PDB-5t5b: CRYSTAL STRUCTURE OF THE COMPLEX OF 10E8 FAB LIGHT CHAIN MUTANT5 ...

ID or keywords:

Entry

Database: PDB / ID: 5t5b

Title

CRYSTAL STRUCTURE OF THE COMPLEX OF 10E8 FAB LIGHT CHAIN MUTANT5 AND T117V2 HIV-1 MPER SCAFFOLD

Components

10E8 EPITOPE SCAFFOLD T117V2
Antibody 10E8 FAB HEAVY CHAIN
Antibody 10E8 FAB LIGHT CHAIN MUTATED

Keywords

IMMUNE SYSTEM / HIV-1 GP41 MPER / 10E8 FAB / LIPID MEMBRANE

Function / homology

Mannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta

Function and homology information

Biological species

Homo sapiens (human)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.07 Å

Authors

Irimia, A. / Wilson, I.A.

Funding support

United States, 2items

Citation

Journal: PLoS Pathog. / Year: 2017
Title: Lipid interactions and angle of approach to the HIV-1 viral membrane of broadly neutralizing antibody 10E8: Insights for vaccine and therapeutic design.
Authors: Irimia, A. / Serra, A.M. / Sarkar, A. / Jacak, R. / Kalyuzhniy, O. / Sok, D. / Saye-Francisco, K.L. / Schiffner, T. / Tingle, R. / Kubitz, M. / Adachi, Y. / Stanfield, R.L. / Deller, M.C. / ...

History

Deposition	Aug 30, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 8, 2017	Provider: repository / Type: Initial release
Revision 1.1	May 10, 2017	Group: Derived calculations
Revision 1.2	Sep 20, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Nov 1, 2017	Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	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 1.6	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5t5b.cif.gz	451.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5t5b_validation.pdf.gz	491.9 KB	Display	wwPDB validaton report
Full document	5t5b_full_validation.pdf.gz	517.6 KB	Display
Data in XML	5t5b_validation.xml.gz	42.8 KB	Display
Data in CIF	5t5b_validation.cif.gz	59.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t5/5t5b ftp://data.pdbj.org/pub/pdb/validation_reports/t5/5t5b	HTTPS FTP

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Related structure data

Related structure data	5sy8C 5t29C 5t6lC 5t80C 5t85C 5tfwC 3lf6S 4g6fS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5c0n-1 5t85-d 5w1m-3 7chz-d 5c0n-2 5t80-d 5mev-d 3u9p-2 5y9j-d 7jtf-1 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 - 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)

Deposited unit

H: Antibody 10E8 FAB HEAVY CHAIN

L: Antibody 10E8 FAB LIGHT CHAIN MUTATED

A: Antibody 10E8 FAB HEAVY CHAIN

B: Antibody 10E8 FAB LIGHT CHAIN MUTATED

O: 10E8 EPITOPE SCAFFOLD T117V2

E: 10E8 EPITOPE SCAFFOLD T117V2

hetero molecules

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

1

H: Antibody 10E8 FAB HEAVY CHAIN

L: Antibody 10E8 FAB LIGHT CHAIN MUTATED

E: 10E8 EPITOPE SCAFFOLD T117V2

hetero molecules

defined by author&software
Evidence: gel filtration
67.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Antibody 10E8 FAB HEAVY CHAIN

B: Antibody 10E8 FAB LIGHT CHAIN MUTATED

O: 10E8 EPITOPE SCAFFOLD T117V2

hetero molecules

defined by author&software
Evidence: gel filtration
67.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	40.931, 159.047, 100.606
Angle α, β, γ (deg.)	90.00, 95.17, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Details

Trimer according to Gel filtration

#1: Antibody	Antibody 10E8 FAB HEAVY CHAIN Mass: 25447.475 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGHV3-1505 / Plasmid: PHCMV3 / Cell line (production host): HEK 293S / Production host: Homo sapiens* (human)
#2: Antibody	Antibody 10E8 FAB LIGHT CHAIN MUTATED Mass: 22811.246 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGLV3-1901 / Plasmid: PHCMV3 / Cell line (production host): HEK 293S / Production host: Homo sapiens* (human)
#3: Protein	10E8 EPITOPE SCAFFOLD T117V2 Mass: 18643.090 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: PET29 / Cell (production host): BL-21 STAR / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 STAR
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.72 Å³/Da / Density % sol: 54.4 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Hepes pH 7.0, 30% PEG 6000;

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Data collection

Diffraction	Mean temperature: 110 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2.067→37.883 Å / Num. obs: 73937 / % possible obs: 94.8 % / Redundancy: 2.1 % / B_iso Wilson estimate: 48 Å² / R_sym value: 0.049 / Net I/σ(I): 9.2
Reflection shell	Resolution: 2.07→2.11 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.456 / Mean I/σ(I) obs: 2.1 / % possible all: 91.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
HKL-2000	Version 2.3.10	data reduction
HKL-2000	Version 2.3.10	data scaling
PHASER	2.6.1	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4G6F AND 3LF6

4g6f

3lf6

Resolution: 2.07→37.88 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.31 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.216	3696	5 %
R_work	0.178	-	-
obs	0.18	73905	94.6 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.07→37.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8404	0	36	209	8649

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	8859
X-RAY DIFFRACTION	f_angle_d	0.879	12128
X-RAY DIFFRACTION	f_dihedral_angle_d	12.776	5197
X-RAY DIFFRACTION	f_chiral_restr	0.058	1351
X-RAY DIFFRACTION	f_plane_restr	0.006	1574

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 (%)
2.0667-2.0939	0.2814	132	0.2697	2495	X-RAY DIFFRACTION	88
2.0939-2.1226	0.284	137	0.2488	2614	X-RAY DIFFRACTION	92
2.1226-2.1529	0.2828	144	0.2404	2729	X-RAY DIFFRACTION	93
2.1529-2.185	0.2745	136	0.2354	2592	X-RAY DIFFRACTION	93
2.185-2.2191	0.2728	137	0.2267	2615	X-RAY DIFFRACTION	93
2.2191-2.2555	0.2879	144	0.2332	2718	X-RAY DIFFRACTION	95
2.2555-2.2944	0.2561	146	0.2109	2767	X-RAY DIFFRACTION	96
2.2944-2.3361	0.2743	141	0.2106	2677	X-RAY DIFFRACTION	95
2.3361-2.381	0.2326	144	0.2029	2750	X-RAY DIFFRACTION	96
2.381-2.4296	0.2277	145	0.1904	2733	X-RAY DIFFRACTION	96
2.4296-2.4825	0.2639	141	0.1941	2700	X-RAY DIFFRACTION	96
2.4825-2.5402	0.2154	147	0.1863	2780	X-RAY DIFFRACTION	97
2.5402-2.6037	0.2425	142	0.1873	2715	X-RAY DIFFRACTION	96
2.6037-2.6741	0.2229	144	0.1741	2726	X-RAY DIFFRACTION	96
2.6741-2.7528	0.2232	145	0.1835	2759	X-RAY DIFFRACTION	95
2.7528-2.8416	0.2515	138	0.1889	2635	X-RAY DIFFRACTION	94
2.8416-2.9431	0.2488	147	0.201	2764	X-RAY DIFFRACTION	95
2.9431-3.0609	0.2375	143	0.1953	2732	X-RAY DIFFRACTION	97
3.0609-3.2001	0.2076	147	0.1902	2793	X-RAY DIFFRACTION	97
3.2001-3.3687	0.2155	146	0.1817	2753	X-RAY DIFFRACTION	96
3.3687-3.5797	0.2359	139	0.1706	2657	X-RAY DIFFRACTION	94
3.5797-3.8558	0.195	144	0.1639	2739	X-RAY DIFFRACTION	95
3.8558-4.2434	0.1951	141	0.1542	2678	X-RAY DIFFRACTION	94
4.2434-4.8563	0.1645	143	0.1374	2715	X-RAY DIFFRACTION	95
4.8563-6.1143	0.1968	143	0.1645	2721	X-RAY DIFFRACTION	94
6.1143-37.8898	0.213	140	0.1872	2652	X-RAY DIFFRACTION	91

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	2.0863	1.1022	-0.987	5.8084	-2.0368	6.0186	0.2682	-0.13	0.1737	0.7824	0.0516	0.6866	-0.5722	-0.3744	-0.2945	0.583	0.062	0.0983	0.4684	0.1085	0.5376	-34.4089	-69.1782	8.4142
2	1.3195	-0.5153	0.0069	5.462	-2.0271	5.968	0.0821	0.3229	0.0263	-1.2031	0.3014	0.5308	0.7047	-0.4252	-0.2789	0.7131	-0.156	-0.1117	0.5911	0.1603	0.6227	-8.9	-14.9875	-59.1481
3	4.0812	0.9198	1.1963	3.8873	0.933	4.2516	-0.1803	0.1737	-0.3987	-0.1652	-0.0082	0.241	0.3855	-0.276	0.1552	0.3659	-0.0407	0.093	0.2869	-0.0139	0.3892	-36.923	-69.5797	-26.7879
4	2.1889	1.3835	-0.7263	3.2554	-0.7558	5.472	-0.2245	0.391	-0.2967	-1.1849	0.3311	-0.4046	-0.4648	-0.2861	-0.0931	1.4739	-0.1577	0.1114	0.977	-0.1449	0.6605	-28.0742	-61.7135	-60.3001
5	1.7132	1.6525	-0.6857	3.7927	-1.6501	3.1214	-0.1336	-0.0868	-0.1668	-0.0176	0.0249	-0.1041	0.0955	0.0647	0.11	0.243	0.0345	0.0149	0.2534	-0.0016	0.2883	-25.3503	-53.9229	-20.934
6	3.3054	1.1366	1.7339	2.3701	0.0536	5.1853	-0.5029	-0.0202	0.6256	-1.4	0.0968	0.5369	-1.543	-0.0044	0.4271	1.6056	-0.1399	-0.1164	0.8292	-0.1206	0.7379	-27.0491	-45.6346	-56.291
7	2.255	-0.7006	-2.294	1.7472	-0.905	3.9944	-0.0332	-0.185	-0.3202	0.4576	-0.344	0.3712	0.7626	-0.0183	0.4349	1.2763	0.0288	-0.0197	1.1857	-0.147	0.8776	-11.6154	-39.3866	5.4344
8	2.0296	-0.7655	0.3106	2.8435	-1.5715	2.5291	-0.1414	0.0257	0.12	-0.0701	0.0182	-0.1962	0.0162	0.119	0.1157	0.2796	-0.0089	0.0068	0.2646	-0.0128	0.3232	-4.7562	-29.9327	-28.3401
9	1.791	-0.2912	0.6817	3.226	-0.5815	4.8263	0.0528	-0.2977	0.1041	0.7328	0.3268	-0.2291	-0.2196	-0.3432	-0.3583	1.3686	0.1289	0.0783	1.236	-0.1077	0.7616	-13.6863	-23.1266	9.9497
10	4.02	-0.49	-1.3519	4.5335	0.3934	4.7334	-0.1486	-0.052	0.3857	0.204	0.0542	0.4358	-0.2463	-0.4134	0.0723	0.3347	0.0279	-0.0422	0.3416	0.0009	0.4672	-18.0754	-15.3291	-24.2985

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'O'
2	X-RAY DIFFRACTION	2	CHAIN 'E'
3	X-RAY DIFFRACTION	3	CHAIN 'B' AND ((RESSEQ 2:109))
4	X-RAY DIFFRACTION	4	CHAIN 'B' AND ((RESSEQ 110:212))
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND ((RESSEQ 1:130))
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND ((RESSEQ 131:231))
7	X-RAY DIFFRACTION	7	CHAIN 'H' AND ((RESSEQ 132:232))
8	X-RAY DIFFRACTION	8	CHAIN 'H' AND ((RESSEQ 1:131))
9	X-RAY DIFFRACTION	9	CHAIN 'L' AND ((RESSEQ 111:212))
10	X-RAY DIFFRACTION	10	CHAIN 'L' AND ((RESSEQ 1:110))

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