PDB-3mod: Crystal structure of the neutralizing HIV antibody 2F5 Fab fragme...

ID or keywords:

Entry

Database: PDB / ID: 3mod

Title

Crystal structure of the neutralizing HIV antibody 2F5 Fab fragment (recombinantly produced IgG) with 11 aa gp41 MPER-derived peptide

Components

ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN
ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN
gp41 MPER-derived peptide

Keywords

IMMUNE SYSTEM / HIV-1 / HIV gp41 MPER / 13H11 / 2F5 / Z13 / 4E10 / Fab antibody

Function / homology

Function and homology information

Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane ...
Similarity search - Function

Biological species

Homo sapiens (human)

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Nicely, N.I. / Dennison, S.M. / Kelsoe, G. / Liao, H.-X. / Alam, S.M. / Haynes, B.F.

Citation

Journal: To be Published
Title: Crystal Structure of a Non-Neutralizing HIV-1 gp41 Envelope Antibody Demonstrates Neutralization Mechanism of gp41 Antibodies
Authors: Nicely, N.I. / Dennison, S.M. / Kelsoe, G. / Ueda, Y. / Liao, H.-X. / Alam, S.M. / Haynes, B.F.

History

Deposition	Apr 22, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 17, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 5, 2014	Group: Source and taxonomy
Revision 1.3	Sep 6, 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_conn / struct_ref_seq Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3mod.cif.gz	193.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3mod.ent.gz	155 KB	Display	PDB format
PDBx/mmJSON format	3mod.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3mod_validation.pdf.gz	435.4 KB	Display	wwPDB validaton report
Full document	3mod_full_validation.pdf.gz	438.8 KB	Display
Data in XML	3mod_validation.xml.gz	20.2 KB	Display
Data in CIF	3mod_validation.cif.gz	29.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mo/3mod ftp://data.pdbj.org/pub/pdb/validation_reports/mo/3mod	HTTPS FTP

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Related structure data

Related structure data	3mnwC 3mnzC 3mo1C 3moaC 3mobC 1tjhS 3mnv C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3mob-d 1tjh-d 1u91-d 4s2s-2 6o3g-1 6o3g-4 6o3j-1 4o5l-d 3moa-d 6o3g-3 6o3l-2 4yaq-2 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 (7) #62 - Feb 2005 Major Histocompatibility Complex similarity (7) #170 - Feb 2014 Broadly Neutralizing Antibodies similarity (6) #252 - Dec 2020 Hepatitis C Virus Protease/Helicase similarity (1)

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 (7)
#62 - Feb 2005
Major Histocompatibility Complex
similarity (7)
#170 - Feb 2014
Broadly Neutralizing Antibodies
similarity (6)
#252 - Dec 2020
Hepatitis C Virus Protease/Helicase
similarity (1)

Deposited unit

P: gp41 MPER-derived peptide

L: ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN

H: ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN

49.9 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)	58.826, 64.434, 178.982
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein/peptide	gp41 MPER-derived peptide Mass: 1372.611 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Chain P is a chemically synthesized peptide of sequence derived from the membrane proximal external region of gp41 Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04580*PLUS
#2: Antibody	ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN Mass: 23305.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T CELL / Organ (production host): KIDNEY / Production host: Homo sapiens (human)
#3: Antibody	ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN Mass: 25257.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T CELL / Organ (production host): KIDNEY / Production host: Homo sapiens (human)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 215 / 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: 3.4 Å³/Da / Density % sol: 63.78 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 5.6 Details: 20% isopropanol, 20% PEG 4000, 0.1 M Na citrate pH 5.6. Drop = 0.5 uL protein + 0.35 uL reservoir., VAPOR DIFFUSION, temperature 298K

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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
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.2→43.4 Å / Num. all: 35419 / Num. obs: 34923 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / R_merge(I) obs: 0.076 / Net I/σ(I): 11.4

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Processing

Software

Name	Version	Classification
PHENIX		model building
PHENIX	(phenix.refine: dev_271)	refinement
d*TREK		data reduction
d*TREK		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1TJH

1tjh

Resolution: 2.2→43.4 Å / SU ML: 0.33 / σ(F): 0.12 / Phase error: 22.13 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2145	1987	5.72 %
R_work	0.1844	-	-
obs	0.1861	34750	98.07 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 34.553 Å² / k_sol: 0.334 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.5348 Å²	0 Å²	-0 Å²
2-	-	0.8793 Å²	0 Å²
3-	-	-	-7.414 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→43.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3511	0	0	215	3726

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.026	3598
X-RAY DIFFRACTION	f_angle_d	1.298	4900
X-RAY DIFFRACTION	f_dihedral_angle_d	15.597	1284
X-RAY DIFFRACTION	f_chiral_restr	0.131	569
X-RAY DIFFRACTION	f_plane_restr	0.009	623

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 (%)
2.2-2.255	0.3248	141	0.2314	2336	X-RAY DIFFRACTION	99
2.255-2.316	0.2709	140	0.2176	2315	X-RAY DIFFRACTION	99
2.316-2.3841	0.25	142	0.2067	2325	X-RAY DIFFRACTION	99
2.3841-2.4611	0.2821	140	0.2094	2327	X-RAY DIFFRACTION	99
2.4611-2.549	0.2432	141	0.2113	2332	X-RAY DIFFRACTION	99
2.549-2.6511	0.2849	142	0.2083	2335	X-RAY DIFFRACTION	99
2.6511-2.7717	0.2543	140	0.2124	2319	X-RAY DIFFRACTION	99
2.7717-2.9178	0.2531	142	0.2098	2343	X-RAY DIFFRACTION	98
2.9178-3.1006	0.2322	143	0.2037	2331	X-RAY DIFFRACTION	98
3.1006-3.3399	0.2154	141	0.1949	2324	X-RAY DIFFRACTION	99
3.3399-3.6758	0.1939	141	0.1704	2357	X-RAY DIFFRACTION	98
3.6758-4.2073	0.1974	143	0.1481	2337	X-RAY DIFFRACTION	97
4.2073-5.2993	0.1335	144	0.1199	2365	X-RAY DIFFRACTION	97
5.2993-43.4523	0.1661	147	0.1672	2417	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	7.6834	0.3342	6.9869	2.1954	1.3031	7.4559	0.3988	0.2305	-1.0598	0.0766	0.1482	0.2581	0.5987	0.0303	-0.5354	0.3275	-0.0211	-0.0636	0.2944	-0.0633	0.385	27.2684	-0.0718	1.1252
2	0.2823	0.106	-0.512	1.2476	-0.2506	1.8971	0.012	0.0109	-0.1415	-0.1218	0.0038	-0.1913	0.1182	0.1355	0.0145	0.2941	0.0056	0.0067	0.2739	0.0204	0.2793	38.7812	2.7996	11.323
3	2.0252	-1.2555	0.3474	1.0502	-0.1291	0.6527	0.0641	-0.029	0.0476	0.0519	0.0615	0.0502	-0.117	-0.0062	-0.0512	0.1718	0.0104	-0.0138	0.1871	0.0342	0.1961	30.1639	11.1757	11.1638
4	1.9185	-0.9079	0.2876	1.9449	-0.8301	0.2641	-0.084	0.0872	0.2141	0.0959	0.0123	-0.1278	-0.0507	-0.0428	0.0737	0.2454	-0.0169	-0.0373	0.24	0.0141	0.2505	39.1599	12.6524	9.84
5	1.5206	-0.9473	0.6065	1.3898	-0.6106	0.4536	0.0823	0.1788	0.0309	-0.0653	-0.0665	-0.0324	0.0196	0.0591	-0.0039	0.2014	-0.0161	-0.0003	0.2424	0.0364	0.1951	28.8166	9.2121	9.5036
6	1.1744	0.2045	1.1398	1.0165	-0.0881	1.0541	0.2163	-0.5605	0.2505	0.5344	-0.1496	0.0263	0.2463	-0.1898	-0.0271	0.465	-0.0244	0.0966	0.2906	-0.0062	0.28	25.5035	-15.7033	43.25
7	1.3252	0.6088	0.0354	0.2679	-0.0676	0.478	-0.0714	0.1232	-0.0427	0.0328	-0.0617	0.0639	-0.0401	-0.0131	0.0813	0.3787	-0.0135	-0.0112	0.2132	0.0101	0.2515	27.9963	-13.5928	36.2664
8	0.8653	0.4036	-0.2439	1.0259	-0.5189	0.2426	-0.1815	0.2651	-0.057	-0.1398	0.154	-0.0782	0.1541	-0.0476	0.0219	0.392	-0.0418	-0.045	0.2614	-0.0165	0.2754	25.1985	-13.8524	33.5496
9	1.4117	-0.5712	-0.7563	0.3095	-0.0901	0.8389	-0.1334	0.1622	-0.1699	-0.2177	0.0908	-0.0226	0.4003	-0.0688	0.078	0.4	-0.0334	0.0248	0.197	0.0268	0.3023	24.6318	-22.6809	36.8047
10	3.1211	-1.5684	3.2683	8.5467	-1.4038	3.4109	-0.0185	-0.5717	0.0272	0.7515	0.8019	-0.7497	-1.0767	-0.9945	-0.5398	0.5532	0.0732	-0.0737	0.3974	0.1023	0.1983	21.5589	-24.6433	50.7651
11	2.8165	2.8265	-1.4688	3.5512	-0.5635	1.372	0.3048	-0.5341	0.0955	0.4503	-0.1749	0.2174	-0.2723	-0.1921	-0.1281	0.3202	0.0376	0.0134	0.4084	0.0846	0.2906	10.2856	13.5184	20.4906
12	1.94	0.3855	-0.6561	0.4343	-0.2906	1.1923	-0.0972	0.0444	-0.1173	-0.1196	0.2155	0.1135	0.0835	-0.3569	-0.1179	0.1489	-0.0039	-0.0161	0.2517	0.0679	0.2192	13.4139	9.3103	9.4048
13	0.3376	-0.1075	-0.084	0.1574	-0.4906	0.8086	-0.021	-0.1959	-0.1878	-0.0066	0.0488	0.0077	0.1098	-0.246	-0.0424	0.1653	0.0006	-0.0169	0.2766	0.0548	0.2179	11.5544	9.1143	14.6462
14	3.0239	2.1688	-0.4119	2.4796	-0.9602	0.4848	0.3591	-0.8106	-0.1891	0.6283	-0.3829	-0.0464	-0.2771	0.0048	0.0498	0.2762	0.0095	0.0223	0.4009	0.1086	0.2942	16.6109	9.4189	19.9154
15	0.6432	0.2462	-0.5089	0.2643	-0.1536	0.8949	-0.1465	-0.068	0.0183	0.1787	0.2221	0.013	0.0356	-0.171	-0.0784	0.2796	0.0013	-0.0135	0.2091	0.0569	0.2072	18.2885	-6.9352	43.7015
16	0.145	0.1267	0.2701	0.968	1.0146	1.122	-0.1424	0.2337	-0.011	0.2022	0.1353	0.4888	0.2864	-0.5803	-0.0234	0.5023	0.0107	0.0208	0.2462	0.0265	0.2778	24.6795	2.1757	48.5988
17	0.7382	-0.0299	1.3481	-0.0068	-0.4372	1.785	-0.0488	0.1645	0.1106	0.0009	0.0739	0.0083	0.1707	0.1067	-0.0248	0.3355	-0.0305	-0.0305	0.3213	0.025	0.2306	18.4029	-6.8893	36.668
18	2.738	-1.3236	-0.3912	1.2071	0.291	0.2312	-0.2999	0.3794	-0.0375	0.4698	0.0843	-0.038	0.3373	0.22	0.156	0.4543	0.0318	-0.0427	0.2457	0.0051	0.2207	26.6241	-4.9106	56.8685
19	4.7536	0.5348	-0.3227	1.1283	1.1928	1.5744	-0.2332	-0.7068	0.8159	0.2048	-0.14	0.2712	-0.1072	-0.8933	0.2064	0.4752	0.0333	0.0584	0.5365	0.0391	0.361	8.3618	-0.1649	46.169
20	4.3599	1.371	-0.514	1.9216	-3.7424	8.6211	0.8691	-0.3967	-1.0035	-0.2189	0.2277	0.2221	0.0261	-0.7205	-0.8799	0.4986	-0.0927	-0.0255	0.2652	0.1012	0.2916	21.1866	-10.4595	59.8832
21	1.1994	0.6445	-0.4811	3.2265	3.4465	6.4919	0.5054	0.139	0.2817	-0.0309	0.3891	-0.668	-0.0962	0.4672	-0.7344	0.2689	-0.0748	-0.0059	0.3073	-0.0402	0.379	27.5474	27.3404	11.8227
22	9.6041	-3.0092	3.3913	1.7484	-0.2788	2.6066	-0.4897	0.3669	0.8922	0.3196	-0.1708	-0.1368	-0.2772	-0.1349	0.5056	0.2689	-0.0603	-0.032	0.2583	0.0295	0.3165	24.9079	24.0251	1.845

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain H and resid 1:5)
2	X-RAY DIFFRACTION	2	(chain H and resid 6:30)
3	X-RAY DIFFRACTION	3	(chain H and resid 31:54)
4	X-RAY DIFFRACTION	4	(chain H and resid 55:82A)
5	X-RAY DIFFRACTION	5	(chain H and resid 82B:114)
6	X-RAY DIFFRACTION	6	(chain H and resid 115:133)
7	X-RAY DIFFRACTION	7	(chain H and resid 134:150)
8	X-RAY DIFFRACTION	8	(chain H and resid 151:178)
9	X-RAY DIFFRACTION	9	(chain H and resid 179:209)
10	X-RAY DIFFRACTION	10	(chain H and resid 210:218)
11	X-RAY DIFFRACTION	11	(chain L and resid 1:29)
12	X-RAY DIFFRACTION	12	(chain L and resid 30:69)
13	X-RAY DIFFRACTION	13	(chain L and resid 70:93)
14	X-RAY DIFFRACTION	14	(chain L and resid 94:107)
15	X-RAY DIFFRACTION	15	(chain L and resid 108:150)
16	X-RAY DIFFRACTION	16	(chain L and resid 151:161)
17	X-RAY DIFFRACTION	17	(chain L and resid 162:184)
18	X-RAY DIFFRACTION	18	(chain L and resid 185:194)
19	X-RAY DIFFRACTION	19	(chain L and resid 195:207)
20	X-RAY DIFFRACTION	20	(chain L and resid 208:214)
21	X-RAY DIFFRACTION	21	(chain P and resid 660:664)
22	X-RAY DIFFRACTION	22	(chain P and resid 665:669)

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