PDB-6flc: 2C8 Fab bound to EDIII of DenV 2

ID or keywords:

Entry

Database: PDB / ID: 6flc

Title

2C8 Fab bound to EDIII of DenV 2

Components

Domain III of Dengue virus 2
Heavy chain of 2C8 Fab
Light chain of 2C8 Fab

Keywords

VIRAL PROTEIN /

Dengue virus /

antibody / macromolecular complex

Function / homology

Function and homology information

symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity /

flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / : /

viral capsid / nucleoside-triphosphate phosphatase /

double-stranded RNA binding / protein complex oligomerization ...
Similarity search - Function

Immunoglobulin-like - #350 / : / Flavivirus envelope glycoprotein E, stem/anchor domain /

RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus ...Immunoglobulin-like - #350 / : / Flavivirus envelope glycoprotein E, stem/anchor domain /

RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M /

RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain /

DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily /

Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain /

RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily /

Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily /

Immunoglobulin-like /

Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology

Biological species

Mus musculus (house mouse)

Dengue virus 2

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Flanagan, A. / Renner, M. / Grimes, J.M.

Funding support

United Kingdom, 2items

Citation

Journal: Nat. Immunol. / Year: 2018
Title: Characterization of a potent and highly unusual minimally enhancing antibody directed against dengue virus.
Authors: Renner, M. / Flanagan, A. / Dejnirattisai, W. / Puttikhunt, C. / Kasinrerk, W. / Supasa, P. / Wongwiwat, W. / Chawansuntati, K. / Duangchinda, T. / Cowper, A. / Midgley, C.M. / Malasit, P. / ...

History

Deposition	Jan 25, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 24, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 31, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6flc.cif.gz	423.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6flc.ent.gz	358.4 KB	Display	PDB format
PDBx/mmJSON format	6flc.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/fl/6flc ftp://data.pdbj.org/pub/pdb/validation_reports/fl/6flc	HTTPS FTP

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Related structure data

Related structure data	6flaC 6flbC C: citing same article (ref.)
Similar structure data	6nmr-2 5b71-1 6nmr-3 6p9h-1 1ob1-2 6k7o-2 6sv2-d 6mvl-d 3s36-d 5b71-2 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	#103 - Jul 2008 Dengue Virus similarity (44) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #197 - May 2016 Zika Virus similarity (43) #145 - Jan 2012 Messenger RNA Capping similarity (1)

Deposited unit

A: Light chain of 2C8 Fab

B: Heavy chain of 2C8 Fab

G: Domain III of Dengue virus 2

H: Heavy chain of 2C8 Fab

I: Domain III of Dengue virus 2

L: Light chain of 2C8 Fab

hetero molecules

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

1

A: Light chain of 2C8 Fab

B: Heavy chain of 2C8 Fab

I: Domain III of Dengue virus 2

hetero molecules

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

2

G: Domain III of Dengue virus 2

H: Heavy chain of 2C8 Fab

L: Light chain of 2C8 Fab

hetero molecules

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

Unit cell

Length a, b, c (Å)	42.560, 61.416, 104.594
Angle α, β, γ (deg.)	77.54, 81.11, 85.53
Int Tables number	1
Space group name H-M	P1

#1: Antibody	Light chain of 2C8 Fab Mass: 23795.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#2: Antibody	Heavy chain of 2C8 Fab Mass: 24805.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#3: Protein	Domain III of Dengue virus 2 Mass: 11063.860 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 2 / Production host: Escherichia coli (E. coli) / References: UniProt: P14340, UniProt: W5RZ25*PLUS
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 595 / 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: 2.28 Å³/Da / Density % sol: 45.95 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: Read the paper

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.98 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2→33.7 Å / Num. obs: 66849 / % possible obs: 97 % / Redundancy: 3.9 % / B_iso Wilson estimate: 30.52 Å² / Net I/σ(I): 15
Reflection shell	Resolution: 2→2.1 Å

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Processing

Software

Name	Version	Classification
BUSTER	2.9.2	refinement
DENZO		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→33.7 Å / Cor.coef. F_o:F_c: 0.9421 / Cor.coef. F_o:F_c free: 0.9231 / Cross valid method: THROUGHOUT / σ(F): 0

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.216	3395	5.08 %	RANDOM
R_work	0.1798	-	-	-
obs	0.1817	66849	97 %	-

Displacement parameters

B_iso mean: 36.86 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.0602 Å²	4.3279 Å²	3.6555 Å²
2-	-	-4.3186 Å²	2.7938 Å²
3-	-	-	5.3788 Å²

Refine analyze

Luzzati coordinate error obs: 0.241 Å

Refinement step

Cycle: 1 / Resolution: 2→33.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8143	0	24	595	8762

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.008	8373	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.13	11392	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		2780	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		181	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		1206	HARMONIC	5
X-RAY DIFFRACTION	t_it		8373	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	3.37
X-RAY DIFFRACTION	t_other_torsion	18.86
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		1122	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		9500	SEMIHARMONIC	4

LS refinement shell

Resolution: 2→2.05 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.2011	268	5.38 %
R_work	0.195	4714	-
all	0.1954	4982	-

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	-0.4838	-1.9748	-0.5027	1.4691	-0.2534	2.8806	-0.0186	0.054	-0.1629	-0.0789	0.0231	0.1277	-0.0875	-0.0625	-0.0045	-0.137	0.0387	-0.0191	0.0088	-0.0003	0.1052	-54.4845	12.5736	58.5153
2	0.5206	-1.671	0.0585	3.9036	-0.6294	2.2678	-0.0203	0.0059	0.1481	-0.0213	-0.0339	-0.0665	-0.195	-0.0168	0.0542	-0.1061	0.0293	-0.0007	-0.0279	-0.0235	-0.0167	-45.0723	13.4734	60.8782
3	0.3594	0.0728	-0.0342	-0.1086	-0.016	1.9469	0.0477	0.1452	0.1801	-0.0548	0.1344	0.0743	-0.195	-0.1737	-0.1821	-0.0655	0.0917	0.0828	-0.071	0.0176	0.0065	-42.486	15.5028	34.5705
4	-0.13	-1.0639	-1.3853	2.125	0.5544	0.5552	0.0004	0.045	0.0739	0.0622	0.0259	0.144	-0.0214	-0.1263	-0.0263	-0.1116	0.0416	0.1206	-0.0485	0.0883	0.0837	-46.7846	19.4233	29.5307
5	-0.0569	-0.5957	0.2178	0.7512	0.5748	0.4279	0.0235	0.1734	0.1982	-0.0161	0.0653	0.2342	-0.0434	-0.1286	-0.0888	-0.07	0.1072	0.0609	0.0703	0.1366	0.0263	-45.2816	19.8745	17.9673
6	1.3473	-0.3788	0.5061	-0.3503	-1.0674	1.0427	-0.0188	-0.0051	0.1009	-0.1169	0.0785	-0.06	0.0813	-0.0003	-0.0597	0.0009	0.0057	0.0349	-0.0256	-0.0036	-0.067	-32.2933	-6.9722	48.9304
7	3.1472	-0.3656	0.1478	2.709	0.1127	1.9562	-0.0598	-0.1583	-0.0336	0.0136	0.091	-0.0704	0.2474	-0.0175	-0.0312	-0.0027	0.0359	0.0296	-0.0549	0.006	-0.0797	-38.21	-7.6965	59.6963
8	0.8779	-0.0622	-0.8776	0.4247	-0.5152	2.5721	-0.0283	0.0336	0.1453	-0.0062	0.1589	0.0504	0.0754	-0.0573	-0.1306	-0.0171	-0.003	0.0022	-0.0404	0.0103	-0.0087	-37.3449	-0.6086	46.3109
9	1.1899	-0.3857	-0.282	1.0583	0.4827	2.4955	0.1356	0.0593	0.2722	0.0122	0.1292	-0.0402	-0.2566	0.0541	-0.2649	-0.0389	-0.0158	0.0752	-0.0753	0.0187	-0.0255	-31.9057	14.0739	29.7776
10	1.808	0.5758	-0.8652	0.0413	0.3156	1.444	0.0412	-0.0613	0.1544	-0.1091	0.0701	-0.0522	-0.0965	0.0926	-0.1113	0.0021	-0.0453	0.0431	0.0112	-0.0024	-0.0127	-23.6114	12.5216	25.646
11	0.2271	1.2329	0.1762	2.4365	-1.3147	1.4993	0.0342	-0.0078	0.0938	-0.1385	0.0298	-0.0514	0.0085	-0.018	-0.064	-0.0018	0.0961	0.0526	0.0142	0.0523	-0.0383	-38.4463	15.0565	-42.2564
12	1.4122	0.5634	-1.9762	0.394	-0.6481	2.3527	0.0338	0.011	0.0723	-0.1252	0.0333	0.0016	0.0412	-0.0271	-0.067	-0.0179	0.0517	0.0131	0.0138	0.0405	-0.063	-39.8677	10.5015	-40.722
13	-0.1057	0.2048	-0.4651	0.3043	-0.1707	0.3077	0.0035	-0.0313	-0.0454	-0.0056	0.0272	0.021	0.0583	-0.0009	-0.0307	0.0091	0.0767	0.0148	0.0321	-0.0156	-0.0138	-35.8645	2.088	-46.9812
14	1.8234	0.0112	-1.5618	1.3267	-1.2199	2.8782	0.0381	0.0878	0.079	-0.0418	0.0204	-0.0475	0.0593	0.0283	-0.0585	-0.0418	0.0617	0.0524	-0.0007	0.0131	-0.064	-36.6792	11.9024	-43.1412
15	0.8394	0.2213	1.3643	-0.2138	-0.4994	0.2484	-0.0091	0.006	-0.0146	-0.0909	0.0011	0.0008	-0.027	-0.0429	0.0079	0.0141	0.0196	0.0178	0.0805	0.0436	-0.1065	-44.2696	8.869	-47.8681
16	1.02	-0.1735	0.4671	2.036	-0.5176	2.317	-0.018	0.1067	-0.1251	-0.0539	0.012	0.024	0.057	0.0099	0.006	-0.0466	0.0467	0.0097	0.0331	-0.0341	-0.0343	-40.3591	-2.3983	-13.8348
17	1.2737	0.4103	-0.2163	0.3498	-0.2654	0.3699	0.0728	-0.0384	-0.1595	-0.005	-0.0778	-0.0077	0.0601	0.1583	0.005	-0.0494	0.039	-0.0242	-0.0583	-0.0516	-0.0303	-45.3199	-6.1713	-3.6482
18	0.2416	1.3047	0.1388	0.8987	-0.1619	0.2633	0.0176	0.0254	-0.091	-0.0065	0.05	0.0143	0.1795	0.0804	-0.0676	-0.0682	-0.0096	-0.0225	-0.0378	0.0106	0.021	-56.615	-20.2628	9.2408
19	3.0446	-1.4733	-1.4227	0.3124	0.2429	2.0375	0.0612	0.0262	-0.0422	-0.0245	-0.0206	0.1007	0.1742	-0.1271	-0.0406	-0.0493	-0.0095	-0.0419	-0.0322	0.0299	-0.0296	-60.9607	-14.9005	11.2767
20	-0.1036	0.9894	-1.6638	1.5902	-0.9028	1.0611	-0.0051	-0.0298	-0.0887	-0.0128	0.0872	-0.0987	0.0065	-0.0731	-0.0821	-0.0315	-0.0401	-0.0805	-0.0799	0.0331	0.2012	-56.5942	-25.5676	14.0475
21	1.2256	-1.4393	1.093	0.7227	1.4594	1.4744	-0.0455	-0.2746	0.2608	-0.164	0.1943	-0.1559	-0.3066	0.0105	-0.1488	-0.0463	0.0143	0.0292	-0.1035	-0.0299	-0.0094	-51.8971	17.1498	-8.3165
22	3.8887	-0.8237	-0.1391	1.9029	1.3171	2.937	-0.0018	0.1486	0.3405	-0.1949	0.0113	0.0405	-0.457	-0.188	-0.0094	-0.0275	0.0453	-0.0057	-0.0906	0.0224	-0.0271	-54.2322	15.9756	-15.5556
23	0.2405	0.0521	0.0796	0.3663	-0.0422	1.3441	0.0703	-0.07	-0.001	0.0036	0.0587	0.0619	0.0494	-0.0766	-0.129	-0.0624	0.0262	-0.0077	-0.011	0.0062	-0.004	-56.4443	4.7854	1.6914
24	1.1031	0.1274	-0.6933	1.8579	-0.1069	0.2313	0.0531	-0.0519	-0.0427	0.0182	-0.0346	0.0316	-0.107	0.0401	-0.0185	-0.0446	0.0047	-0.004	0.043	0.0371	-0.0225	-54.4692	-2.2736	16.3732
25	2.1796	-0.0716	0.2313	1.0909	1.197	1.0755	0.0594	-0.2245	-0.0931	0.164	0.0199	-0.0421	-0.0253	-0.0208	-0.0793	-0.0282	-0.0395	0.0069	0.0367	0.0511	-0.0514	-58.0706	-3.5695	23.6724
26	0.7514	1.1839	-0.4142	-0.8187	-1.5807	0.7381	-0.0213	-0.0389	-0.0315	0.0354	0.0268	0.0122	0.0482	0.0164	-0.0055	0.0918	0.1129	0.0876	-0.0409	0.0177	-0.0501	-51.8847	-5.8006	87.169
27	-0.1549	0.1332	-0.4289	0.8409	0.19	2.1109	-0.0008	0.0222	0.0098	0.0227	0.0658	0.0411	0.0848	0.0603	-0.0649	0.0156	0.0642	0.0704	-0.0523	0.0064	-0.0391	-51.8598	-4.1186	83.2556
28	-0.2316	-1.1152	-0.1398	-0.1329	-0.3659	3.0763	0.025	0.0286	0.0378	-0.0132	-0.0416	0.0523	0.091	0.0436	0.0166	-0.0381	0.0561	0.0468	-0.0824	-0.1281	0.0379	-58.8637	-0.6725	85.2523
29	0.6155	0.4872	0.6187	0.9575	-0.1848	0.2027	0.0028	0.0184	0.0029	0.0126	-0.0155	0.0029	0.0014	0.0421	0.0127	0.0283	0.1387	0.0472	-0.0155	-0.0255	-0.0542	-52.0192	-3.5183	90.3633
30	0.6908	1.271	0.4753	1.9829	-0.1809	-0.233	0.0033	0.0073	-0.0354	0.037	0.0024	0.0319	0.0432	-0.0242	-0.0057	0.0988	-0.1154	0.14	-0.0592	-0.0284	-0.056	-62.4058	-9.0635	86.2485

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|1 - A\|31 }
2	X-RAY DIFFRACTION	2	{ A\|32 - A\|92 }
3	X-RAY DIFFRACTION	3	{ A\|93 - A\|139 }
4	X-RAY DIFFRACTION	4	{ A\|140 - A\|173 }
5	X-RAY DIFFRACTION	5	{ A\|174 - A\|211 }
6	X-RAY DIFFRACTION	6	{ B\|2 - B\|24 }
7	X-RAY DIFFRACTION	7	{ B\|25 - B\|83 }
8	X-RAY DIFFRACTION	8	{ B\|84 - B\|135 }
9	X-RAY DIFFRACTION	9	{ B\|136 - B\|196 }
10	X-RAY DIFFRACTION	10	{ B\|197 - B\|221 }
11	X-RAY DIFFRACTION	11	{ G\|299 - G\|317 }
12	X-RAY DIFFRACTION	12	{ G\|318 - G\|343 }
13	X-RAY DIFFRACTION	13	{ G\|344 - G\|354 }
14	X-RAY DIFFRACTION	14	{ G\|355 - G\|379 }
15	X-RAY DIFFRACTION	15	{ G\|380 - G\|394 }
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