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- PDB-6s8c: Post-fusion conformation of the envelope protein of tick-borne en... -

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Basic information

Entry
Database: PDB / ID: 6s8c
TitlePost-fusion conformation of the envelope protein of tick-borne encephalitis virus with longer stem
ComponentsGenome polyprotein,Genome polyprotein
KeywordsVIRAL PROTEIN / ENVELOPE PROTEIN / MEMBRANE FUSION / STEM / VIRUS/VIRAL PROTEIN
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / 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 perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C ...: / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus envelope glycoprotein E, stem/anchor domain / : / 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. / 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, flavivirus / Flavivirus envelope glycoprotein M / 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 / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesTick-borne encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.57 Å
AuthorsVaney, M.C. / Rouvinski, A. / Rey, F.A.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-13-ISV8-0002-01 France
Citation
Journal: Embo Rep. / Year: 2020
Title: Extensive flavivirus E trimer breathing accompanies stem zippering of the post-fusion hairpin.
Authors: Medits, I. / Vaney, M.C. / Rouvinski, A. / Rey, M. / Chamot-Rooke, J. / Rey, F.A. / Heinz, F.X. / Stiasny, K.
#1: Journal: EMBO J. / Year: 2004
Title: Structure of a flavivirus envelope glycoprotein in its low-pH-induced membrane fusion conformation.
Authors: Bressanelli, S. / Stiasny, K. / Allison, S.L. / Stura, E.A. / Duquerroy, S. / Lescar, J. / Heinz, F.X. / Rey, F.A.
History
DepositionJul 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 2, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 24, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein,Genome polyprotein
B: Genome polyprotein,Genome polyprotein
C: Genome polyprotein,Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)146,8183
Polymers146,8183
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11410 Å2
ΔGint-25 kcal/mol
Surface area41410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.435, 169.435, 123.567
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Genome polyprotein,Genome polyprotein


Mass: 48939.246 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tick-borne encephalitis virus (WESTERN SUBTYPE), (gene. exp.) Tick-borne encephalitis virus
Variant: Neudoerfl / Plasmid: PT389 / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly)
References: UniProt: P14336, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6
Details: 19% isopropanol, 100mM tris-sodium citrate pH 5.6, 19% PEG 4000, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2014
RadiationMonochromator: Fixed-exit LN2 cooled Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.57→48.91 Å / Num. obs: 41959 / % possible obs: 99.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 70.83 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.072 / Rrim(I) all: 0.136 / Net I/σ(I): 7.9 / Num. measured all: 147146
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.5 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.57-2.671.1671517443560.290.7311.3821.197.5
9.61-48.910.03727647930.9970.0230.04426.298.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.86 Å48.91 Å
Translation7.86 Å48.91 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.28data scaling
PHASER2.5.1phasing
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1URZ

1urz


Resolution: 2.57→48.91 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU R Cruickshank DPI: 0.401 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.356 / SU Rfree Blow DPI: 0.23 / SU Rfree Cruickshank DPI: 0.241
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2028 4.84 %RANDOM
Rwork0.182 ---
obs0.184 41941 99.6 %-
Displacement parametersBiso max: 151.15 Å2 / Biso mean: 63.69 Å2 / Biso min: 24.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.9176 Å20 Å20 Å2
2--0.9176 Å20 Å2
3----1.8352 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: final / Resolution: 2.57→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7755 0 0 78 7833
Biso mean---44.86 -
Num. residues----1019
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3605SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes176HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1140HARMONIC5
X-RAY DIFFRACTIONt_it7926HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1066SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8005SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7926HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10764HARMONIC21.21
X-RAY DIFFRACTIONt_omega_torsion3.46
X-RAY DIFFRACTIONt_other_torsion2.99
LS refinement shellResolution: 2.57→2.64 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2755 139 4.61 %
Rwork0.2286 2875 -
all0.2307 3014 -
obs--97.48 %
Refinement TLS params.

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

IDL11 (°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)
14.20230.1321-2.19280.8795-0.00683.58560.15150.61030.5119-0.3706-0.1111-0.3329-0.45270.2105-0.0404-0.15680.02710.0434-0.14350.1022-0.1092-43.101178.0658-73.3319
21.88130.71290.63891.752-0.32182.5851-0.0393-0.29950.30420.2559-0.16250.149-0.5279-0.17420.2018-0.18530.0062-0.0104-0.3363-0.1015-0.2946-58.9692181.9339-40.724
30.8841-0.51040.2786-0.88411.226800.0345-0.1008-0.02260.0530.09480.1445-0.0295-0.2158-0.1294-0.01890.2275-0.05560.0694-0.2076-0.0745-68.9248188.3508-32.0045
45.7991-0.5817-1.21092.2444-3.72351.0692-0.11420.046-0.0198-0.00440.1124-0.1410.2416-0.05590.00180.10040.07210.1850.3681-0.01650.1024-68.4614184.1808-19.3997
53.9522-0.2383-1.01831.12210.07342.5612-0.04290.11520.55970.20870.0786-0.3053-0.25520.4811-0.0357-0.1719-0.1629-0.15390.07990.08660.304-28.0256176.8034-52.7851
61.6878-0.5742-0.71311.4277-0.02944.03960.17620.3406-0.3101-0.3824-0.22170.07540.27980.02570.0455-0.13810.0876-0.0507-0.2581-0.1081-0.1754-53.5584157.2365-77.5716
71.5475-0.8773-0.3961.15751.11942.57160.02070.0445-0.12-0.0162-0.12590.26820.1376-0.5490.1052-0.2695-0.0843-0.0158-0.1154-0.0381-0.1765-73.1772161.8329-47.2354
81.29470.35011.8096-0.0273-0.74050-0.08340.09410.04570.0630.0166-0.0058-0.05760.220.0667-0.2175-0.22540.14840.2175-0.08980.0946-82.4535156.3583-37.3212
98.5667-2.18042.86344.36310.86132.3394-0.1049-0.22040.19920.26420.56710.7435-0.6251-0.0057-0.4622-0.0937-0.07760.1060.3469-0.11430.0278-90.327167.7612-23.1457
101.4614-0.8591-0.14931.5768-0.73763.46290.20550.2654-0.0152-0.2277-0.24350.07130.0609-0.27070.0381-0.21640.0942-0.0898-0.2244-0.0363-0.1943-66.4028179.0509-75.1151
111.7758-0.9416-0.42322.42111.25513.60610.07670.242-0.0939-0.1007-0.0742-0.68270.17120.6326-0.0026-0.30750.07950.0175-0.11980.0298-0.013-33.1173157.6436-65.8038
121.93970.4605-1.44821.68680.33623.27390.0425-0.2476-0.07040.444-0.0967-0.13450.390.25530.0541-0.16340.0059-0.099-0.26870.0309-0.304-51.6881158.3071-34.4763
13-0.57160.6765-0.66972.2404-0.81410.4453-0.09010.1710.1581-0.1160.1942-0.27070.0835-0.0596-0.10420.3746-0.04080.05560.23330.2076-0.304-51.5459160.0139-19.8638
149.02651.6788-1.06530.3667-3.975700.0214-0.12350.06280.1386-0.0960.6647-0.1986-0.74310.07460.2273-0.19620.20270.1029-0.04720.1409-65.2233156.9138-12.9378
151.8994-0.5046-1.27982.24712.06764.37570.12610.0676-0.33780.2489-0.1484-0.13520.6332-0.00830.0223-0.05960.03120.0004-0.3494-0.0616-0.0132-50.4341139.325-61.8374
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1{A|1:51 138:191 285:302}0
2X-RAY DIFFRACTION2{A|52:62 122:137 192:241 257:284}0
3X-RAY DIFFRACTION3{A|63:121}0
4X-RAY DIFFRACTION4{A|242:256}0
5X-RAY DIFFRACTION5{A|303:403}0
6X-RAY DIFFRACTION6{B|1:51 138:191 285:302}0
7X-RAY DIFFRACTION7{B|52:62 122:137 192:241 257:284}0
8X-RAY DIFFRACTION8{B|63:121}0
9X-RAY DIFFRACTION9{B|242:256}0
10X-RAY DIFFRACTION10{B|303:403}0
11X-RAY DIFFRACTION11{C|1:51 138:191 285:302}0
12X-RAY DIFFRACTION12{C|52:62 122:137 192:241 257:284}0
13X-RAY DIFFRACTION13{C|63:121}0
14X-RAY DIFFRACTION14{C|242:256}0
15X-RAY DIFFRACTION15{C|303:403}0

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