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- PDB-7qrg: Structure of the post-fusion complex between precursor membrane e... -

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Basic information

Entry
Database: PDB / ID: 7qrg
TitleStructure of the post-fusion complex between precursor membrane ectodomain (prM) and envelope ectodomain protein (E) from tick-borne encephalitis virus
Components
  • Envelope protein E
  • Genome polyprotein
KeywordsVIRAL PROTEIN / class II fusion envelope protein / precursor membrane protein / chaperone / post-fusion / flavivirus
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 / viral capsid / double-stranded RNA binding / 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 / viral capsid / double-stranded RNA binding / 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 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 / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb 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 envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb 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. / 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 / 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 / Resolution: 2.8 Å
AuthorsVaney, M.C. / Rouvinski, A. / Rey, F.A.
Funding support France, 3items
OrganizationGrant numberCountry
Pasteur Institute France
Centre National de la Recherche Scientifique (CNRS) France
Agence Nationale de la Recherche (ANR)ANR-13-ISV8-0002-01 France
Citation
Journal: Nat Commun / Year: 2022
Title: Evolution and activation mechanism of the flavivirus class II membrane-fusion machinery.
Authors: Vaney, M.C. / Dellarole, M. / Duquerroy, S. / Medits, I. / Tsouchnikas, G. / Rouvinski, A. / England, P. / Stiasny, K. / Heinz, F.X. / Rey, F.A.
#1: 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.
History
DepositionJan 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope protein E
D: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2724
Polymers63,0882
Non-polymers1842
Water25214
1
A: Envelope protein E
D: Genome polyprotein
hetero molecules

A: Envelope protein E
D: Genome polyprotein
hetero molecules

A: Envelope protein E
D: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,81612
Polymers189,2636
Non-polymers5536
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_895-y+3,x-y+4,z1
crystal symmetry operation3_485-x+y-1,-x+3,z1
Unit cell
Length a, b, c (Å)97.935, 97.935, 115.164
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Envelope protein E /


Mass: 47796.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The N-terminal end of E (Molecule 1) is linked to the C-terminal of ectodomain prM (Molecule 2) by a linker of 14 residues (GGGGENLYFQGGGG). This linker of 14 residues is only described in ...Details: The N-terminal end of E (Molecule 1) is linked to the C-terminal of ectodomain prM (Molecule 2) by a linker of 14 residues (GGGGENLYFQGGGG). This linker of 14 residues is only described in the sequence of E (Molecule 1) at its N-terminal. For purification, at the C-terminal of E it is added an enterokinase site with a dstrep-tag sequence : (GPFEDDDDKAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK). The residue TRP 101 from the fusion loop is mutated to ASP 101.
Source: (gene. exp.) Tick-borne encephalitis virus (WESTERN SUBTYPE)
Strain: Neudoerfl / Plasmid: PT389 / Cell (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P14336
#2: Protein Genome polyprotein


Mass: 15290.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The C-terminal end of prM (Molecule 3) is linked to the N-terminal of E (Molecule 1) by a linker of 14 residues (GGGGENLYFQGGGG). This linker is described in the sequence of E (Molecule 1). ...Details: The C-terminal end of prM (Molecule 3) is linked to the N-terminal of E (Molecule 1) by a linker of 14 residues (GGGGENLYFQGGGG). This linker is described in the sequence of E (Molecule 1). The furin site is deleted from one amino acid (Arginine). Intact furin site : ...RTRRSVL... Mutated furin site: ...RTRSVL...
Source: (gene. exp.) Tick-borne encephalitis virus (WESTERN SUBTYPE)
Strain: Neudoerfl / Plasmid: PT389 / Cell (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P14336
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: 0.1M Na Malonate, 0.1M HEPES pH 6.7, 18.9% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→48.97 Å / Num. obs: 15904 / % possible obs: 98.9 % / Redundancy: 5.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.238 / Rpim(I) all: 0.117 / Rrim(I) all: 0.286 / Net I/σ(I): 6.3
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 2.73 / Num. unique obs: 2299 / CC1/2: 0.306 / Rpim(I) all: 1.31 / Rrim(I) all: 3.25

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1URZ, 3C5X

1urz

3c5x


Resolution: 2.8→48.97 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.861 / SU R Cruickshank DPI: 1.105 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.116 / SU Rfree Blow DPI: 0.351 / SU Rfree Cruickshank DPI: 0.356
RfactorNum. reflection% reflectionSelection details
Rfree0.264 826 5.19 %RANDOM
Rwork0.228 ---
obs0.23 15902 98.2 %-
Displacement parametersBiso max: 241.56 Å2 / Biso mean: 79.9 Å2 / Biso min: 33.62 Å2
Baniso -1Baniso -2Baniso -3
1--13.7134 Å20 Å20 Å2
2---13.7134 Å20 Å2
3---27.4269 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: final / Resolution: 2.8→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3642 0 12 14 3668
Biso mean--81.62 49.59 -
Num. residues----479
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1276SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes90HARMONIC2
X-RAY DIFFRACTIONt_gen_planes543HARMONIC5
X-RAY DIFFRACTIONt_it3732HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion490SEMIHARMONIC5
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_contact3756SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3732HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg5061HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion1.73
X-RAY DIFFRACTIONt_other_torsion18.88
LS refinement shellResolution: 2.8→2.99 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2821 140 4.93 %
Rwork0.2585 2697 -
all0.2598 2837 -
obs--99.06 %
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)
12.52120.1419-1.75845.0411-1.68711.7225-0.02830.1055-0.0985-0.08510.0315-0.1170.1043-0.003-0.00320.034-0.17630.1941-0.088-0.0375-0.0673-23.676818.4511-33.2327
20.9544-0.37321.62020.2563-0.00292.27330.0927-0.2372-0.06240.1142-0.0739-0.23180.08520.28-0.0188-0.04090.0326-0.0060.05520.0391-0.0578-33.554925.471143.7362
31.1831-0.7486-1.0895-0.4729-1.59675.3815-0.01510.03110.10630.0258-0.053-0.14880.00610.20830.068-0.109-0.0123-0.0209-0.1064-0.02960.0788-34.299427.57277.6421
40.0118-0.0027-0.0006-0.0036-0.0080.00880.0002-0.00130.00020.0011-0.00040.001-0.0007-0.00030.0002-0.01270.01690.02090.0256-0.0106-0.0006-29.334221.6731-4.758
50.330.5188-0.46710.4891-0.59650.1851-0.00170.00450.0259-0.01960.00910.001-0.0016-0.0136-0.00750.0254-0.0410.03190.07180.03440.028-33.719728.4646-23.4209
64.00722.519-1.92382.99151.01492.85350.0537-0.10940.05730.0248-0.01640.078-0.16840.1647-0.0373-0.0616-0.2144-0.0372-0.0803-0.1336-0.071-33.807849.107733.9212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{D|1:80}D1 - 80
2X-RAY DIFFRACTION2{A|-1:51}A-1 - 51
3X-RAY DIFFRACTION2{A|138:191}A138 - 191
4X-RAY DIFFRACTION2{A|285:302}A285 - 302
5X-RAY DIFFRACTION3{A|52:62}A52 - 62
6X-RAY DIFFRACTION3{A|122:137}A122 - 137
7X-RAY DIFFRACTION3{A|192:241}A192 - 241
8X-RAY DIFFRACTION3{A|257:284}A257 - 284
9X-RAY DIFFRACTION4{A|63:121}A63 - 121
10X-RAY DIFFRACTION5{A|242:256}A242 - 256
11X-RAY DIFFRACTION6{A|303:403}A303 - 403

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