PDB-4g6f: Crystal Structure of 10E8 Fab in Complex with an HIV-1 gp41 Peptide

ID or keywords:

Entry

Database: PDB / ID: 4g6f

Title

Crystal Structure of 10E8 Fab in Complex with an HIV-1 gp41 Peptide

Components

10E8 Heavy Chain
10E8 Light Chain
gp41 MPER Peptide

Keywords

IMMUNE SYSTEM / Immunoglobulin / MPER / Antibody

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Ofek, G. / Huang, J. / Connors, M. / Kwong, P.D.

Citation

Journal: Nature / Year: 2012
Title: Broad and potent neutralization of HIV-1 by a gp41-specific human antibody.
Authors: Huang, J. / Ofek, G. / Laub, L. / Louder, M.K. / Doria-Rose, N.A. / Longo, N.S. / Imamichi, H. / Bailer, R.T. / Chakrabarti, B. / Sharma, S.K. / Alam, S.M. / Wang, T. / Yang, Y. / Zhang, B. ...

History

Deposition	Jul 19, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 26, 2012	Provider: repository / Type: Initial release
Revision 1.1	Dec 12, 2012	Group: Database references
Revision 1.2	Sep 16, 2015	Group: Refinement description
Revision 1.3	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.4	Oct 30, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4g6f.cif.gz	378.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4g6f.ent.gz	309.4 KB	Display	PDB format
PDBx/mmJSON format	4g6f.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4g6f_validation.pdf.gz	464.8 KB	Display	wwPDB validaton report
Full document	4g6f_full_validation.pdf.gz	475.6 KB	Display
Data in XML	4g6f_validation.xml.gz	39.5 KB	Display
Data in CIF	4g6f_validation.cif.gz	57.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g6/4g6f ftp://data.pdbj.org/pub/pdb/validation_reports/g6/4g6f	HTTPS FTP

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Related structure data

Similar structure data	4pl5-1 6isp-d 1k6m-d 1pkq-d 6g5k-d 3ghb-d 3kse-d 1y4s-d 4m1d-d 2jd4-d 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

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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

H: 10E8 Heavy Chain

B: 10E8 Heavy Chain

L: 10E8 Light Chain

D: 10E8 Light Chain

P: gp41 MPER Peptide

F: gp41 MPER Peptide

106 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

2

H: 10E8 Heavy Chain

L: 10E8 Light Chain

P: gp41 MPER Peptide

B: 10E8 Heavy Chain

D: 10E8 Light Chain

F: gp41 MPER Peptide

defined by software
106 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	68.021, 71.432, 129.236
Angle α, β, γ (deg.)	90.00, 104.50, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	10E8 Heavy Chain Mass: 25447.475 Da / Num. of mol.: 2 / Fragment: Fragment of Antigen Binding Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGHV3-1505 / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Production host: Homo sapiens* (human)
#2: Antibody	10E8 Light Chain Mass: 22989.459 Da / Num. of mol.: 2 / Fragment: Fragment of Antigen Binding Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGLV3-1901 / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Production host: Homo sapiens* (human)
#3: Protein/peptide	gp41 MPER Peptide Mass: 4628.267 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.86 Å³/Da / Density % sol: 57.05 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 40% PEG 400, 0.1 M NaCitrate, 0.1 M Tris pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 200 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 10, 2011

Radiation

Monochromator: SI220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.1→50 Å / Num. obs: 61890 / % possible obs: 88.6 % / Redundancy: 2.7 % / R_merge(I) obs: 0.074 / Net I/σ(I): 12

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
2.1-2.14	1.5	0.242	1	52.2
2.14-2.18	1.6	0.271	1	61.2
2.18-2.22	1.7	0.259	1	70
2.22-2.26	1.9	0.249	1	76.6
2.26-2.31	2	0.237	1	82.9
2.31-2.37	2.2	0.233	1	87.6
2.37-2.42	2.4	0.232	1	91.1
2.42-2.49	2.6	0.22	1	94.1
2.49-2.56	2.7	0.201	1	96.2
2.56-2.65	2.9	0.175	1	96.8
2.65-2.74	3.1	0.161	1	97.1
2.74-2.85	3.2	0.138	1	97.1
2.85-2.98	3.2	0.118	1	97.3
2.98-3.14	3.2	0.105	1	96.8
3.14-3.33	3.2	0.086	1	96.5
3.33-3.59	3.1	0.076	1	96.2
3.59-3.95	3.1	0.067	1	96.5
3.95-4.52	3.1	0.059	1	95.4
4.52-5.7	3.1	0.057	1	95.2
5.7-50	3.1	0.056	1	93.7

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	1.8_1069	refinement
PDB_EXTRACT	3.11	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→42.59 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.22 / σ(F): 1.33 / Phase error: 25.09 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.218	2011	3.25 %
R_work	0.18	-	-
obs	0.181	61862	88.4 %

Solvent computation

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

Displacement parameters

B_iso mean: 51.7 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→42.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7244	0	0	484	7728

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7446
X-RAY DIFFRACTION	f_angle_d	1.064	10131
X-RAY DIFFRACTION	f_dihedral_angle_d	13.405	2641
X-RAY DIFFRACTION	f_chiral_restr	0.074	1102
X-RAY DIFFRACTION	f_plane_restr	0.005	1297

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 (%)
2.1-2.1549	0.2622	82	0.2265	2501	X-RAY DIFFRACTION	52
2.1549-2.2132	0.2929	108	0.2323	3217	X-RAY DIFFRACTION	67
2.2132-2.2783	0.3062	135	0.2312	3680	X-RAY DIFFRACTION	77
2.2783-2.3518	0.2681	131	0.218	4127	X-RAY DIFFRACTION	85
2.3518-2.4359	0.2621	150	0.2133	4360	X-RAY DIFFRACTION	90
2.4359-2.5334	0.2474	149	0.1998	4564	X-RAY DIFFRACTION	95
2.5334-2.6487	0.2238	158	0.1936	4661	X-RAY DIFFRACTION	97
2.6487-2.7883	0.2598	158	0.192	4656	X-RAY DIFFRACTION	97
2.7883-2.9629	0.2291	150	0.1875	4744	X-RAY DIFFRACTION	97
2.9629-3.1916	0.2415	156	0.1834	4653	X-RAY DIFFRACTION	97
3.1916-3.5127	0.1823	156	0.1675	4688	X-RAY DIFFRACTION	96
3.5127-4.0206	0.1983	160	0.1592	4673	X-RAY DIFFRACTION	96
4.0206-5.0643	0.1871	160	0.1503	4638	X-RAY DIFFRACTION	95
5.0643-42.593	0.2182	158	0.1931	4689	X-RAY DIFFRACTION	94

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	1.6675	0.0837	0.2263	1.5801	-0.003	0.2692	0.4283	-0.6452	-1.1778	0.9275	-0.9607	-1.0809	0.747	0.5808	-0.0116	-2.6628	1.2326	-0.3922	-0.696	-0.0689	-0.4234	54.0263	14.2755	18.1739
2	4.2112	1.994	-0.0935	3.4268	-0.5643	1.6397	-0.0026	-0.4152	-1.221	0.1603	-0.0192	0.9242	0.125	0.0257	-0.0002	0.2982	0.0175	-0.0068	0.4755	0.2544	1.1681	43.5615	3.4102	47.7764
3	2.8039	-0.6852	-0.8333	0.9403	1.2393	1.6466	-0.3062	-0.8222	-1.713	0.2799	0.0304	0.2058	0.4714	0.2263	0.3138	0.3873	0.0611	0.0303	0.6013	0.3708	1.2111	51.278	-0.6329	51.9214
4	0.2617	-0.0246	-0.0365	0.0873	-0.0317	0.2622	0.0377	0.0634	0.021	-0.0336	-0.0657	-0.0486	-0.0506	-0.2137	0	0.2178	0.0112	-0.0514	0.2543	0.0011	0.1196	33.9401	16.648	15.4822
5	2.5908	2.9962	4.4564	4.37	3.5357	2.0878	-0.0748	0.1533	0.358	0.3579	-0.0706	-0.5594	-0.1235	0.6267	0.3985	0.2556	-0.0536	-0.0266	0.5261	0.1945	0.4364	37.6426	10.974	52.6744
6	8.8414	0.3931	1.8548	4.1073	0.1005	7.4821	-0.2246	1.0471	0.5376	-0.2163	-0.0106	-0.4142	-0.5298	0.4727	0.2081	0.2166	0.0175	0.0067	0.427	0.1528	0.421	32.1595	15.8586	45.2783
7	2.0276	0.581	3.2303	3.4207	-0.0219	7.7558	-0.2876	-0.5002	0.9113	0.6994	-0.1946	-1.0829	-0.7119	1.1765	0.2814	0.4935	-0.1184	-0.2561	0.6654	0.0558	0.8074	42.3477	18.9811	58.788
8	9.6226	0.157	1.8636	5.5818	0.0185	8.3071	-0.1361	-0.5278	0.7029	0.3003	-0.0284	-0.3696	-0.5537	-0.3471	0.3023	0.2689	0.0029	-0.0124	0.3159	-0.0175	0.3879	29.0797	16.5477	55.0534
9	5.3296	5.2953	5.0332	5.8525	5.4398	5.0759	0.0364	-0.5166	-1.1338	0.8151	0.283	0.1705	1.1736	-0.807	-0.2756	0.9957	-0.0365	0.1642	0.9917	-0.028	0.5213	49.096	0.4964	-3.1853
10	9.7256	-5.1586	3.1222	6.1883	0.696	2.593	0.1392	0.4534	0.5481	-0.9549	-0.0566	-0.3433	-0.0632	0.3269	-0.0632	0.7381	-0.0441	0.0845	0.7202	0.0126	0.286	48.3866	20.073	-6.9722
11	0.2392	0.2337	0.1155	0.1018	0.0653	0.2734	0.1988	0.2211	0.0209	0.1446	-0.1898	0.0425	-0.1729	-0.2009	-0	0.2492	-0.0255	0.0677	0.0498	0.0177	0.1824	19.0469	9.2341	88.1207
12	5.1918	-2.4289	3.5376	3.8163	-3.5929	5.5244	0.0507	-0.2354	-0.2078	0.0749	0.0515	0.2881	0.2012	-0.3012	-0.1165	0.2347	0.0111	0.0229	0.2215	-0.0187	0.2466	11.361	8.5559	57.0482
13	2.1862	0.618	1.3447	2.4542	0.2217	2.2946	-0.2232	0.0683	0.3452	-0.0299	0.0773	-0.0234	-0.2151	0.1044	0.2892	0.2293	-0.0053	-0.001	0.195	-0.014	0.2536	12.0072	16.3985	51.8627
14	0.1756	0.2194	-0.0995	0.2923	0.0013	0.2348	0.0796	-0.021	-0.0762	0.099	-0.0199	0.1982	-0.0564	-0.5003	-0	0.2592	0.0307	0.0529	0.4638	0.0335	0.3054	-0.251	4.4096	90.2816
15	4.811	-1.7205	-8.5639	0.6202	3.069	2.0264	-0.6354	0.1377	-0.8947	0.5245	0.0185	0.5108	0.7022	-0.5534	0.7718	0.3543	0.072	0.1183	0.6485	0.1006	0.4886	-5.5706	5.4032	56.9599
16	7.0484	-1.1758	-3.6177	4.6279	0.3377	6.3433	-0.1871	-0.0901	-0.5025	0.1412	0.1746	0.4837	0.2717	-0.1277	0.0104	0.2211	0.0246	-0.0262	0.164	0.0596	0.3495	1.373	-0.9983	51.6821
17	0.7587	1.4058	-0.7138	2.0019	8.0004	6.9009	-0.6228	0.4527	0.2318	0.034	2.0004	-1.6431	-0.0252	-1.3715	-1.3973	0.9597	-0.1824	0.1052	1.2978	-0.0516	0.9177	20.1786	27.0669	108.4308
18	1.8672	-2.9913	-1.1433	4.8919	2.7092	8.601	-0.0692	-0.5462	-0.1282	0.4769	0.0184	0.3034	-0.2261	-0.0796	0.0453	0.5968	-0.1028	0.1064	0.5583	-0.0852	0.3607	12.9333	9.3207	112.9666

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN H AND RESID 1:124 )	H	1 - 124
2	X-RAY DIFFRACTION	2	( CHAIN H AND RESID 125:203 )	H	125 - 203
3	X-RAY DIFFRACTION	3	( CHAIN H AND RESID 204:214 )	H	204 - 214
4	X-RAY DIFFRACTION	4	( CHAIN L AND RESID 2:107 )	L	2 - 107
5	X-RAY DIFFRACTION	5	( CHAIN L AND RESID 108:137 )	L	108 - 137
6	X-RAY DIFFRACTION	6	( CHAIN L AND RESID 138:173 )	L	138 - 173
7	X-RAY DIFFRACTION	7	( CHAIN L AND RESID 174:189 )	L	174 - 189
8	X-RAY DIFFRACTION	8	( CHAIN L AND RESID 190:210 )	L	190 - 210
9	X-RAY DIFFRACTION	9	( CHAIN P AND RESID 656:669 )	P	656 - 669
10	X-RAY DIFFRACTION	10	( CHAIN P AND RESID 670:684 )	P	670 - 684
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 1:111 )	B	1 - 111
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 112:177 )	B	112 - 177
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 178:217 )	B	178 - 217
14	X-RAY DIFFRACTION	14	( CHAIN D AND RESID 2:107 )	D	2 - 107
15	X-RAY DIFFRACTION	15	( CHAIN D AND RESID 108:121 )	D	108 - 121
16	X-RAY DIFFRACTION	16	( CHAIN D AND RESID 122:209 )	D	122 - 209
17	X-RAY DIFFRACTION	17	( CHAIN F AND RESID 659:671 )	F	659 - 671
18	X-RAY DIFFRACTION	18	( CHAIN F AND RESID 672:685 )	F	672 - 685

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