PDB-5u3m: Crystal Structure of DH511.11P Fab in Complex with HIV-1 gp41 MPE...

ID or keywords:

Entry

Database: PDB / ID: 5u3m

Title

Crystal Structure of DH511.11P Fab in Complex with HIV-1 gp41 MPER Peptide

Components

DH511.11P Fab Heavy Chain
DH511.11P 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 / 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 / viral envelope ...
Similarity search - Function

Biological species

Homo sapiens (human)

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.418 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 / Category: pdbx_audit_support / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5u3m.cif.gz	278.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5u3m.ent.gz	231.3 KB	Display	PDB format
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Validation report

Summary document	5u3m_validation.pdf.gz	425.8 KB	Display	wwPDB validaton report
Full document	5u3m_full_validation.pdf.gz	427.8 KB	Display
Data in XML	5u3m_validation.xml.gz	18.2 KB	Display
Data in CIF	5u3m_validation.cif.gz	24.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u3/5u3m ftp://data.pdbj.org/pub/pdb/validation_reports/u3/5u3m	HTTPS FTP

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Related structure data

Related structure data	5u3jC 5u3kC 5u3lSC 5u3nC 5u3oC 5u3pC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5kn5-2 5epm-1 6z7w-3 6s3d-3 6snd-1 6i9i-1 6s3d-1 6z7w-1 5kn5-1 6snc-1 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: DH511.11P Fab Heavy Chain

L: DH511.11P Fab Light Chain

A: gp41 MPER peptide

52.8 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)	65.760, 102.110, 197.131
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

Components on special symmetry positions

ID	Model	Components
1	1	L-302- HOH

#1: Antibody	DH511.11P Fab Heavy Chain Mass: 25297.572 Da / Num. of mol.: 1 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	DH511.11P Fab Light Chain Mass: 23794.516 Da / Num. of mol.: 1 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: 3733.408 Da / Num. of mol.: 1 / Fragment: gp41 656-683 / Source method: obtained synthetically / Details: gp41 MPER 656-683 Peptide / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q73372*PLUS
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.13 Å³/Da / Density % sol: 60.73 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 4% Isopropanol, 3% PEG 3350, 0.75 M NH4SO4, 0.1 M C2H3NaO2 pH 4.5

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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: Feb 27, 2016

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.41→39.509 Å / Num. obs: 24106 / % possible obs: 93.6 % / Redundancy: 8.5 % / B_iso Wilson estimate: 42.82 Å² / R_merge(I) obs: 0.2 / Net I/σ(I): 7.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	Diffraction-ID	% possible all
2.41-2.48	4.1	0.325	1748	0.845	1	69.4
2.48-2.56	4.8	0.355		0.835	1	79.8
2.56-2.65	5	0.435		0.638	1	85.7
2.65-2.76	5.7	0.546		0.636	1	90.7
2.76-2.88	6.9	0.618		0.859	1	97.1
2.88-3.04	8.5	0.568		0.917	1	99.6
3.04-3.23	9.8	0.444		0.961	1	99.9
3.23-3.48	10.9	0.36		0.976	1	100
3.48-3.83	11.1	0.258		0.983	1	100
3.83-4.38	11	0.165		0.991	1	100
4.38-5.52	10.9	0.127		0.992	1	100
5.52-50	10.7	0.119		0.993	1	99.6

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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: 5U3L

5u3l

Resolution: 2.418→39.509 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.47 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2698	1996	8.29 %
R_work	0.227	-	-
obs	0.2306	24069	93.15 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.418→39.509 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3683	0	0	73	3756

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	3769
X-RAY DIFFRACTION	f_angle_d	0.5	5129
X-RAY DIFFRACTION	f_dihedral_angle_d	11.348	2233
X-RAY DIFFRACTION	f_chiral_restr	0.044	570
X-RAY DIFFRACTION	f_plane_restr	0.002	644

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 (%)
2.4184-2.4789	0.3366	99	0.2892	1092	X-RAY DIFFRACTION	66
2.4789-2.5459	0.3792	115	0.2839	1273	X-RAY DIFFRACTION	77
2.5459-2.6208	0.2954	126	0.2798	1396	X-RAY DIFFRACTION	84
2.6208-2.7054	0.3318	131	0.2709	1456	X-RAY DIFFRACTION	87
2.7054-2.802	0.3227	141	0.2617	1551	X-RAY DIFFRACTION	93
2.802-2.9142	0.2984	147	0.2521	1630	X-RAY DIFFRACTION	98
2.9142-3.0468	0.3206	152	0.2594	1679	X-RAY DIFFRACTION	100
3.0468-3.2074	0.2817	152	0.2447	1669	X-RAY DIFFRACTION	100
3.2074-3.4082	0.2945	153	0.2297	1698	X-RAY DIFFRACTION	100
3.4082-3.6712	0.2211	152	0.2141	1677	X-RAY DIFFRACTION	100
3.6712-4.0403	0.284	154	0.2193	1706	X-RAY DIFFRACTION	100
4.0403-4.6242	0.2395	155	0.1862	1721	X-RAY DIFFRACTION	100
4.6242-5.823	0.2244	156	0.2058	1717	X-RAY DIFFRACTION	100
5.823-39.5146	0.2674	163	0.2324	1808	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	2.0788	0.0806	-1.2596	1.2633	0.279	5.9838	0.1916	0.4161	-0.2863	-0.0189	-0.1253	0.335	-0.3323	-0.4783	-0.0226	0.2762	-0.0004	0.019	0.5775	-0.0952	0.4863	72.7321	7.499	218.7636
2	2.8118	-1.2493	-1.2933	1.3664	1.2822	1.9744	0.0271	0.0959	-0.0535	-0.1242	0.031	0.013	-0.1355	0.1667	-0.0263	0.293	-0.0452	-0.0017	0.4081	-0.0265	0.3635	69.2571	16.0694	226.7225
3	4.5302	-2.9462	-0.6498	3.446	-0.2038	1.7386	0.0027	0.2421	-0.3765	0.1145	0.046	0.5167	0.0823	-0.0684	-0.0537	0.254	-0.0594	-0.0325	0.4504	-0.115	0.4289	44.2609	24.7	237.697
4	6.0489	-2.2948	-1.7144	3.1775	0.6418	3.471	0.0329	-0.3218	-0.0604	0.0282	0.0746	0.5175	-0.0971	-0.1628	-0.1168	0.1984	0.0642	0.0494	0.6495	-0.0615	0.4606	45.0783	26.2599	244.1839
5	3.1004	-0.2923	-0.8365	3.1939	0.2733	1.9417	0.6308	0.4235	0.6694	-0.1421	-0.0767	-0.0046	-0.8934	0.0613	-0.2457	0.6624	-0.1235	0.2865	0.619	0.028	0.4349	79.9579	27.7469	212.9286
6	2.0013	0.2048	-1.8826	0.3115	0.2644	2.4954	0.2166	0.6188	0.5067	-0.1837	-0.0681	-0.1879	-0.9285	-0.1828	-0.4925	1.2152	-0.1556	0.3651	0.5218	0.0786	0.4791	80.5301	32.6731	208.363
7	2.3886	-1.483	-1.3144	3.2798	2.6252	2.0868	0.2186	0.3007	0.3444	-0.3595	0.0723	-0.7102	-0.418	0.2059	-0.2289	0.5406	-0.1124	0.1643	0.4591	0.0688	0.3607	76.5094	28.4956	218.9428
8	1.7236	0.3275	-0.0223	3.2315	-1.4844	6.21	0.0463	-0.1528	0.4075	0.0128	-0.0893	-0.043	-0.1099	-0.1047	-0.0338	0.206	0.0386	0.0521	0.3491	-0.0594	0.5578	62.8405	34.5362	243.2602
9	0.7093	0.5629	0.5829	1.7069	1.1574	0.8629	-0.164	-0.5426	0.278	0.3274	0.4091	0.2378	-0.0668	0.4475	0.4821	0.2335	-0.0326	0.1317	0.8296	-0.1092	0.4069	83.4733	-5.9878	196.9747
10	5.1847	0.3697	-1.0943	0.8943	-0.6588	0.6189	0.3361	-0.5481	0.585	0.1483	0.1923	-0.1012	-0.2122	0.3701	0.757	0.2444	0.0024	0.1329	0.9157	-0.2189	0.408	97.7961	7.2398	203.2043

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 45 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 46 through 188 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 189 through 203 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 204 through 216 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 1 through 61 )
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 62 through 79 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 80 through 113 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 114 through 214 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 661 through 671 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 672 through 685 )

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