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

ID or keywords:

Entry

Database: PDB / ID: 3moa

Title

Crystal structure of the neutralizing HIV antibody 2F5 Fab fragment (recombinantly produced Fab) with 17 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)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 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	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	3moa.cif.gz	197.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3moa.ent.gz	158.5 KB	Display	PDB format
PDBx/mmJSON format	3moa.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3moa_validation.pdf.gz	440 KB	Display	wwPDB validaton report
Full document	3moa_full_validation.pdf.gz	444.9 KB	Display
Data in XML	3moa_validation.xml.gz	21.7 KB	Display
Data in CIF	3moa_validation.cif.gz	31.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mo/3moa ftp://data.pdbj.org/pub/pdb/validation_reports/mo/3moa	HTTPS FTP

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Related structure data

Related structure data	3mnwC 3mnzC 3mo1C 3mobC 3modC 1tjiS 1tjh 3mnv C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3mob-d 3idm-d 4s2s-2 1u91-d 3mod-d 1u8j-d 1u8m-d 1tjh-d 4yaq-2 6o3l-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

50.7 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)	58.820, 65.229, 174.205
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: 2131.364 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.: 294 / 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: 3.3 Å³/Da / Density % sol: 62.7 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 5.6 Details: Reservoir; Hampton Research Crystal Screen 40 = 20% isopropanol, 20% PEG 4000, 100 mM Na citrate pH 5.6. Drop: 0.5 uL protein + 0.35 uL reservoir. Reservoir was NOT supplemented with 100 mM ...Details: Reservoir; Hampton Research Crystal Screen 40 = 20% isopropanol, 20% PEG 4000, 100 mM Na citrate pH 5.6. Drop: 0.5 uL protein + 0.35 uL reservoir. Reservoir was NOT supplemented with 100 mM NaCl as in Ofek et al. 2004., VAPOR DIFFUSION, temperature 298K

Crystal

Density Matthews: 3.3 Å³/Da / Density % sol: 62.7 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion / pH: 5.6
Details: Reservoir; Hampton Research Crystal Screen 40 = 20% isopropanol, 20% PEG 4000, 100 mM Na citrate pH 5.6. Drop: 0.5 uL protein + 0.35 uL reservoir. Reservoir was NOT supplemented with 100 mM ...

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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: 2.3→43.7 Å / Num. all: 30678 / Num. obs: 30678 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / R_merge(I) obs: 0.062 / Net I/σ(I): 15.4

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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: 1TJI

1tji

Resolution: 2.3→43.683 Å / SU ML: 0.3 / σ(F): 0.19 / Phase error: 20.2 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2193	1986	6.52 %
R_work	0.1839	-	-
obs	0.1862	30459	99.47 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 38.922 Å² / k_sol: 0.336 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.4653 Å²	-0 Å²	-0 Å²
2-	-	0.1352 Å²	0 Å²
3-	-	-	-2.6005 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→43.683 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3506	0	0	294	3800

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.027	3598
X-RAY DIFFRACTION	f_angle_d	1.348	4901
X-RAY DIFFRACTION	f_dihedral_angle_d	15.999	1285
X-RAY DIFFRACTION	f_chiral_restr	0.142	569
X-RAY DIFFRACTION	f_plane_restr	0.009	624

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 (%)
2.3-2.3575	0.2916	138	0.2176	1996	X-RAY DIFFRACTION	99
2.3575-2.4213	0.2466	140	0.2106	1977	X-RAY DIFFRACTION	99
2.4213-2.4925	0.256	138	0.2092	2000	X-RAY DIFFRACTION	100
2.4925-2.5729	0.2529	139	0.1946	1996	X-RAY DIFFRACTION	99
2.5729-2.6649	0.2386	140	0.2017	1998	X-RAY DIFFRACTION	99
2.6649-2.7716	0.2379	139	0.199	1988	X-RAY DIFFRACTION	100
2.7716-2.8977	0.2339	141	0.2044	2027	X-RAY DIFFRACTION	100
2.8977-3.0504	0.233	143	0.2067	2037	X-RAY DIFFRACTION	100
3.0504-3.2415	0.249	141	0.1986	2018	X-RAY DIFFRACTION	100
3.2415-3.4917	0.2236	142	0.1824	2035	X-RAY DIFFRACTION	100
3.4917-3.8429	0.2102	144	0.1706	2050	X-RAY DIFFRACTION	100
3.8429-4.3985	0.2089	143	0.1419	2052	X-RAY DIFFRACTION	100
4.3985-5.5398	0.1463	147	0.1261	2094	X-RAY DIFFRACTION	100
5.5398-43.6905	0.1744	151	0.1725	2205	X-RAY DIFFRACTION	100

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	4.2578	5.6608	4.7963	7.7547	7.0042	7.0536	0.7157	-0.0981	-0.6595	0.3273	-0.2578	-0.6643	0.9123	-0.358	-0.4807	0.2949	0.0037	-0.0581	0.2463	0.0536	0.2619	2.0615	0.1199	-0.1587
2	0.057	0.2516	0.1472	0.9281	0.2311	1.1249	-0.3425	0.0608	0.0658	-0.1279	0.0873	0.308	-0.0783	-0.265	0.1955	0.2196	-0.0289	-0.0373	0.2634	-0.0626	0.283	-12.5479	-0.495	-19.3667
3	2.2724	0.6834	-0.0942	1.4691	0.2548	0.1585	-0.1012	-0.0004	0.0261	-0.0548	0.1027	0.009	-0.0636	0.087	0.005	0.1406	-0.002	-0.0246	0.1645	-0.0228	0.14	-3.252	10.6506	-9.0241
4	0.982	0.52	-0.8482	1.9436	0.3271	1.0219	-0.0651	-0.0908	-0.0002	0.0601	-0.2077	0.3696	-0.2303	0.2279	0.1389	0.1257	0.0053	-0.052	0.1646	-0.0162	0.1392	-10.7631	9.9434	-9.1
5	0.8796	0.2624	-0.028	1.1277	-0.0254	0.0029	-0.1466	-0.0443	0.092	-0.1463	-0.019	0.1792	-0.1584	-0.2828	0.075	0.2359	-0.0231	-0.0098	0.273	-0.0387	0.1655	-1.5664	8.3798	-12.2746
6	2.3135	1.2304	0.4758	0.6893	0.244	0.1309	0.1122	-0.2025	0.0693	-0.0069	-0.189	0.2138	0.0723	-0.0213	0.0348	0.1959	-0.0009	-0.0323	0.2073	-0.0326	0.1908	2.6514	9.3008	-6.5328
7	1.162	-0.1706	0.1332	2.6178	0.6901	0.3002	0.1252	0.3134	0.2937	-0.7193	0.0177	-0.0503	-0.0043	-0.0164	-0.0846	0.4231	-0.0397	0.0566	0.1926	-0.0115	0.2433	3.8018	-16.3881	-42.3058
8	0.3962	0.2671	0.2533	0.8546	0.6787	0.7672	-0.1994	-0.1034	0.0743	0.1475	-0.0097	-0.1324	0.0738	0.053	0.1505	0.2851	0.0403	-0.017	0.2195	0.0015	0.2247	3.7698	-18.0729	-33.7272
9	2.0945	1.2912	0.3799	0.9888	0.735	1.0547	-0.2384	-0.0178	-0.004	0.0291	0.0864	0.0858	0.215	0.0703	0.1676	0.3723	0.0398	0.017	0.2229	-0.0297	0.2901	3.7897	-18.2849	-35.0977
10	3.0322	1.928	0.1523	5.0947	-1.1226	0.385	-0.7048	1.0497	-0.2523	-1.1161	0.4581	-0.0754	0.7024	-0.0116	0.2272	0.6215	-0.1242	0.0497	0.5027	-0.0942	0.2378	7.1045	-23.4339	-49.7064
11	9.3119	-4.7368	-4.0585	4.4621	3.9839	3.5614	0.111	1.4004	-0.3974	-0.4757	-0.1422	0.0437	-0.3301	-0.171	0.0681	0.2759	-0.0957	0.0646	0.4317	-0.1136	0.2712	15.3615	13.46	-23.0564
12	0.5544	-1.584	0.0387	6.3308	1.3654	1.1297	-0.0596	0.547	0.3869	-0.5525	0.4533	-1.1758	-0.0011	0.5872	-0.4429	0.1619	-0.038	0.059	0.5457	-0.1603	0.4137	26.0394	5.7039	-18.417
13	3.7521	-2.4381	0.2576	2.7628	-0.4364	2.826	0.0287	0.2245	-0.1506	-0.2877	0.3228	-0.1601	-1.1136	0.176	-0.3589	0.4903	-0.1221	0.0906	0.5076	-0.08	0.2539	14.1331	23.2585	-20.0675
14	0.6209	0.4072	0.3679	1.4504	0.3151	1.335	-0.0718	0.1081	-0.1572	-0.0173	0.1989	-0.3449	0.0004	0.3029	-0.3009	0.1071	-0.023	0.0151	0.21	-0.1045	0.2115	15.9556	9.6179	-9.0645
15	0.4112	-0.2206	0.6861	4.2651	0.5283	1.9929	0.0312	0.3434	-0.1805	0.4663	0.2812	-0.2009	0.1115	0.7351	-0.2593	0.1642	-0.0239	0.0598	0.333	-0.1435	0.3151	23.6629	6.2676	-13.3276
16	0.2419	0.4394	0.6487	1.843	1.5351	1.8593	0.0003	0.3541	-0.0474	-0.5483	0.0877	-0.3089	-0.2989	0.3973	-0.142	0.1933	-0.0902	0.0274	0.3061	-0.0699	0.207	11.4961	10.7712	-16.5364
17	1.2722	-0.3814	-0.9672	0.7255	0.2763	0.8958	-0.0209	-0.2818	0.0599	-0.2346	0.2373	-0.0841	0.0121	0.1185	-0.1888	0.317	-0.021	-0.0262	0.2441	-0.0694	0.2619	11.8186	-7.5363	-41.5091
18	0.0271	-0.129	0.2464	0.4888	-0.8736	1.5582	-0.0405	0.1204	0.1231	-0.4556	-0.1267	-0.4248	-0.1762	-0.0023	0.1556	0.4687	0.0352	0.0188	0.2367	0.0038	0.302	4.562	1.4908	-47.7978
19	0.3436	0.1002	-0.2371	1.1591	0.7569	0.8394	-0.1369	0.0039	0.2311	-0.2021	0.1377	-0.1104	0.0062	0.2123	-0.0548	0.3347	-0.0309	0.0068	0.2946	-0.0391	0.2798	11.0086	-5.3019	-42.6925
20	2.2298	0.1569	2.9747	0.6847	1.225	5.3653	0.4597	0.4913	-0.4056	0.1476	0.1031	0.0911	0.8131	0.4746	-0.4689	0.5254	0.0567	0.0085	0.3766	-0.0718	0.3267	10.145	-9.9637	-55.6267
21	5.8296	-1.4983	2.2637	5.8535	-1.7891	1.1565	-0.3111	0.032	0.1848	-2.3455	-0.2367	0.5176	1.3911	2.1882	0.5851	0.7939	0.0752	0.0013	0.7877	0.1444	0.3482	1.9144	28.3861	-16.628
22	8.1148	-3.2396	2.2658	2.1948	-1.6669	4.5791	-0.2462	0.2371	0.8633	-0.2194	0.303	-0.3932	0.1805	0.5321	-0.0402	0.2571	0.0034	-0.0433	0.3028	-0.0688	0.2898	4.2909	24.2904	-3.8125

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 6:16)
3	X-RAY DIFFRACTION	3	(chain H and resid 17:62)
4	X-RAY DIFFRACTION	4	(chain H and resid 63:82A)
5	X-RAY DIFFRACTION	5	(chain H and resid 82B:100)
6	X-RAY DIFFRACTION	6	(chain H and resid 100A:114)
7	X-RAY DIFFRACTION	7	(chain H and resid 115:133)
8	X-RAY DIFFRACTION	8	(chain H and resid 134:160)
9	X-RAY DIFFRACTION	9	(chain H and resid 161:209)
10	X-RAY DIFFRACTION	10	(chain H and resid 210:217)
11	X-RAY DIFFRACTION	11	(chain L and resid 2:11)
12	X-RAY DIFFRACTION	12	(chain L and resid 12:23)
13	X-RAY DIFFRACTION	13	(chain L and resid 24:27)
14	X-RAY DIFFRACTION	14	(chain L and resid 28:69)
15	X-RAY DIFFRACTION	15	(chain L and resid 70:81)
16	X-RAY DIFFRACTION	16	(chain L and resid 82:105)
17	X-RAY DIFFRACTION	17	(chain L and resid 106:149)
18	X-RAY DIFFRACTION	18	(chain L and resid 150:161)
19	X-RAY DIFFRACTION	19	(chain L and resid 162:204)
20	X-RAY DIFFRACTION	20	(chain L and resid 205:214)
21	X-RAY DIFFRACTION	21	(chain P and resid 659:662)
22	X-RAY DIFFRACTION	22	(chain P and resid 663:669)

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Yorodumi