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- PDB-6vg5: DengueV-2 Capsid ST148 inhibitor Complex -

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Basic information

Entry
Database: PDB / ID: 6vg5
TitleDengueV-2 Capsid ST148 inhibitor Complex
ComponentsCapsid premembrane protein
KeywordsVIRAL PROTEIN/INHIBITOR / Dengue / Capsid / Inhibitor / VIRAL PROTEIN / VIRAL PROTEIN-INHIBITOR 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 ...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 / monoatomic ion channel activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #930 / : / 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 ...Arc Repressor Mutant, subunit A - #930 / : / 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 / Arc Repressor Mutant, subunit A / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / Chem-QWY / Capsid premembrane protein / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsWhite, M. / Xia, H. / Shi, P.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI142759 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI127744 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI136126 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI145617 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: A cocrystal structure of dengue capsid protein in complex of inhibitor.
Authors: Xia, H. / Xie, X. / Zou, J. / Noble, C.G. / Russell, W.K. / Holthauzen, L.M.F. / Choi, K.H. / White, M.A. / Shi, P.Y.
History
DepositionJan 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid premembrane protein
B: Capsid premembrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,27519
Polymers18,8012
Non-polymers1,47417
Water97354
1
A: Capsid premembrane protein
B: Capsid premembrane protein
hetero molecules

A: Capsid premembrane protein
B: Capsid premembrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,55038
Polymers37,6024
Non-polymers2,94834
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)40.400, 25.500, 68.500
Angle α, β, γ (deg.)90.000, 92.550, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-203-

NO3

21A-315-

HOH

31A-322-

HOH

41B-307-

HOH

51B-311-

HOH

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Components

#1: Protein Capsid premembrane protein


Mass: 9400.506 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2D2BF61, UniProt: P07564*PLUS
#2: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-QWY / 3-amino-N-(5-phenyl-1,3,4-thiadiazol-2-yl)-6,7,8,9-tetrahydro-5H-cyclohepta[b]thieno[3,2-e]pyridine-2-carboxamide


Mass: 421.538 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H19N5OS2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 3.0 M NaNO3, 100 mM HEPES pH 6.8, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07812 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 10, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07812 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 21285 / % possible obs: 93.4 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.042 / Rrim(I) all: 0.103 / Χ2: 0.922 / Net I/σ(I): 8.7 / Num. measured all: 129277
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.535.80.8298150.6950.3690.910.70575.9
1.53-1.556.10.79810130.7220.3490.8730.71988.4
1.55-1.586.40.71810420.8480.3050.7820.7592.5
1.58-1.626.30.62810610.8740.2690.6840.77394.5
1.62-1.656.40.57410590.8860.2440.6250.79494.3
1.65-1.696.20.50510900.9160.2170.5510.82994.8
1.69-1.736.20.4310390.9310.1850.4690.86194.9
1.73-1.786.20.37811020.9420.1630.4130.90996.2
1.78-1.836.20.32510960.9580.140.3550.9695.7
1.83-1.896.20.27510590.9660.1190.3010.98195.3
1.89-1.9660.22210970.9770.0980.2431.05194.6
1.96-2.045.80.1569700.9880.070.1721.0687.2
2.04-2.136.10.12410710.9920.0540.1351.09392.7
2.13-2.246.40.10310990.9930.0440.1121.10897.4
2.24-2.386.30.08511080.9960.0370.0921.08396.9
2.38-2.566.20.07411140.9950.0330.0811.0696.9
2.56-2.8260.06511220.9960.0290.0721.06197
2.82-3.235.70.05110990.9960.0230.0560.91296.2
3.23-4.075.30.04110420.9970.020.0460.83488.3
4.07-505.80.04111870.9960.020.0460.80697.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.85 Å20.37 Å
Translation1.85 Å20.37 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.7.17phasing
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1sfk

1sfk


Resolution: 1.5→40.39 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.814 / SU ML: 0.047 / SU R Cruickshank DPI: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.086
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 973 4.8 %RANDOM
Rwork0.1454 ---
obs0.1478 19240 88.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.5 Å2 / Biso mean: 17.535 Å2 / Biso min: 6.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å2-0 Å2-0.07 Å2
2---0.05 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 1.5→40.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1309 0 126 54 1489
Biso mean--26.73 28.01 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131466
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171489
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.671949
X-RAY DIFFRACTIONr_angle_other_deg1.3231.5833404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8475166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.45215.97477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33515284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.071524
X-RAY DIFFRACTIONr_chiral_restr0.0640.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0191585
X-RAY DIFFRACTIONr_gen_planes_other0.0010.019353
X-RAY DIFFRACTIONr_mcbond_it1.5851.525652
X-RAY DIFFRACTIONr_mcbond_other1.5821.523651
X-RAY DIFFRACTIONr_mcangle_it2.1242.277813
X-RAY DIFFRACTIONr_rigid_bond_restr1.10232954
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.197 36 -
Rwork0.165 743 -
all-779 -
obs--48.03 %

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