PDB-3ley: 2F5 Epitope scaffold elicited anti-HIV-1 monoclonal antibody 6a7 ...

ID or keywords:

Entry

Database: PDB / ID: 3ley

Title

2F5 Epitope scaffold elicited anti-HIV-1 monoclonal antibody 6a7 in complex with HIV-1 GP41

Components

6a7 Antibody Heavy Chain
6a7 Antibody Light Chain
Envelope glycoprotein gp41

Keywords

IMMUNE SYSTEM /

HIV-1 / GP-41 /

MONOCLONAL ANTIBODY / 2F5 /

SCAFFOLD /

EPITOPE / TRANSPLANT / GRAFT / RE-ELCITATION /

Envelope protein /

VACCINE DESIGN

Function / homology

Function and homology information

viral envelope / host cell plasma membrane / virion membrane / structural molecule activity /

plasma membrane
Similarity search - Function

Biological species

Mus musculus (house mouse)

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.99 Å

Authors

Ofek, G. / Guenaga, F.J. / Schief, W.R. / Skinner, J. / Baker, D. / Wyatt, R. / Kwong, P.D.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Elicitation of structure-specific antibodies by epitope scaffolds.
Authors: Ofek, G. / Guenaga, F.J. / Schief, W.R. / Skinner, J. / Baker, D. / Wyatt, R. / Kwong, P.D.

History

Deposition	Jan 15, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 29, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3ley.cif.gz	188.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3ley.ent.gz	156.3 KB	Display	PDB format
PDBx/mmJSON format	3ley.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/le/3ley ftp://data.pdbj.org/pub/pdb/validation_reports/le/3ley	HTTPS FTP

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Related structure data

Related structure data	3lesC 3levC 3lexC 1tji C: citing same article (ref.)
Similar structure data	4hgw-d 3i2c-d 1mjj-1 5bk3-2 4jn1-d 5uix-d 5dlm-1 4k3d-2 5mu2-1 4k8r-2 6dwc-2 6bzw-4 4ojf-d 1m71-d 4yhi-1 6nov-2 6mns-1 1f90-d 1fl6-1 1y0l-1 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 (2) #170 - Feb 2014 Broadly Neutralizing Antibodies similarity (2) #62 - Feb 2005 Major Histocompatibility Complex similarity (2)

Deposited unit

H: 6a7 Antibody Heavy Chain

L: 6a7 Antibody Light Chain

P: Envelope glycoprotein gp41

hetero molecules

49.3 kDa, 3 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)	36.249, 80.160, 72.139
Angle α, β, γ (deg.)	90.00, 97.07, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	6a7 Antibody Heavy Chain Mass: 23891.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma / Cell line: myeloma cell line FO / Strain: BALB/c
#2: Antibody	6a7 Antibody Light Chain Mass: 24198.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma / Cell line: myeloma cell line FO / Strain: BALB/c
#3: Protein/peptide	Envelope glycoprotein gp41 Mass: 986.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HIV-1 gp41 peptide / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9IJQ0
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.13 Å³/Da / Density % sol: 42.27 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 31.5 % PEG 1000, 0.2 M Zn(CH3COO)2, 0.1 M CH3COONA PH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
Detector	Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 2, 2009
Radiation	Monochromator: SI (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.98→50 Å / Num. obs: 26922 / % possible obs: 96.7 % / Observed criterion σ(I): 5 / B_iso Wilson estimate: 29.3 Å² / R_sym value: 0.081 / Net I/σ(I): 31.5
Reflection shell	Resolution: 1.98→2.05 Å / Mean I/σ(I) obs: 5.2 / R_sym value: 0.342 / % possible all: 86.9

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Processing

Software

Name	Version	Classification
PHENIX		refinement
PDB_EXTRACT	3.005	data extraction
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.99→27.1 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.2 / σ(F): 0.05 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.215	1916	7.38 %
R_work	0.177	-	-
obs	0.18	25977	92 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 50.67 Å² / k_sol: 0.32 e/Å³

Displacement parameters

B_iso mean: 41.75 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	7.708 Å²	0 Å²	5.834 Å²
2-	-	0.711 Å²	-0 Å²
3-	-	-	-8.419 Å²

Refinement step

Cycle: LAST / Resolution: 1.99→27.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3402	0	3	331	3736

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	3491
X-RAY DIFFRACTION	f_angle_d	0.768	4756
X-RAY DIFFRACTION	f_dihedral_angle_d	15.031	1215
X-RAY DIFFRACTION	f_chiral_restr	0.051	542
X-RAY DIFFRACTION	f_plane_restr	0.003	598

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 (%)
1.988-2.038	0.311	89	0.223	1125	X-RAY DIFFRACTION	60
2.038-2.093	0.258	123	0.199	1547	X-RAY DIFFRACTION	84
2.093-2.155	0.269	127	0.196	1678	X-RAY DIFFRACTION	90
2.155-2.224	0.257	142	0.204	1703	X-RAY DIFFRACTION	92
2.224-2.304	0.314	133	0.203	1721	X-RAY DIFFRACTION	93
2.304-2.396	0.248	145	0.197	1773	X-RAY DIFFRACTION	95
2.396-2.505	0.293	146	0.201	1769	X-RAY DIFFRACTION	95
2.505-2.637	0.253	134	0.205	1771	X-RAY DIFFRACTION	95
2.637-2.802	0.253	141	0.202	1801	X-RAY DIFFRACTION	96
2.802-3.018	0.246	147	0.197	1839	X-RAY DIFFRACTION	98
3.018-3.321	0.19	147	0.171	1819	X-RAY DIFFRACTION	98
3.321-3.801	0.219	146	0.154	1825	X-RAY DIFFRACTION	98
3.801-4.784	0.156	147	0.138	1838	X-RAY DIFFRACTION	98
4.784-27.098	0.18	149	0.173	1852	X-RAY DIFFRACTION	96

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	1.464	-0.5831	-2.0358	0.9435	0.068	2.1133	-0.1758	0.2695	-0.1441	0.4536	0.0109	0.1885	-0.2362	-0.5715	0.2159	0.334	0.0663	-0.0174	0.3294	-0.0628	0.2085	6.897	-21.0727	3.8943
2	1.7552	0.1544	-1.3752	1.715	0.8551	2.4446	-0.0877	0.176	-0.1769	-0.0211	-0.0457	-0.0455	-0.0318	0.1306	0.1253	0.1866	0.0757	-0.0194	0.2225	-0.0281	0.1603	14.1935	-19.9172	6.3434
3	2.9695	-1.7733	-1.865	2.027	1.9544	3.6864	0.1121	-0.1916	0.4271	-0.2699	0.073	-0.0795	-0.2044	-0.0988	-0.0859	0.3545	-0.0338	0.0687	0.2664	-0.001	0.3382	-10.8774	-15.9718	38.801
4	1.701	0.2218	-0.5834	1.9502	0.1116	3.817	-0.0771	0.0758	-0.0143	-0.0552	0.0877	0.1727	0.2411	-0.5177	-0.0159	0.1588	-0.0017	-0.0393	0.2591	0.0351	0.1592	-7.6121	-18.1842	30.578
5	2.6799	0.1339	-1.0719	1.0933	0.9517	2.463	0.4534	-0.057	0.4009	-0.2256	-0.0362	0.0137	-0.5937	0.0266	-0.4147	0.5041	-0.0474	0.1617	0.2124	-0.0085	0.2759	18.6894	2.1866	12.3026
6	1.6452	0.15	-1.7461	0.6355	-0.3906	3.3416	0.2205	-0.0276	0.2115	-0.0766	0.0793	0.0819	-0.2631	0.1191	-0.2693	0.2345	0.004	-0.0061	0.1466	-0.0469	0.1799	7.3563	-8.486	27.3458
7	1.694	0.018	-1.8577	1.5019	1.7493	2.2713	0.0569	-0.4196	0.1974	-0.0329	0.1219	-0.0296	0.0404	0.4519	-0.1763	0.1353	0.0298	-0.041	0.2736	-0.0191	0.1914	4.5769	-11.7083	40.1609
8	0.6578	-0.8061	-0.7898	0.1273	0.4765	1.9841	-0.1801	-0.4046	0.0398	0.2527	0.2906	-0.0284	0.1878	0.7346	-0.0704	0.3182	0.0516	0.007	0.4012	-0.0142	0.1814	-1.8486	-16.5386	51.3723
9	0.4364	-0.0973	0.1441	-0.0066	-0.1112	0.1656	-0.15	0.3061	0.1169	-0.485	0.483	0.4176	-0.4887	-0.483	-0.33	0.5462	0.0721	0.0455	0.5343	0.0628	0.33	18.6053	-4.4647	-4.9447

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN H AND RESID 1:32
2	X-RAY DIFFRACTION	2	CHAIN H AND RESID 33:121
3	X-RAY DIFFRACTION	3	CHAIN H AND RESID 122:139
4	X-RAY DIFFRACTION	4	CHAIN H AND RESID 140:220
5	X-RAY DIFFRACTION	5	CHAIN L AND RESID 1:82
6	X-RAY DIFFRACTION	6	CHAIN L AND RESID 83:141
7	X-RAY DIFFRACTION	7	CHAIN L AND RESID 142:188
8	X-RAY DIFFRACTION	8	CHAIN L AND RESID 189:219
9	X-RAY DIFFRACTION	9	CHAIN P AND RESID 659:668

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