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- PDB-3g7t: Crystal structure of dengue virus type 1 envelope protein in the ... -

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Basic information

Entry
Database: PDB / ID: 3g7t
TitleCrystal structure of dengue virus type 1 envelope protein in the postfusion conformation
ComponentsEnvelope proteinViral envelope
KeywordsVIRAL PROTEIN / Membrane fusion protein / envelope protein / membrane anchor / fusion loop / IgC domain / beta sandwich / glycoprotein / Membrane / Transmembrane / Virion
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / 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 ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / 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 / membrane => GO:0016020 / protein dimerization activity / 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 / endoplasmic reticulum membrane / virion membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus ...Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Envelope protein E / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsModis, Y.
CitationJournal: J.Virol. / Year: 2009
Title: Crystal structure of dengue virus type 1 envelope protein in the postfusion conformation and its implications for membrane fusion.
Authors: Nayak, V. / Dessau, M. / Kucera, K. / Anthony, K. / Ledizet, M. / Modis, Y.
History
DepositionFeb 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Apr 23, 2014Group: Other
Revision 1.4Nov 1, 2017Group: Refinement description / Category: software
Revision 1.5Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7862
Polymers43,7511
Non-polymers351
Water181
1
A: Envelope protein
hetero molecules

A: Envelope protein
hetero molecules

A: Envelope protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,3596
Polymers131,2533
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area12310 Å2
ΔGint-104 kcal/mol
Surface area48470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.650, 75.650, 292.802
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

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Components

#1: Protein Envelope protein / Viral envelope


Mass: 43750.883 Da / Num. of mol.: 1 / Fragment: Soluble ectodomain residues 1-400
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 1 / Strain: 98901518 DHF DV-1 / Gene: E / Plasmid: pMTBip/V5-His / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider 2 / References: UniProt: Q5USP2, UniProt: Q689G3*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS STATE THAT THERE ARE NO SEQUENCE CONFLICTS BETWEEN THE SEQUENCE IN THE PDB FILE AND ...THE AUTHORS STATE THAT THERE ARE NO SEQUENCE CONFLICTS BETWEEN THE SEQUENCE IN THE PDB FILE AND SEQUENCE DATABASE REFERENCE NCBI BAD42413.

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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: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12.5% PEG 550 MME, 0.1 M MES pH 6.5, 10 mM ZnSO4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.97949
SYNCHROTRONNSLS X2520.97949
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDJul 20, 2007Kohzu HLD*-24 monchromator followed by vertical and horizontal focusing mirrors
ADSC QUANTUM 3152CCDAug 25, 2007Pt-coated toroidal Si mirror for horizontal and vertical focussing followed by double flat Si crystal monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Kohzu HLD*-24SINGLE WAVELENGTHMx-ray1
2Si crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 6794 / Num. obs: 6794 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 73.8 Å2 / Rmerge(I) obs: 0.223
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 1.64 / Num. unique all: 607 / % possible all: 92

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.4.0077refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OK8
Resolution: 3.5→25 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.839 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 71.167 / SU ML: 0.511 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.711 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.297 311 4.6 %RANDOM
Rwork0.208 ---
obs0.212 6786 98.32 %-
all-6786 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 157.41 Å2 / Biso mean: 63.849 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--4.11 Å2-2.06 Å20 Å2
2---4.11 Å20 Å2
3---6.17 Å2
Refine analyzeLuzzati coordinate error free: 0.711 Å / Luzzati sigma a free: 0.511 Å
Refinement stepCycle: LAST / Resolution: 3.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2905 0 1 1 2907
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222961
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.9634014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4015375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.06625.133113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg26.03715530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4241511
X-RAY DIFFRACTIONr_chiral_restr0.1140.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212138
X-RAY DIFFRACTIONr_mcbond_it7.2012.51873
X-RAY DIFFRACTIONr_mcangle_it11.62143035
X-RAY DIFFRACTIONr_scbond_it8.82.51088
X-RAY DIFFRACTIONr_scangle_it13.3664979
LS refinement shellResolution: 3.5→3.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 26 -
Rwork0.228 418 -
all-444 -
obs-418 91.36 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.13550.764-0.80981.63820.27941.1817-0.0201-0.1462-0.08970.03120.093-0.2524-0.00620.3016-0.07280.3383-0.03-0.0090.3835-0.01780.3475-21.55328.69548.152
20.38370.10671.73470.78511.06768.2967-0.15330.2302-0.102-0.09230.23-0.0764-0.14930.7129-0.07670.2569-0.15230.0220.5526-0.0240.4318-25.11117.2981.753
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 51
2X-RAY DIFFRACTION1A133 - 191
3X-RAY DIFFRACTION1A275 - 298
4X-RAY DIFFRACTION1A299 - 395
5X-RAY DIFFRACTION1A398 - 500
6X-RAY DIFFRACTION2A52 - 132
7X-RAY DIFFRACTION2A192 - 274
8X-RAY DIFFRACTION2A501 - 1396

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