PDB-8g8d: Crystal structure of DH1346 Fab in complex with HIV proximal MPER...

ID or keywords:

Entry

Database: PDB / ID: 8g8d

Title

Crystal structure of DH1346 Fab in complex with HIV proximal MPER peptide

Components

DH1346 heavy chain
DH1346 light chain
gp41 MPER peptide

Keywords

IMMUNE SYSTEM / HIV / Neutralizing Antibody / MPER / gp41

Function / homology

FLUORIDE ION

Function and homology information

Biological species

Homo sapiens (human)

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.02 Å

Authors

Niyongabo, A. / Janus, B.M. / Ofek, G.

Funding support

1items

Citation

Journal: Cell / Year: 2024
Title: Vaccine induction of heterologous HIV-1-neutralizing antibody B cell lineages in humans.
Authors: Wilton B Williams / S Munir Alam / Gilad Ofek / Nathaniel Erdmann / David C Montefiori / Michael S Seaman / Kshitij Wagh / Bette Korber / Robert J Edwards / Katayoun Mansouri / Amanda Eaton ...
Abstract: A critical roadblock to HIV vaccine development is the inability to induce B cell lineages of broadly neutralizing antibodies (bnAbs) in humans. In people living with HIV-1, bnAbs take years to ...

History

Deposition	Feb 17, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 22, 2024	Provider: repository / Type: Initial release
Revision 1.1	May 29, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jun 19, 2024	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8g8d.cif.gz	532.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8g8d_validation.pdf.gz	465.5 KB	Display	wwPDB validaton report
Full document	8g8d_full_validation.pdf.gz	477.3 KB	Display
Data in XML	8g8d_validation.xml.gz	39 KB	Display
Data in CIF	8g8d_validation.cif.gz	55.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g8/8g8d ftp://data.pdbj.org/pub/pdb/validation_reports/g8/8g8d	HTTPS FTP

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Related structure data

Related structure data	44246C 8g8aC 8g8cC C: citing same article (ref.)
Similar structure data	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 (1) #170 - Feb 2014 Broadly Neutralizing Antibodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

H: DH1346 heavy chain

L: DH1346 light chain

P: gp41 MPER peptide

A: DH1346 heavy chain

B: DH1346 light chain

C: gp41 MPER peptide

hetero molecules

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

1

H: DH1346 heavy chain

L: DH1346 light chain

P: gp41 MPER peptide

hetero molecules

defined by author
Evidence: surface plasmon resonance
52.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: DH1346 heavy chain

B: DH1346 light chain

C: gp41 MPER peptide

hetero molecules

defined by author
52.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	41.069, 115.513, 231.322
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein / Antibody / Protein/peptide , 3 types, 6 molecules HALBPC

#1: Protein	DH1346 heavy chain Mass: 24642.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody	DH1346 light chain Mass: 23203.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide	gp41 MPER peptide Mass: 4460.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1

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Non-polymers , 3 types, 459 molecules

#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-F / FLUORIDE ION Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
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: 2.63 Å³/Da / Density % sol: 53.27 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 25% PEG 1500, 0.1M Sodium acetate/acetic acid pH4.5, 30% MPD, and 30% dextran sulfate sodium salt

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 22, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.02→37.98 Å / Num. obs: 67030 / % possible obs: 91.7 % / Redundancy: 3 % / R_merge(I) obs: 0.075 / Net I/σ(I): 12.1
Reflection shell	Resolution: 2.02→2.1 Å / R_merge(I) obs: 0.53 / Num. unique obs: 5929

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Processing

Software

Name	Version	Classification
PHENIX	1.2	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.02→37.98 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2335	5094	7.6 %
R_work	0.1978	-	-
obs	0.2005	67012	91.69 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.02→37.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7113	0	11	448	7572

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005
X-RAY DIFFRACTION	f_angle_d	0.723
X-RAY DIFFRACTION	f_dihedral_angle_d	11.364	2531
X-RAY DIFFRACTION	f_chiral_restr	0.048	1122
X-RAY DIFFRACTION	f_plane_restr	0.005	1267

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 (%)
2.02-2.05	0.3014	130	0.2674	1586	X-RAY DIFFRACTION	71
2.05-2.07	0.2997	156	0.253	1924	X-RAY DIFFRACTION	88
2.07-2.1	0.3058	162	0.2489	1965	X-RAY DIFFRACTION	89
2.1-2.12	0.3038	160	0.2387	1965	X-RAY DIFFRACTION	88
2.12-2.15	0.2629	166	0.233	2005	X-RAY DIFFRACTION	88
2.15-2.18	0.265	161	0.237	1963	X-RAY DIFFRACTION	89
2.18-2.21	0.2576	158	0.2356	1937	X-RAY DIFFRACTION	89
2.21-2.25	0.272	165	0.2313	1983	X-RAY DIFFRACTION	90
2.25-2.28	0.29	165	0.2266	2005	X-RAY DIFFRACTION	88
2.28-2.32	0.2621	159	0.2201	1943	X-RAY DIFFRACTION	89
2.32-2.36	0.2798	162	0.2157	1968	X-RAY DIFFRACTION	88
2.36-2.4	0.2701	165	0.2215	1996	X-RAY DIFFRACTION	90
2.4-2.45	0.2592	168	0.2213	2028	X-RAY DIFFRACTION	91
2.45-2.5	0.2763	165	0.227	2000	X-RAY DIFFRACTION	91
2.5-2.55	0.2611	158	0.218	1907	X-RAY DIFFRACTION	85
2.55-2.61	0.2578	163	0.212	1985	X-RAY DIFFRACTION	89
2.61-2.68	0.2213	175	0.2123	2128	X-RAY DIFFRACTION	96
2.68-2.75	0.2735	180	0.2144	2193	X-RAY DIFFRACTION	97
2.75-2.83	0.2425	179	0.2138	2141	X-RAY DIFFRACTION	97
2.83-2.92	0.2083	189	0.2008	2250	X-RAY DIFFRACTION	99
2.92-3.02	0.2468	176	0.1982	2168	X-RAY DIFFRACTION	98
3.02-3.15	0.2203	185	0.1967	2275	X-RAY DIFFRACTION	99
3.15-3.29	0.2197	179	0.1995	2185	X-RAY DIFFRACTION	99
3.29-3.46	0.2418	180	0.1954	2208	X-RAY DIFFRACTION	96
3.46-3.68	0.2373	176	0.1835	2117	X-RAY DIFFRACTION	93
3.68-3.96	0.1899	168	0.1768	2084	X-RAY DIFFRACTION	92
3.96-4.36	0.1949	182	0.1617	2238	X-RAY DIFFRACTION	97
4.36-4.99	0.1865	179	0.1537	2160	X-RAY DIFFRACTION	94
4.99-6.28	0.2092	190	0.1847	2281	X-RAY DIFFRACTION	97
6.28-37.98	0.251	193	0.2036	2330	X-RAY DIFFRACTION	93

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	3.1662	0.3758	-0.9085	1.3627	0.3654	1.4844	-0.0456	0.3644	-0.0509	-0.0863	-0.026	0.1788	0.0324	-0.3912	0.0693	0.165	-0.0136	-0.0293	0.3516	-0.0063	0.2226	-4.182	14.558	-33.52
2	2.2755	-0.3797	-2.4557	0.8817	0.3384	3.2645	-0.0466	0.1675	0.0156	-0.0262	0.0299	0.0424	0.0812	-0.1022	-0.0071	0.1352	-0.0389	-0.0157	0.2238	-0.0152	0.1957	-1.349	15.738	-26.96
3	1.4401	1.399	-0.8642	4.6084	0.8795	0.634	0.1401	-0.0791	-0.2494	-0.0048	-0.003	0.0126	0.0838	0.0593	-0.1234	0.3748	-0.1026	-0.1454	0.2618	0.0772	0.3032	7.008	-9.175	-48.936
4	2.4992	-0.9928	-1.7286	3.6422	0.1761	2.5572	-0.4666	-0.2044	-0.4989	0.696	0.0629	0.2397	0.8038	0.1636	0.2852	0.4995	0.0057	0.1647	0.287	0.0674	0.3101	-3.542	0.207	-13.876
5	0.1329	-0.3642	0.2547	0.1589	-0.1966	0.3156	-0.6741	0.116	-0.133	1.3698	0.1309	0.6181	1.0506	0.4209	0.3188	0.771	0.1465	0.2938	0.2892	-0.0042	0.3558	3.87	-8.121	-20.418
6	1.9753	-1.5732	1.2998	6.0146	-2.3976	5.6321	-0.9536	0.444	1.0143	2.4407	-0.471	-1.2866	-2.0648	0.8264	0.138	0.802	-0.0749	-0.336	0.282	0.0618	0.4747	19.509	-16.406	-42.011
7	3.6406	1.6162	2.3118	3.1826	0.4988	2.0221	0.2231	-0.4666	-0.1187	0.5084	-0.1584	-0.0328	-0.39	-0.1103	0.0781	0.3322	-0.0769	0.0716	0.3904	-0.0027	0.2308	-8.039	23.699	-4.065
8	3.0158	-0.4959	0.1719	2.5945	1.075	3.0108	-0.1093	-0.3022	0.5712	0.2146	0.0499	-0.3236	0.0638	-0.1111	0.0205	0.18	-0.0078	0.0091	0.2133	-0.0388	0.218	4.483	-12.955	-73.689
9	4.4356	0.963	0.3691	2.8153	0.5764	1.9649	0.006	0.0875	0.1556	0.0755	-0.0497	0.3406	-0.1215	-0.524	0.0535	0.1676	0.0112	-0.0059	0.3009	-0.078	0.2642	-4.442	-14.983	-81.456
10	1.1298	-0.1095	1.4416	3.6611	-0.033	3.1084	-0.07	0.1043	-0.3418	-0.2151	-0.0674	-0.3125	0.099	-0.0019	0.0583	0.1399	0.013	0.0249	0.2427	-0.0566	0.2554	1.63	-20.011	-85.457
11	2.0084	0.1023	1.9211	2.1196	0.0686	3.5566	0.0536	0.1304	-0.0862	-0.1138	-0.0356	-0.1736	0.0282	-0.0101	-0.0703	0.1719	0.0053	0.0004	0.2071	-0.0722	0.2231	3.158	-15.485	-82.525
12	3.5406	0.0532	2.5	1.501	0.728	6.4727	-0.3254	0.0235	0.2898	-0.4831	-0.2911	0.353	-0.6524	-0.6355	0.6386	0.2487	0.0268	-0.0483	0.2543	-0.0042	0.252	-7.332	-11.638	-96.223
13	2.0948	-1.5222	-1.4893	1.9684	0.3769	1.5675	-0.0191	0.1707	-0.3693	0.5328	0.3241	-0.527	-0.1071	0.4483	-0.1979	0.2885	0.0442	-0.1479	0.252	-0.0608	0.3971	14.961	-9.253	-69.497
14	5.2487	0.0014	1.558	0.1449	0.7903	4.4877	0.0121	0.3646	1.6267	0.1416	-0.5034	-0.993	-0.7469	0.0232	0.468	0.22	0.0374	0.0201	0.3001	-0.0036	0.5802	10.715	19.024	-62.027
15	1.1302	0.4885	0.0416	4.6449	1.9868	3.0869	0.1131	0.0982	-0.0754	-0.0854	-0.0519	0.1241	0.0321	-0.0812	-0.0606	0.1395	0.0148	-0.0326	0.1966	0.0104	0.2014	8.991	8.358	-67.941
16	4.9996	-2.5853	-1.5434	2.8496	3.6028	4.6967	0.2321	-0.1776	-0.0489	0.2289	-0.1761	0.1536	0.1558	-0.2751	-0.0329	0.1251	-0.0265	0.0033	0.2043	0.0115	0.1602	4.138	7.323	-59.838
17	2.7702	1.4796	0.9978	7.6082	-0.1949	2.3623	-0.2095	0.6452	0.1969	-1.6911	0.0112	-0.6763	-1.0737	0.5762	0.2163	0.9412	-0.2663	0.0037	0.5683	-0.0017	0.3065	7.016	4.818	-100.272
18	1.7205	1.7493	0.5808	4.8187	0.0037	2.3548	-0.4374	0.1213	0.0462	-0.6543	0.062	0.2871	-0.4709	0.3214	0.1886	0.4051	-0.0228	-0.1131	0.2926	0.0206	0.2215	0.492	-3.257	-97.761
19	2.2327	0.5096	-0.7331	3.4289	-0.5841	1.099	-0.3745	0.5359	0.1947	-0.9974	0.0853	0.6585	-0.778	-0.3191	0.1519	0.7564	-0.0169	-0.2755	0.4353	0.0899	0.4415	-6.067	1.026	-100.734
20	2.7164	1.5407	1.4063	7.7017	0.3956	3.4033	-0.2586	0.2771	0.1997	-0.5119	-0.0264	-0.1713	-0.6778	0.358	0.1865	0.3019	-0.0959	-0.0576	0.3504	0.0099	0.1899	1.844	-4.061	-96.514
21	0.3336	0.3784	0.3405	0.7241	0.4044	1.2901	-0.5595	-0.2215	0.1152	-0.894	0.1477	0.1521	-0.7405	0.1975	0.3253	0.53	-0.0916	-0.2236	0.3668	-0.0484	0.3664	6.941	7.59	-92.373
22	4.387	-1.4568	2.1579	4.3143	-3.8403	3.9689	0.0855	-0.6617	-0.0332	0.0144	-0.1474	-0.1631	0.2796	-0.0618	0.1212	0.2621	-0.0329	-0.0249	0.2707	-0.0045	0.2435	18.062	13.944	-59.478
23	5.6322	-0.8921	3.0187	3.5799	-1.4127	2.5591	-0.1481	0.3352	0.1927	-0.9966	0.1936	-0.0171	0.2629	0.2556	0.121	0.3997	-0.0632	-0.0275	0.2158	-0.0091	0.2238	18.258	18.063	-75.209
24	6.4155	1.6612	1.1821	5.3273	-0.4772	6.1231	-0.3235	-0.0373	-0.0223	-0.5204	0.1616	0.1954	-0.2726	-0.2269	0.1025	0.3763	-0.0113	0.0045	0.2688	-0.0161	0.1784	18.166	14.974	-75.873
25	5.0504	1.2464	1.504	6.0071	1.0249	5.6714	-0.1896	-0.0145	-0.032	-0.0811	-0.0199	-0.5391	-0.2204	0.809	0.0913	0.1634	-0.0604	0.0409	0.2258	-0.0193	0.2534	23.44	14	-64.752
26	8.2517	-1.9389	5.2599	9.1289	-3.9036	4.8602	0.6597	-0.2173	-0.1681	-0.5543	0.0246	-0.6941	0.2504	-0.2985	-0.434	0.1908	-0.1569	0.0517	0.3315	0.0376	0.3775	24.825	22.838	-69.589
27	4.1668	-0.2315	0.7722	7.0734	-4.641	3.1283	-0.4344	-0.0962	0.1055	-0.3133	-0.1275	-0.076	-1.096	-0.0774	0.4066	0.3181	-0.0611	0.0075	0.1936	-0.0448	0.3405	21.043	25.574	-71.046
28	3.2109	-1.5961	-1.9699	3.9056	0.418	7.1704	0.2582	0.4009	0.158	-0.6056	-0.4101	-0.1083	-0.0278	-0.423	0.1885	0.2579	0.0294	-0.047	0.3514	0.0138	0.2451	-4.533	-23.504	-107.861

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 1:40 )	H	1 - 40
2	X-RAY DIFFRACTION	2	( CHAIN H AND RESID 41:133 )	H	41 - 133
3	X-RAY DIFFRACTION	3	( CHAIN H AND RESID 134:214 )	H	134 - 214
4	X-RAY DIFFRACTION	4	( CHAIN L AND RESID 3:97 )	L	3 - 97
5	X-RAY DIFFRACTION	5	( CHAIN L AND RESID 98:116 )	L	98 - 116
6	X-RAY DIFFRACTION	6	( CHAIN L AND RESID 117:209 )	L	117 - 209
7	X-RAY DIFFRACTION	7	( CHAIN P AND RESID 655:683 )	P	655 - 683
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 1:17 )	A	1 - 17
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 18:40 )	A	18 - 40
10	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 41:76 )	A	41 - 76
11	X-RAY DIFFRACTION	11	( CHAIN A AND RESID 77:103 )	A	77 - 103
12	X-RAY DIFFRACTION	12	( CHAIN A AND RESID 104:120 )	A	104 - 120
13	X-RAY DIFFRACTION	13	( CHAIN A AND RESID 121:133 )	A	121 - 133
14	X-RAY DIFFRACTION	14	( CHAIN A AND RESID 134:148 )	A	134 - 148
15	X-RAY DIFFRACTION	15	( CHAIN A AND RESID 149:202 )	A	149 - 202
16	X-RAY DIFFRACTION	16	( CHAIN A AND RESID 203:216 )	A	203 - 216
17	X-RAY DIFFRACTION	17	( CHAIN B AND RESID 2:17 )	B	2 - 17
18	X-RAY DIFFRACTION	18	( CHAIN B AND RESID 18:47 )	B	18 - 47
19	X-RAY DIFFRACTION	19	( CHAIN B AND RESID 48:74 )	B	48 - 74
20	X-RAY DIFFRACTION	20	( CHAIN B AND RESID 75:97 )	B	75 - 97
21	X-RAY DIFFRACTION	21	( CHAIN B AND RESID 98:116 )	B	98 - 116
22	X-RAY DIFFRACTION	22	( CHAIN B AND RESID 117:132 )	B	117 - 132
23	X-RAY DIFFRACTION	23	( CHAIN B AND RESID 133:153 )	B	133 - 153
24	X-RAY DIFFRACTION	24	( CHAIN B AND RESID 154:174 )	B	154 - 174
25	X-RAY DIFFRACTION	25	( CHAIN B AND RESID 175:190 )	B	175 - 190
26	X-RAY DIFFRACTION	26	( CHAIN B AND RESID 191:200 )	B	191 - 200
27	X-RAY DIFFRACTION	27	( CHAIN B AND RESID 201:209 )	B	201 - 209
28	X-RAY DIFFRACTION	28	( CHAIN C AND RESID 655:683 )	C	655 - 683

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