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

ID or keywords:

Entry

Database: PDB / ID: 3mob

Title

Crystal structure of the neutralizing HIV antibody 2F5 Fab fragment (recombinantly produced Fab) 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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 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	Sep 6, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.3	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3mob.cif.gz	190.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3mob.ent.gz	152.6 KB	Display	PDB format
PDBx/mmJSON format	3mob.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3mob_validation.pdf.gz	444.9 KB	Display	wwPDB validaton report
Full document	3mob_full_validation.pdf.gz	452 KB	Display
Data in XML	3mob_validation.xml.gz	21.9 KB	Display
Data in CIF	3mob_validation.cif.gz	29.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mo/3mob ftp://data.pdbj.org/pub/pdb/validation_reports/mo/3mob	HTTPS FTP

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Related structure data

Related structure data	3mnwC 3mnzC 3mo1C 3moaC 3modC 1tjhS 3mnv C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1u91-d 3mod-d 5dd0-d 6fy3-2 6o3g-3 4s2s-2 2p8p-d 3moa-d 6mtp-1 3lev-3 6o3l-2 1tjh-d 6fy2-1 2a6d-2 6o3g-1 4ris-d 6o3j-1 6o3g-4 1u8m-d 3u46-2 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)	58.505, 64.976, 173.046
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. 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.: 93 / 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: 3.29 Å³/Da / Density % sol: 62.65 %
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. 0.5 uL protein + 0.35 uL drop., 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 / Date: Aug 10, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.6→43.5 Å / Num. all: 21061 / Num. obs: 21061 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / R_merge(I) obs: 0.094 / Net I/σ(I): 10.8

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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: 2.6→43.478 Å / SU ML: 0.44 / σ(F): 0.37 / Phase error: 23.47 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2356	1990	9.48 %
R_work	0.1902	-	-
obs	0.1946	20983	99.81 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 46.277 Å² / k_sol: 0.342 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.4905 Å²	0 Å²	-0 Å²
2-	-	4.0835 Å²	0 Å²
3-	-	-	-5.574 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→43.478 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3477	0	0	93	3570

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.026	3564
X-RAY DIFFRACTION	f_angle_d	1.365	4855
X-RAY DIFFRACTION	f_dihedral_angle_d	16.3	1271
X-RAY DIFFRACTION	f_chiral_restr	0.121	564
X-RAY DIFFRACTION	f_plane_restr	0.012	617

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 (%)
2.6-2.665	0.3278	138	0.2573	1332	X-RAY DIFFRACTION	100
2.665-2.7371	0.3479	141	0.2531	1331	X-RAY DIFFRACTION	100
2.7371-2.8176	0.3045	137	0.2336	1331	X-RAY DIFFRACTION	100
2.8176-2.9085	0.275	141	0.2325	1337	X-RAY DIFFRACTION	100
2.9085-3.0125	0.3116	136	0.2432	1321	X-RAY DIFFRACTION	100
3.0125-3.133	0.2907	143	0.2298	1350	X-RAY DIFFRACTION	100
3.133-3.2756	0.2939	140	0.2235	1337	X-RAY DIFFRACTION	100
3.2756-3.4482	0.2501	142	0.2069	1346	X-RAY DIFFRACTION	100
3.4482-3.6641	0.2758	141	0.1776	1353	X-RAY DIFFRACTION	100
3.6641-3.9469	0.1936	142	0.1713	1341	X-RAY DIFFRACTION	100
3.9469-4.3437	0.1906	142	0.1465	1371	X-RAY DIFFRACTION	100
4.3437-4.9715	0.1524	146	0.1278	1379	X-RAY DIFFRACTION	100
4.9715-6.2606	0.1919	146	0.1518	1390	X-RAY DIFFRACTION	100
6.2606-43.4836	0.2055	155	0.1715	1474	X-RAY DIFFRACTION	99

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	2.4617	3.7478	-1.4142	9.7105	-6.9178	6.4758	1.0819	0.1032	-0.6466	0.6263	-1.1389	0.4513	-2.0193	0.439	0.061	0.3548	-0.0045	0.024	0.2854	-0.0276	0.3434	-0.8957	0.2532	-1.2677
2	2.4414	0.5586	-0.9895	0.9226	-0.0387	0.5894	-0.0238	-0.0328	0.1825	0.0037	0.1161	0.0143	0.0419	0.0146	-0.069	0.2233	-0.0071	0.0112	0.1857	0.0367	0.2061	4.5784	-6.3346	-10.8215
3	3.32	0.1291	2.4377	0.246	-0.4805	4.1691	0.1125	-0.2048	-0.8802	0.0711	0.213	-0.1551	0.1038	-0.2406	-0.2508	0.343	0.027	0.077	0.2639	-0.0506	0.3648	6.8171	-17.7902	-11.5288
4	0.441	1.0335	-0.6333	2.4718	-1.6542	1.1142	-0.0567	0.0015	0.0328	-0.0744	0.1264	-0.1538	0.1273	-0.0313	-0.0307	0.1727	0.0153	0.0237	0.2291	0.0113	0.2205	6.1965	-8.259	-10.0143
5	0.7079	0.6654	-0.028	1.0524	-0.3012	0.677	0.1561	-0.1439	-0.1189	0.2116	-0.2572	-0.3179	-0.172	0.107	0.1115	0.2368	0.0111	-0.0303	0.2118	0.0367	0.2593	-1.0264	-6.8813	-8.8569
6	2.7893	-0.62	0.6508	1.3778	-0.1867	0.6556	0.8252	0.172	-0.6008	-0.3601	-0.1366	-0.0395	-0.0731	0.0691	-0.444	0.4141	0.0577	-0.0493	0.2874	0.1036	0.3848	-8.8046	18.5318	-44.1125
7	4.5267	1.6811	-0.0474	0.6786	0.191	0.8315	-0.1039	-0.1439	-0.067	-0.3784	-0.1154	-0.0148	-0.4455	0.0558	0.2092	0.3822	-0.0004	0.0128	0.2527	0.0486	0.2994	0.4414	14.7431	-34.8936
8	1.1924	0.8333	0.0511	2.0369	-0.8873	0.5812	-0.1871	-0.2919	-0.0953	0.0338	0.0421	0.1499	-0.1275	-0.119	0.0565	0.3628	0.0659	0.0202	0.379	0.0729	0.3362	-6.3928	18.1027	-31.0556
9	2.1893	0.6775	-0.0927	0.4645	-0.3007	0.7624	-0.1935	-0.0271	-0.0597	0.0389	0.0649	-0.0806	-0.2308	-0.0928	0.1537	0.4097	0.0223	0.0096	0.2537	0.0508	0.3718	-3.1513	21.5106	-35.2312
10	2.5929	-2.0912	-0.6431	5.4513	-3.9736	5.5213	0.2991	-0.0024	-0.3039	0.0594	0.4623	0.669	-0.6024	0.2131	-0.5671	0.4621	-0.0383	-0.0668	0.3421	0.052	0.3652	-6.5197	26.1544	-45.9876
11	5.0944	-4.637	3.8636	9.7786	-6.3144	4.3895	0.2041	1.5457	0.0839	-1.0866	-0.4572	0.2947	0.481	0.1535	0.239	0.3885	-0.0614	0.0619	0.6334	0.0941	0.3294	-15.478	-12.7741	-23.1617
12	0.7796	0.1517	0.867	6.2352	-1.6658	1.4804	0.0874	0.0669	-0.1852	-0.8489	0.3434	1.1134	0.2831	-0.7031	-0.5202	0.3135	-0.1041	-0.0143	0.6177	0.1138	0.2969	-22.522	-10.4638	-18.8236
13	1.8286	0.8971	0.1761	3.7098	0.5233	0.3583	-0.0868	0.0949	0.2327	0.0358	-0.0067	0.6331	-0.0164	0.0274	0.0306	0.2751	-0.0412	-0.0134	0.308	0.0593	0.3041	-12.3575	-7.0117	-12.1667
14	0.7876	-0.3492	0.4522	1.9914	-0.1984	1.8702	-0.0707	-0.1691	0.0495	0.1801	0.4736	0.3336	0.1479	-0.7224	-0.3646	0.1833	-0.0327	-0.017	0.3296	0.1339	0.2534	-19.9808	-11.2085	-8.3419
15	1.0581	-1.432	0.2594	3.4028	-1.6678	1.1642	0.0713	0.2166	-0.0401	-0.5454	0.1165	0.1192	0.1731	-0.1959	-0.1852	0.2457	-0.0439	-0.0351	0.3278	0.0989	0.2297	-14.1546	-7.5165	-15.9523
16	3.2782	-1.0247	0.6235	0.3333	-0.0519	1.4182	0.1441	-0.2841	0.0725	-0.1573	0.1619	0.1359	-0.2729	-0.1671	-0.2764	0.3047	-0.0109	0.0163	0.2416	0.0857	0.2848	-11.728	8.5381	-41.4875
17	0.4659	-0.0291	-0.5807	0.1883	0.0954	0.728	-0.1191	-0.1484	-0.3165	-0.1222	-0.1022	0.4066	-0.103	-0.0437	0.1959	0.5768	0.0328	-0.0733	0.2774	0.0501	0.4971	-4.6081	-0.4844	-47.512
18	1.6457	-0.544	0.8753	0.6141	-0.3715	1.3591	0.0119	-0.4115	-0.0974	-0.0882	0.1094	0.0952	-0.2742	0.1167	-0.1009	0.4194	0.0035	-0.0025	0.2846	0.0331	0.2701	-9.5137	8.4115	-37.1268
19	1.949	0.1036	-0.3729	0.6809	-1.0036	2.3641	-0.0281	0.1366	-0.4956	-0.4997	-0.0375	0.2017	0.2366	-0.011	-0.0282	0.5026	-0.0782	0.0011	0.3378	0.0744	0.3599	-8.626	4.3074	-51.6787
20	5.7358	3.9967	-4.0406	5.4688	-3.3994	2.9703	-0.4089	0.953	-0.3057	-0.576	0.3816	-0.2169	0.0628	-0.7939	-0.0297	0.4653	-0.02	-0.1143	0.4369	0.0858	0.3402	-15.1396	7.4549	-51.2532
21	3.4666	5.1844	4.9242	7.9018	7.7267	8.8755	0.4264	0.2328	-0.8998	-0.4514	0.8163	-1.6257	0.1954	0.0702	-0.9395	0.4058	0.0464	0.058	0.2754	-0.0747	0.4179	-1.7111	-26.2435	-12.7418
22	8.4529	-0.0146	1.9218	1.1911	-2.4491	5.6925	0.1667	0.1805	-1.369	-1.0857	0.2482	-0.3388	0.4371	-0.4385	-0.198	0.4299	0.0562	0.1367	0.2771	0.1492	0.5725	-4.6035	-24.1785	-2.4877

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain H and resid 1:6)
2	X-RAY DIFFRACTION	2	(chain H and resid 7:53)
3	X-RAY DIFFRACTION	3	(chain H and resid 54:64)
4	X-RAY DIFFRACTION	4	(chain H and resid 65:100)
5	X-RAY DIFFRACTION	5	(chain H and resid 100A:117)
6	X-RAY DIFFRACTION	6	(chain H and resid 118:135)
7	X-RAY DIFFRACTION	7	(chain H and resid 136:148)
8	X-RAY DIFFRACTION	8	(chain H and resid 149:171)
9	X-RAY DIFFRACTION	9	(chain H and resid 172:209)
10	X-RAY DIFFRACTION	10	(chain H and resid 210:214)
11	X-RAY DIFFRACTION	11	(chain L and resid 2:11)
12	X-RAY DIFFRACTION	12	(chain L and resid 12:28)
13	X-RAY DIFFRACTION	13	(chain L and resid 29:45)
14	X-RAY DIFFRACTION	14	(chain L and resid 46:76)
15	X-RAY DIFFRACTION	15	(chain L and resid 77:106)
16	X-RAY DIFFRACTION	16	(chain L and resid 107:149)
17	X-RAY DIFFRACTION	17	(chain L and resid 150:161)
18	X-RAY DIFFRACTION	18	(chain L and resid 162:186)
19	X-RAY DIFFRACTION	19	(chain L and resid 187:198)
20	X-RAY DIFFRACTION	20	(chain L and resid 199:214)
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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Yorodumi