PDB-3mo1: Crystal structure of the non-neutralizing HIV antibody 13H11 Fab ...

ID or keywords:

Entry

Database: PDB / ID: 3mo1

Title

Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment

Components

ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN
ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN

Keywords

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

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION

Function and homology information

Biological species

Mus musculus (house mouse)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 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 ...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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3mo1.cif.gz	191.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3mo1.ent.gz	153.2 KB	Display	PDB format
PDBx/mmJSON format	3mo1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3mo1_validation.pdf.gz	458.4 KB	Display	wwPDB validaton report
Full document	3mo1_full_validation.pdf.gz	463.2 KB	Display
Data in XML	3mo1_validation.xml.gz	25.5 KB	Display
Data in CIF	3mo1_validation.cif.gz	34.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mo/3mo1 ftp://data.pdbj.org/pub/pdb/validation_reports/mo/3mo1	HTTPS FTP

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Related structure data

Related structure data	3mnwC 3mnzC 3moaC 3mobC 3modC 3mnvS 1tjh S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6rlm-5 5mp5-4 1xf3-2 3nzh-d 2g2r-1 5ggq-d 6wj0-d 3e8u-d 5mvj-4 2mcp-d 3l7f-3 3g6j-3 3uo1-d 6dca-2 5waw-d 5mp1-2 1gpo-1 1ucb-d 1nd0-3 4kte-d 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	#163 - Jul 2013 HIV Capsid similarity (2) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN

B: ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN

hetero molecules

48.6 kDa, 2 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)	90.365, 60.436, 80.118
Angle α, β, γ (deg.)	90.00, 91.22, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-233- ACT
2	1	B-234- SO4
3	1	B-394- HOH

Details

The biological unit is a heterodimer of one light chain (A) and one heavy chain fragment (B). The biological unit in this structure is the same as the asymmetric unit.

#1: Antibody	ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN Mass: 24719.545 Da / Num. of mol.: 1 / Fragment: FUSION PROTEIN between mouse Fv and a human Fc Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus,Homo sapiens / Cell line (production host): HEK293T CELL / Organ (production host): KIDNEY / Production host: Homo sapiens (human)
#2: Antibody	ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN Mass: 23521.475 Da / Num. of mol.: 1 / Fragment: FUSION PROTEIN between mouse Fv and a human Fc Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus,Homo sapiens / Cell line (production host): HEK293T CELL / Organ (production host): KIDNEY / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.27 Å³/Da / Density % sol: 45.74 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 7.2 Details: Reservoir: Qiagen AmSO4 suite condition with 2 M ammonium sulfate, 0.2 M ammonium acetate. Drop: 0.5 uL protein + 0.5 uL reservoir., pH 7.2, VAPOR DIFFUSION, temperature 298K

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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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 1, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→42.3 Å / Num. all: 40173 / Num. obs: 38807 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / R_merge(I) obs: 0.073 / Net I/σ(I): 13.2

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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: 3MNV

3mnv

Resolution: 1.8→40.05 Å / SU ML: 0.25 / σ(F): 0.25 / Phase error: 23.5 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2208	1997	5.16 %
R_work	0.1869	-	-
obs	0.1886	38721	96.38 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 44.331 Å² / k_sol: 0.377 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.5595 Å²	0 Å²	0.8531 Å²
2-	-	6.5605 Å²	0 Å²
3-	-	-	-1.001 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→40.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3323	0	25	345	3693

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3464
X-RAY DIFFRACTION	f_angle_d	1.155	4702
X-RAY DIFFRACTION	f_dihedral_angle_d	15.112	1226
X-RAY DIFFRACTION	f_chiral_restr	0.081	529
X-RAY DIFFRACTION	f_plane_restr	0.005	599

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 (%)
1.8-1.845	0.2901	144	0.2185	2637	X-RAY DIFFRACTION	97
1.845-1.8949	0.2495	141	0.2062	2605	X-RAY DIFFRACTION	97
1.8949-1.9507	0.2758	141	0.2141	2621	X-RAY DIFFRACTION	96
1.9507-2.0136	0.2519	142	0.1841	2597	X-RAY DIFFRACTION	96
2.0136-2.0856	0.2152	140	0.1752	2573	X-RAY DIFFRACTION	95
2.0856-2.1691	0.2249	141	0.1743	2582	X-RAY DIFFRACTION	95
2.1691-2.2678	0.2585	141	0.1982	2564	X-RAY DIFFRACTION	95
2.2678-2.3874	0.2528	138	0.196	2561	X-RAY DIFFRACTION	95
2.3874-2.5369	0.266	140	0.195	2567	X-RAY DIFFRACTION	95
2.5369-2.7328	0.231	142	0.1964	2619	X-RAY DIFFRACTION	95
2.7328-3.0077	0.2537	142	0.2029	2613	X-RAY DIFFRACTION	96
3.0077-3.4427	0.2366	145	0.1846	2673	X-RAY DIFFRACTION	98
3.4427-4.3366	0.1767	149	0.1506	2734	X-RAY DIFFRACTION	100
4.3366-40.0598	0.1586	151	0.1664	2778	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	6.1767	-2.5537	-3.0604	3.1727	3.339	3.8165	-0.095	-1.0126	0.812	0.067	0.4857	-0.4009	0.1216	0.699	-0.4024	0.1968	0.0452	-0.0377	0.3176	-0.1204	0.2169	-11.9907	241.1655	32.346
2	3.6644	-0.9337	-1.3216	1.1375	0.4758	0.5967	-0.2068	-0.395	-0.1984	-0.0145	0.2218	0.0616	0.0825	0.0767	0.0497	0.2227	0.0877	-0.0007	0.2164	0.006	0.12	-16.7702	230.4173	30.1585
3	3.9962	-1.3751	-0.6158	0.9572	1.0025	0.6998	0.0313	-0.1281	0.2842	0.0021	0.0694	-0.1703	0.1538	0.1338	-0.0974	0.2075	0.0516	-0.0012	0.2263	-0.0467	0.1409	-10.7202	233.8277	26.4327
4	3.0295	-2.1269	-1.6301	1.4629	0.9571	2.2365	0.1942	-0.2767	0.5668	-0.1917	0.1919	-0.2363	-0.3942	0.127	-0.209	0.1758	0.027	0.0194	0.2008	-0.0844	0.1864	-19.9477	241.7997	30.6732
5	1.3016	-0.1388	-0.022	0.5603	0.7504	2.1127	0.0352	0.208	-0.0505	-0.0638	0.0015	0.0653	0.0785	0.219	-0.0255	0.1813	-0.02	-0.0226	0.2193	-0.0187	0.1421	-18.4556	229.2069	-5.8779
6	0.248	-0.143	0.3955	0.4024	-0.4443	0.6085	-0.0853	-0.1063	0.0164	-0.043	0.1276	0.0403	-0.2731	-0.0602	-0.0153	0.2146	0.0485	-0.0212	0.3043	-0.0323	0.1249	-17.9476	234.3519	-5.7562
7	3.4789	-0.1804	0.6898	1.1162	-0.1489	0.1648	0.1231	0.6537	0.2367	-0.34	0.0442	-0.0178	-0.2151	0.2902	-0.0832	0.2949	0.0461	-0.0002	0.36	0.011	0.1214	-18.9866	241.1996	-14.0195
8	0.5182	-0.5888	0.4209	0.9114	-0.478	0.4538	0.0554	-0.1456	-0.1014	-0.0234	0.1505	0.1507	0.2047	-0.1229	-0.0909	0.2338	0.043	-0.0121	0.2397	-0.0156	0.1501	-16.6945	231.6493	2.647
9	1.5939	0.053	-0.2396	0.4914	-0.0458	0.0646	-0.0757	0.7306	-0.1393	-0.2591	-0.1349	0.0391	0.1068	0.007	0.1651	0.2741	0.0621	-0.0813	0.4809	-0.004	0.1173	-26.3294	237.5953	-20.8119
10	1.3405	-0.2424	-0.7873	0.3975	-0.2202	0.7042	-0.029	-0.1426	0.0982	-0.0429	-0.0514	-0.0342	-0.2715	0.2345	0.059	0.1988	0.0249	0.0009	0.31	-0.0608	0.1068	-11.1627	232.2135	-12.9946
11	3.149	-3.0324	2.3527	4.5414	-4.5818	5.0983	-0.047	-0.1427	-1.0368	-1.9357	-0.2192	0.5899	1.2066	0.0467	0.4129	0.6594	0.1265	0.1992	0.3227	0.0948	0.6456	-32.5225	222.3349	29.5503
12	1.5712	-0.3526	-0.8968	0.23	0.5123	2.1138	0.0999	0.1887	-0.5652	-0.1291	-0.1794	0.4114	0.323	-0.107	0.0728	0.2355	0.0355	-0.0027	0.2211	-0.0586	0.3635	-41.0945	235.2831	23.4785
13	3.7917	-1.9231	1.3628	2.8193	-0.6879	0.5999	0.1536	0.463	-0.4031	-0.1545	-0.0356	0.2512	0.0735	0.1232	-0.1275	0.1775	0.04	0.0277	0.1474	-0.0383	0.2079	-30.2526	239.0093	27.8625
14	3.5781	0.4701	-1.3189	0.2798	0.0954	1.0117	0.0076	-0.43	-0.0987	-0.0189	-0.1301	0.1697	-0.1217	0.2164	0.1089	0.1835	0.0307	0.0302	0.2128	-0.0047	0.2578	-37.0972	241.53	37.0759
15	0.978	-0.4984	-0.6537	2.3676	-0.3712	1.1569	0.0968	0.1376	-0.057	0.1402	-0.1551	0.1918	-0.1126	-0.2262	0.0669	0.188	0.0387	-0.0002	0.1779	-0.0512	0.2542	-42.267	241.8545	28.7975
16	1.8174	-0.4576	-0.6859	0.3049	0.7244	1.4503	0.1997	0.2395	-0.3069	-0.0594	-0.1673	0.2112	0.1862	-0.0869	0.0023	0.22	0.0771	0.0002	0.1851	-0.0208	0.2274	-32.7416	239.1216	22.7092
17	2.2663	-2.6384	-1.7678	5.2161	3.7433	3.7103	-0.246	0.4117	-0.3716	0.0001	-0.237	0.6735	-0.0104	-0.3458	0.3838	0.1993	0.0539	-0.0048	0.2792	-0.0311	0.2772	-35.3251	233.0283	-3.7467
18	1.9981	-2.3176	0.5295	3.3935	-0.037	0.2637	0.1807	0.3394	0.006	-0.4889	-0.1557	0.0114	-0.1403	-0.2791	-0.0036	0.2115	0.0068	0.0245	0.2243	-0.0009	0.2295	-27.2353	229.0155	-3.2987
19	0.0987	-0.0092	0.157	0.2869	0.1336	-0.0279	-0.0945	0.0048	-0.018	0.0065	0.0843	0.0991	-0.0306	-0.2183	-0.0216	0.212	0	0.0029	0.2469	0.0262	0.1786	-27.0679	225.0016	-0.802
20	0.6202	0.748	0.9766	2.3472	-0.6473	3.7248	0.099	0.1794	0.1833	-0.0352	0.0649	0.5396	0.4153	-0.7676	-0.1484	0.2093	-0.046	-0.0198	0.3699	0.0492	0.3128	-37.2547	225.5577	-0.9589

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 0:30F)
2	X-RAY DIFFRACTION	2	(chain A and resid 31:65)
3	X-RAY DIFFRACTION	3	(chain A and resid 66:88)
4	X-RAY DIFFRACTION	4	(chain A and resid 89:105)
5	X-RAY DIFFRACTION	5	(chain A and resid 106:125)
6	X-RAY DIFFRACTION	6	(chain A and resid 126:147)
7	X-RAY DIFFRACTION	7	(chain A and resid 148:162)
8	X-RAY DIFFRACTION	8	(chain A and resid 163:180)
9	X-RAY DIFFRACTION	9	(chain A and resid 181:194)
10	X-RAY DIFFRACTION	10	(chain A and resid 195:211)
11	X-RAY DIFFRACTION	11	(chain B and resid 0:4)
12	X-RAY DIFFRACTION	12	(chain B and resid 5:30)
13	X-RAY DIFFRACTION	13	(chain B and resid 31:46)
14	X-RAY DIFFRACTION	14	(chain B and resid 47:61)
15	X-RAY DIFFRACTION	15	(chain B and resid 62:82C)
16	X-RAY DIFFRACTION	16	(chain B and resid 83:112)
17	X-RAY DIFFRACTION	17	(chain B and resid 113:127)
18	X-RAY DIFFRACTION	18	(chain B and resid 128:154)
19	X-RAY DIFFRACTION	19	(chain B and resid 156:210)
20	X-RAY DIFFRACTION	20	(chain B and resid 211:226)

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