PDB-4l5f: Crystal Structure of DENV1-E106 Fab bound to DENV-1 Envelope prot...

ID or keywords:

Entry

Database: PDB / ID: 4l5f

Title

Crystal Structure of DENV1-E106 Fab bound to DENV-1 Envelope protein DIII

Components

Envelope proteinViral envelope
Heavy chain of E106 antibody (VH and CH1 of IgG2c)
Light chain of E106 antibody (kappa)

Keywords

VIRAL PROTEIN /

IMMUNE SYSTEM /

antibody /

FAB /

neutralizing /

virus /

envelope / antibody epitope /

infectious disease / Center for Structural Genomics of Infectious Diseases (CSGID) / NIAID /

National Institute of Allergy and Infectious Diseases

Function / homology

Function and homology information

membrane => GO:0016020 / host cell endoplasmic reticulum membrane /

protein dimerization activity / fusion of virus membrane with host endosome membrane /

viral envelope / virion attachment to host cell / endoplasmic reticulum membrane / virion membrane
Similarity search - Function

Biological species

Dengue virus 1

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.45 Å

Authors

Edeling, M.A. / Nelson, C.A. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: Crystal Structure of DENV1-E106 Fab bound to DENV-1 Envelope protein DIII
Authors: Edeling, M.A. / Austin, S.K. / Shrestha, B. / Dowd, K.A. / Mukherjee, S. / Nelson, C.A. / Johnson, S. / Mabila, M.N. / Christian, E.A. / Rucker, J. / Pierson, T.C. / Diamond, M.S. / Fremont, D.H.

History

Deposition	Jun 11, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 11, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4l5f.cif.gz	218.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4l5f.ent.gz	181.9 KB	Display	PDB format
PDBx/mmJSON format	4l5f.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l5/4l5f ftp://data.pdbj.org/pub/pdb/validation_reports/l5/4l5f	HTTPS FTP

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Related structure data

Similar structure data	6p50-d 5kvf-d 6fla-2 6svl-1 5tzu-d 6fla-1 6o9h-2 6bfs-d 1tqc-d 6plk-2 5ikc-1 6ute-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
Other databases	TargetTrack: CSGID-IDP00272

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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) #103 - Jul 2008 Dengue Virus similarity (11) #197 - May 2016 Zika Virus similarity (11)

Deposited unit

H: Heavy chain of E106 antibody (VH and CH1 of IgG2c)

E: Envelope protein

L: Light chain of E106 antibody (kappa)

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	82.6610, 91.8230, 92.5990
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	Heavy chain of E106 antibody (VH and CH1 of IgG2c) Mass: 23538.461 Da / Num. of mol.: 1 / Fragment: VH and CH1 domains / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: IFN-ABR-/- C57BL/6 MICE
#2: Protein	Envelope protein / Viral envelope Mass: 11985.743 Da / Num. of mol.: 1 / Fragment: domain III (UNP residues 293-399) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 1 / Strain: 16007 / Gene: E / Plasmid: PET21(A)+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8BE40
#3: Antibody	Light chain of E106 antibody (kappa) Mass: 23564.875 Da / Num. of mol.: 1 / Fragment: VL anD CL domains / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: IFN-ABR-/- C57BL/6 MICE
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.99 Å³/Da / Density % sol: 58.93 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 14 mg/mL in a well solution of 22% PEG 6000, and 0.1 M MES pH 5.0 (final pH 5.7), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 4.2.2 / Wavelength: 0.97625 Å

Detector

Type: NOIR-1 / Detector: CCD / Date: Aug 1, 2009

Radiation

Monochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97625 Å / Relative weight: 1

Reflection

Resolution: 2.45→20 Å / Num. obs: 26014 / % possible obs: 99.5 % / Redundancy: 6.4 % / R_merge(I) obs: 0.083 / Χ²: 1.001 / Net I/σ(I): 13.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.45-2.54	4.8	0.546	2448	0.707	1	95.9
2.54-2.64	5.6	0.462	2577	0.786	1	98.9
2.64-2.76	6.2	0.368	2545	0.893	1	100
2.76-2.9	6.5	0.251	2597	1.044	1	100
2.9-3.08	6.6	0.184	2594	1.016	1	100
3.08-3.32	6.7	0.131	2590	1.1	1	100
3.32-3.65	6.8	0.102	2596	1.117	1	100
3.65-4.18	6.9	0.077	2631	1.019	1	100
4.18-5.25	7	0.057	2647	1.001	1	100
5.25-20	6.8	0.051	2789	1.148	1	100

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 50.83 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	4 Å	20 Å
Translation	4 Å	20 Å

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHASER	2.1.4	phasing
PHENIX	1.8.2_1309	refinement
PDB_EXTRACT	3.11	data extraction
HKL-2000		data collection
DENZO		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.45→19.998 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7753 / SU ML: 0.34 / σ(F): 1.34 / Phase error: 28.04 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2387	1314	5.07 %
R_work	0.1897	-	-
obs	0.1921	25912	97.88 %

Solvent computation

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

Displacement parameters

B_iso max: 158.05 Å² / B_iso mean: 58.9307 Å² / B_iso min: 29.83 Å²

Refinement step

Cycle: LAST / Resolution: 2.45→19.998 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4063	0	0	94	4157

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	4158
X-RAY DIFFRACTION	f_angle_d	0.822	5650
X-RAY DIFFRACTION	f_chiral_restr	0.054	649
X-RAY DIFFRACTION	f_plane_restr	0.004	717
X-RAY DIFFRACTION	f_dihedral_angle_d	11.24	1505

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.4501-2.548	0.3495	108	0.2738	2284	2392	83
2.548-2.6637	0.3614	149	0.2699	2724	2873	99
2.6637-2.8038	0.3216	151	0.2557	2735	2886	100
2.8038-2.9789	0.3078	142	0.2436	2765	2907	100
2.9789-3.2081	0.2836	156	0.2285	2754	2910	100
3.2081-3.5293	0.2485	147	0.2171	2795	2942	100
3.5293-4.0364	0.2403	150	0.1858	2784	2934	100
4.0364-5.0717	0.1718	157	0.1429	2809	2966	100
5.0717-19.9986	0.2133	154	0.1597	2948	3102	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	5.7548	0.7034	-2.7741	2.2529	-1.5646	5.6103	0.135	-0.194	-0.465	0.1037	-0.151	-0.3314	0.2245	0.2519	0.0296	0.4704	0.0169	-0.1375	0.3155	0.024	0.6086	44.5929	-9.8706	-18.0531
2	1.139	0.8949	-1.128	1.9081	-0.3	1.7832	-0.0158	-0.2392	-0.0381	0.1767	0.0859	-0.1375	-0.0356	0.1702	-0.0762	0.4434	0.0595	-0.0672	0.348	0.0552	0.5601	36.784	-8.7934	-15.3131
3	8.5017	0.7417	2.4887	4.2591	-0.7537	4.744	-0.0544	0.7741	-0.3677	-0.369	0.0121	0.3262	0.3725	-0.3678	0.0182	0.4209	0.0231	0.0047	0.517	-0.0563	0.334	10.9187	-18.8723	-16.5386
4	1.9663	3.8317	-0.2165	7.7791	1.1385	7.6598	-0.175	0.7769	-0.5521	0.7915	-0.0573	-1.3202	0.5268	1.1965	0.2078	0.4206	-0.0189	0.033	0.4884	-0.0284	0.8301	60.8258	-2.2762	-36.4775
5	5.3809	4.8725	-5.4749	4.5032	-4.972	5.4432	-0.0096	1.2301	0.1614	-0.1238	0.5156	0.3494	0.0682	-0.6921	-0.5204	0.5346	-0.0481	0.032	0.5944	-0.0185	0.6631	59.304	18.2282	-42.7562
6	8.6579	4.8009	-5.1087	9.4251	-6.3081	7.9781	0.0094	0.133	-1.0489	0.2654	-0.1176	0.1765	0.2107	0.6715	0.1787	0.2843	0.0162	-0.0417	0.3988	-0.084	0.4739	58.5972	2.0872	-35.7827
7	1.8725	-2.8036	1.7951	9.5659	-6.6407	4.6899	0.3702	1.1738	-0.8869	-1.9913	-0.9231	-0.37	1.8395	-0.0066	0.6438	0.9469	0.0009	0.1811	1.2737	-0.3396	0.7944	58.8836	4.3476	-54.6396
8	5.1786	-4.666	3.6401	4.2868	-3.2857	2.5634	-1.5372	3.611	-1.4511	-2.4261	-0.6493	-2.9848	-0.1878	2.0812	2.1826	1.2954	0.0175	0.4507	1.6864	0.2201	1.4283	66.5705	5.6368	-52.2671
9	8.6845	1.3977	-0.7185	5.0297	-4.341	3.7934	1.0145	-0.5572	0.2428	-2.2191	-1.6808	-1.2486	1.347	1.3833	0.6713	0.7632	0.1012	0.2174	0.6484	0.1302	1.2539	69.1671	7.3154	-41.2666
10	7.8591	0.7126	-0.801	3.3708	-3.3034	3.2295	0.2717	-1.3522	-0.5198	1.0956	-0.222	-1.6989	-0.0503	1.0122	-0.0276	0.5774	-0.0306	-0.1702	0.6341	0.1123	0.7525	63.1069	1.9999	-31.7272
11	5.2991	6.9585	-6.2044	9.379	-8.2506	7.3427	0.6413	-0.1506	0.5827	0.6078	-0.2867	0.344	-0.4078	1.1749	-0.4724	0.4686	-0.0872	0.0012	0.5252	-0.057	0.5511	60.0189	7.7304	-33.6201
12	3.094	-3.9048	0.0215	5.3922	-1.7942	6.7162	0.5106	1.1802	2.1551	-0.1775	0.7931	0.2688	-0.4215	-0.07	-1.1468	0.7462	-0.4316	0.2982	1.5557	0.1885	0.8992	61.7426	13.7207	-54.4963
13	7.5791	-5.1236	3.345	9.0647	-6.482	4.641	0.3409	0.7447	-0.7716	-0.6307	0.0474	0.3901	1.1301	0.1987	-0.4771	0.5128	0.0307	-0.0061	0.5994	-0.2379	0.5458	54.5701	1.4921	-47.0351
14	5.9228	4.9533	0.7962	4.1784	1.5403	9.1073	-0.6415	0.9038	1.2228	-1.1199	0.9544	1.2419	0.005	-0.2574	-0.167	0.4612	-0.096	0.0029	0.4756	-0.0618	0.6545	55.7865	13.078	-51.0253
15	3.6023	1.5746	-1.1017	3.6014	-0.1265	3.5586	0.1792	0.4269	0.4562	0.2196	0.2676	0.0682	-0.5411	-0.3259	-0.4093	0.4518	0.0504	0.0489	0.3134	0.122	0.5303	32.8221	7.7194	-28.8988
16	4.4787	0.8062	-1.6141	5.6098	-1.1717	2.6954	0.3237	0.6698	0.6881	0.2451	0.1779	0.2875	-0.3458	-0.2445	-0.4525	0.4439	0.0428	0.0876	0.3491	0.1016	0.513	32.2009	6.8406	-26.9753
17	5.2564	1.9822	-3.7595	0.5949	-1.4896	3.5585	0.2098	0.4411	0.4575	0.0252	0.0336	0.0168	-0.1589	-0.2652	-0.2481	0.3809	0.0361	-0.0284	0.3897	0.1245	0.4462	6.7162	-5.3855	-13.0685
18	7.5318	-0.0199	-2.344	5.0688	-4.9202	7.2621	-0.1643	0.2056	0.0431	0.2884	0.2782	0.1226	0.022	-0.6422	-0.0578	0.4086	-0.0668	-0.0199	0.2966	-0.0088	0.388	-1.6063	-9.8791	-5.5211

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 82 )	H
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 82A through 119 )	H
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 120 through 214 )	H
4	X-RAY DIFFRACTION	4	chain 'E' and (resid 297 through 308 )	E
5	X-RAY DIFFRACTION	5	chain 'E' and (resid 309 through 319 )	E
6	X-RAY DIFFRACTION	6	chain 'E' and (resid 320 through 336 )	E
7	X-RAY DIFFRACTION	7	chain 'E' and (resid 337 through 345 )	E
8	X-RAY DIFFRACTION	8	chain 'E' and (resid 346 through 350 )	E
9	X-RAY DIFFRACTION	9	chain 'E' and (resid 351 through 355 )	E
10	X-RAY DIFFRACTION	10	chain 'E' and (resid 356 through 360 )	E
11	X-RAY DIFFRACTION	11	chain 'E' and (resid 361 through 369 )	E
12	X-RAY DIFFRACTION	12	chain 'E' and (resid 370 through 375 )	E
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 376 through 386 )	E
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 387 through 394 )	E
15	X-RAY DIFFRACTION	15	chain 'L' and (resid 1 through 69 )	L
16	X-RAY DIFFRACTION	16	chain 'L' and (resid 70 through 101 )	L
17	X-RAY DIFFRACTION	17	chain 'L' and (resid 102 through 174 )	L
18	X-RAY DIFFRACTION	18	chain 'L' and (resid 175 through 213 )	L

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