PDB-5u3l: Crystal Structure of DH511.2 Fab in Complex with HIV-1 gp41 MPER ...

ID or keywords:

Entry

Database: PDB / ID: 5u3l

Title

Crystal Structure of DH511.2 Fab in Complex with HIV-1 gp41 MPER 670-683 Peptide

Components

DH511.2 Fab Heavy Chain
DH511.2 Fab Light Chain
gp41 MPER peptide

Keywords

IMMUNE SYSTEM/VIRAL PROTEIN / HIV-1 / Neutralizing / Antibody / gp41 / MPER / IMMUNE SYSTEM-VIRAL PROTEIN complex

Function / homology

Function and homology information

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)

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.165 Å

Authors

Ofek, G. / Wu, L. / Lougheed, C.S. / Williams, L.D. / Nicely, N.I. / Haynes, B.F.

Funding support

United States, 1items

Citation

Journal: Sci Immunol / Year: 2017
Title: Potent and broad HIV-neutralizing antibodies in memory B cells and plasma.
Authors: Williams, L.D. / Ofek, G. / Schatzle, S. / McDaniel, J.R. / Lu, X. / Nicely, N.I. / Wu, L. / Lougheed, C.S. / Bradley, T. / Louder, M.K. / McKee, K. / Bailer, R.T. / O'Dell, S. / Georgiev, I. ...

History

Deposition	Dec 2, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jul 5, 2017	Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2	Aug 23, 2017	Group: Author supporting evidence / Database references / Refinement description Category: citation / citation_author ...citation / citation_author / pdbx_audit_support / software Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.3	Dec 11, 2019	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Oct 4, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5	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	5u3l.cif.gz	512.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5u3l.ent.gz	432.9 KB	Display	PDB format
PDBx/mmJSON format	5u3l.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5u3l_validation.pdf.gz	463.3 KB	Display	wwPDB validaton report
Full document	5u3l_full_validation.pdf.gz	471.2 KB	Display
Data in XML	5u3l_validation.xml.gz	34 KB	Display
Data in CIF	5u3l_validation.cif.gz	47.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u3/5u3l ftp://data.pdbj.org/pub/pdb/validation_reports/u3/5u3l	HTTPS FTP

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Related structure data

Related structure data	5u3jC 5u3kC 5u3mC 5u3nC 5u3oC 5u3pSC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4x0k-2 4u6g-1 6bli-1 6blh-d 5e08-d 6bli-3 5u3o-d 2fr4-1 5w4v-2 4u6g-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #163 - Jul 2013 HIV Capsid similarity (1) #169 - Jan 2014 HIV Envelope Glycoprotein similarity (6) #170 - Feb 2014 Broadly Neutralizing Antibodies similarity (6) #62 - Feb 2005 Major Histocompatibility Complex similarity (6)

Deposited unit

H: DH511.2 Fab Heavy Chain

L: DH511.2 Fab Light Chain

A: DH511.2 Fab Heavy Chain

B: DH511.2 Fab Light Chain

P: gp41 MPER peptide

C: gp41 MPER peptide

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

1

H: DH511.2 Fab Heavy Chain

L: DH511.2 Fab Light Chain

P: gp41 MPER peptide

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

2

A: DH511.2 Fab Heavy Chain

B: DH511.2 Fab Light Chain

C: gp41 MPER peptide

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

Unit cell

Length a, b, c (Å)	110.072, 75.644, 123.427
Angle α, β, γ (deg.)	90.00, 94.11, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	H-100- PHE

#1: Antibody	DH511.2 Fab Heavy Chain Mass: 25101.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IgG Heavy Chain / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#2: Antibody	DH511.2 Fab Light Chain Mass: 23466.990 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IgG Light Chain / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#3: Protein/peptide	gp41 MPER peptide Mass: 2789.345 Da / Num. of mol.: 2 / Fragment: gp41 656-683 / Source method: obtained synthetically / Details: gp41 MPER 670-683 Peptide / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q73372*PLUS
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.49 Å³/Da / Density % sol: 50.7 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20% PEG 8000, 10% PEG 400, 0.5 M NaCl, 0.1 M C2H3NaO2 pH 5.5

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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: RAYONIX MX300-HS / Detector: CCD / Date: Jul 8, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.17→42.51 Å / Num. obs: 51031 / % possible obs: 93.5 % / Redundancy: 5.1 % / B_iso Wilson estimate: 36.98 Å² / R_merge(I) obs: 0.098 / R_pim(I) all: 0.045 / R_rim(I) all: 0.109 / Χ²: 0.93 / Net I/σ(I): 8.3 / Num. measured all: 259846

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	Diffraction-ID	% possible all
2.17-2.23	2.6	0.498	3495	0.815	1	52.5
2.23-2.31	3.1	0.539		0.785	1	85.2
2.31-2.39	3.8	0.505		0.859	1	94.2
2.39-2.48	4.4	0.445		0.895	1	95.8
2.48-2.6	5	0.393		0.927	1	96.2
2.6-2.73	5.5	0.335		0.934	1	97.7
2.73-2.91	5.9	0.262		0.966	1	99.8
2.91-3.13	6	0.177		0.986	1	100
3.13-3.44	5.9	0.12		0.991	1	100
3.44-3.94	5.8	0.088		0.994	1	100
3.94-4.97	5.8	0.065		0.996	1	100
4.97-50	5.7	0.057		0.997	1	99.7

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
HKL-2000		data collection
HKL-2000		data scaling
PDB_EXTRACT	3.22	data extraction
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5U3P

5u3p

Resolution: 2.165→42.51 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.11 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2309	2611	5.12 %
R_work	0.2048	-	-
obs	0.2061	50955	94.34 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.165→42.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6983	0	0	213	7196

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	7178
X-RAY DIFFRACTION	f_angle_d	0.554	9769
X-RAY DIFFRACTION	f_dihedral_angle_d	10.497	4213
X-RAY DIFFRACTION	f_chiral_restr	0.044	1080
X-RAY DIFFRACTION	f_plane_restr	0.003	1239

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 (%)
2.165-2.2044	0.2994	65	0.272	1497	X-RAY DIFFRACTION	56
2.2044-2.2468	0.2771	103	0.2728	2037	X-RAY DIFFRACTION	76
2.2468-2.2926	0.3215	138	0.2622	2378	X-RAY DIFFRACTION	88
2.2926-2.3425	0.2782	149	0.2467	2464	X-RAY DIFFRACTION	94
2.3425-2.397	0.275	143	0.2559	2559	X-RAY DIFFRACTION	95
2.397-2.4569	0.2727	135	0.2415	2563	X-RAY DIFFRACTION	95
2.4569-2.5233	0.2658	130	0.2363	2572	X-RAY DIFFRACTION	95
2.5233-2.5976	0.3013	136	0.2403	2598	X-RAY DIFFRACTION	97
2.5976-2.6814	0.2623	170	0.237	2626	X-RAY DIFFRACTION	98
2.6814-2.7772	0.2304	141	0.2382	2638	X-RAY DIFFRACTION	99
2.7772-2.8884	0.2893	146	0.2351	2696	X-RAY DIFFRACTION	100
2.8884-3.0198	0.2535	128	0.226	2706	X-RAY DIFFRACTION	100
3.0198-3.179	0.2329	157	0.2252	2687	X-RAY DIFFRACTION	100
3.179-3.3781	0.2377	142	0.2106	2669	X-RAY DIFFRACTION	100
3.3781-3.6388	0.2208	128	0.1988	2723	X-RAY DIFFRACTION	100
3.6388-4.0047	0.2015	141	0.1888	2718	X-RAY DIFFRACTION	100
4.0047-4.5836	0.1897	139	0.1584	2725	X-RAY DIFFRACTION	100
4.5836-5.7726	0.1978	166	0.163	2712	X-RAY DIFFRACTION	100
5.7726-42.5183	0.2303	154	0.208	2776	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	4.1702	0.6498	0.282	1.7036	-0.385	1.8838	-0.0933	0.4751	0.2121	-0.0764	0.0176	-0.0592	-0.2794	0.034	0.1357	0.3037	-0.0609	-0.034	0.5617	0.0617	0.2826	-35.2434	16.6801	42.7261
2	4.4266	-2.0748	-0.1212	5.0398	-0.006	1.348	0.0521	1.1282	-0.0567	-0.3018	0.0183	0.0045	0.1809	0.6268	-0.099	0.3797	0.028	-0.0088	0.988	0.0922	0.5837	0.8479	10.5755	36.2284
3	5.8942	-2.1573	-1.9787	4.6257	6.1036	8.5517	0.342	-0.3362	-0.3113	0.0248	-0.147	-0.5317	0.2484	-0.2077	-0.2087	0.354	-0.0952	-0.052	0.5191	0.0951	0.4551	-24.0624	-1.8783	56.9784
4	4.8469	-0.6117	0.622	2.7072	-0.7668	2.6978	-0.044	-0.2192	-0.523	0.0423	-0.021	0.0011	0.3886	-0.2294	-0.057	0.291	-0.0607	-0.0157	0.5167	0.0739	0.3793	-33.564	0.1198	51.7011
5	4.3859	-1.2011	0.4848	3.9468	0.2089	2.0513	-0.0415	-0.1577	-0.5237	0.1861	0.0906	0.039	0.0755	-0.2872	-0.05	0.269	-0.1017	0.0065	0.5614	0.1073	0.359	-30.9419	0.7553	53.7466
6	4.6817	-4.8309	1.1075	5.1497	-0.6756	2.6522	-0.2829	0.1454	-0.9691	0.1336	-0.0434	0.5963	-0.2597	0.0468	0.3148	0.4494	0.0256	-0.2002	0.5059	-0.0957	0.7589	-9.6787	-8.0928	51.372
7	6.8279	3.4922	0.7207	1.7969	0.3527	3.0178	-0.049	1.5989	0.3588	-0.4545	0.0439	-0.0293	-0.0112	0.5936	0.0112	0.3309	0.0157	0.0046	1.0228	0.2045	0.6956	10.8879	12.7404	43.3539
8	6.9949	4.8957	1.2957	8.1076	1.0085	1.3866	0.1721	0.4047	0.2401	0.2927	-0.0976	0.5229	0.0449	0.109	-0.2093	0.3627	0.0956	-0.0221	0.6828	0.0367	0.5044	1.6351	4.656	52.5876
9	9.8177	3.0639	4.056	5.4991	1.5668	2.6013	-0.096	1.0114	-0.0879	0.0351	0.2874	0.5904	0.0331	0.4689	-0.0786	0.4664	0.1505	0.0726	0.688	0.0473	0.4627	-1.6814	5.3295	50.7371
10	5.7721	5.4217	0.8301	5.6298	0.8771	2.3942	-0.4116	0.5828	0.9257	-0.0897	0.5293	0.8636	-0.2395	0.5458	-0.0875	0.3789	0.0211	-0.0476	0.7237	0.1193	0.7227	6.8715	14.8537	50.2426
11	7.9497	4.8411	0.8652	3.8272	-1.1351	3.2379	0.4504	0.162	-0.7661	0.6162	-0.4269	-0.6719	0.1365	0.6934	-0.1219	0.5202	0.0771	-0.0518	0.5878	0.0046	0.4257	10.2698	4.608	56.0196
12	3.5643	2.4884	3.3272	1.9369	2.3983	5.8767	-0.1303	0.1899	-0.1142	0.114	0.4198	-0.1801	-0.1376	1.252	-0.2532	0.2542	-0.0533	0.0275	0.6615	-0.0369	0.3213	-0.9824	38.8903	16.5143
13	2.1068	-0.2713	0.8871	1.9542	2.183	6.2323	-0.0203	-0.0501	-0.1779	0.1078	0.0421	0.0105	0.1901	0.379	-0.0166	0.3094	-0.0304	-0.0152	0.372	0.0633	0.3114	-7.7859	35.8297	23.1448
14	3.271	-1.4141	-0.1588	4.4355	-0.1483	2.1291	0.4429	0.7168	0.1391	-0.8581	-0.4069	0.0581	-0.5026	-0.4495	-0.027	0.5872	0.135	0.045	0.4928	0.0511	0.2635	-20.3762	45.9704	-9.3326
15	3.1264	-2.0294	3.3908	7.6675	-5.1037	4.9471	0.5127	0.6695	0.6032	-0.5681	-0.3328	-0.5099	-1.3557	-0.0285	0.1075	0.9467	0.245	0.2153	0.7618	0.0956	0.4086	-14.7196	49.5236	-15.8292
16	4.1797	-1.802	0.9486	2.6099	-0.2775	7.2434	-0.1169	-0.2411	0.1133	0.1711	-0.1818	0.3704	-0.8821	-0.7543	0.1995	0.3892	0.0435	-0.0408	0.4101	-0.058	0.3023	-22.1053	48.1733	26.3739
17	8.4845	-3.8692	6.8066	5.255	-6.281	8.3225	-0.5149	-0.9869	-0.0589	0.8423	0.5661	-0.1643	0.2824	-0.2598	0.0494	0.5715	0.2507	-0.0533	0.5489	-0.024	0.5107	-32.8603	57.9566	8.2931
18	1.3125	-0.6019	-0.1843	5.2377	2.2387	2.5977	0.5072	0.7097	-0.7428	-0.8392	-0.1711	0.786	0.2325	0.1775	0.4021	0.7142	0.2558	-0.3049	0.6822	-0.1055	0.6177	-33.3242	46.2125	-9.9155
19	2.5439	-0.9732	-0.2195	3.1158	1.3661	2.6988	0.4182	0.6768	-0.6489	-0.5024	-0.3818	1.0737	0.3135	-0.0146	-0.0015	0.6462	0.1147	-0.3108	0.5268	-0.1001	0.7253	-36.4753	45.713	-8.3026
20	5.8126	-0.0704	-3.5592	2.8462	-0.9625	4.132	0.0401	-0.4069	0.117	0.0861	0.14	0.4004	-1.1399	0.1822	-0.3586	0.3168	0.0075	-0.0067	0.7549	0.1153	0.37	-56.4365	12.1277	49.1453
21	8.293	0.8591	3.1804	4.2527	0.8344	1.2826	-0.0132	0.6729	-0.8807	1.2623	-0.1545	-1.9729	-0.078	0.5945	0.1284	0.5055	-0.072	-0.1125	0.6436	0.098	0.53	6.0601	41.8635	37.7854
22	4.8017	1.3725	-2.9197	3.8417	-0.1177	9.7709	0.1409	-0.0818	-0.979	-0.014	0.076	0.1387	0.9036	-0.277	-0.3246	0.3717	-0.0563	-0.0822	0.5616	0.1629	0.3654	-3.8606	37.6915	45.2082

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 111 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 112 through 213 )
3	X-RAY DIFFRACTION	3	chain 'L' and (resid 1 through 18 )
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 19 through 61 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 62 through 102 )
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 103 through 113 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 114 through 128 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 129 through 150 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 151 through 172 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 173 through 188 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 189 through 212 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 1 through 33 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 34 through 111 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 112 through 188 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 189 through 213 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 1 through 102 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 103 through 113 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 114 through 150 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 151 through 211 )
20	X-RAY DIFFRACTION	20	chain 'P' and (resid 668 through 685 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 667 through 671 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 672 through 685 )

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Open data

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Download

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Validation report

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Assembly

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Experimental details

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Data collection

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi