	-0.4403	0.5834	0.7076	-0.3854	1.4866	73.189	2.302	-27.919
14	0.5864	1.8737	0.1801	6.7625	-1.5207	10.992	-0.1561	0.0147	-0.1876	-0.9074	-0.0181	-0.3082	0.9747	0.3326	0.1742	0.9641	0.0083	0.1656	0.0188	-0.014	0.4762	72.36	0.037	-16.596
15	0.8573	-0.3805	0.1922	2.156	-2.6405	3.5946	0.0262	0.2904	-0.1993	-0.5044	-0.0612	0.0905	1.1042	0.0245	0.035	0.9529	0.022	0.1407	0.1882	-0.1504	0.3299	69.241	16.232	-33.575
16	3.1152	1.8319	-0.2352	17.3509	0.1304	5.8346	-0.07	0.5236	0.2095	-0.0874	-0.4153	-0.5808	1.4288	0.265	0.4852	0.6437	0.1329	0.1714	0.4851	-0.0349	0.172	72.873	25.466	-51.65

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 51
2	X-RAY DIFFRACTION	2	A	52 - 126
3	X-RAY DIFFRACTION	3	A	133 - 173
4	X-RAY DIFFRACTION	4	A	174 - 214
5	X-RAY DIFFRACTION	5	B	1 - 43
6	X-RAY DIFFRACTION	6	B	44 - 67
7	X-RAY DIFFRACTION	7	B	68 - 133
8	X-RAY DIFFRACTION	8	B	134 - 212
9	X-RAY DIFFRACTION	9	H	1 - 41
10	X-RAY DIFFRACTION	10	H	42 - 73
11	X-RAY DIFFRACTION	11	H	74 - 126
12	X-RAY DIFFRACTION	12	H	133 - 214
13	X-RAY DIFFRACTION	13	L	1 - 17
14	X-RAY DIFFRACTION	14	L	18 - 50
15	X-RAY DIFFRACTION	15	L	51 - 193
16	X-RAY DIFFRACTION	16	L	194 - 213

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