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- PDB-7qre: Structure of the hetero-tetramer complex between precursor membra... -

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Basic information

Entry
Database: PDB / ID: 7qre
TitleStructure of the hetero-tetramer complex between precursor membrane protein fragment (pr) and envelope protein (E) from tick-borne encephalitis virus
Components
  • Envelope protein E
  • Genome polyprotein
KeywordsVIRAL PROTEIN / class II fusion envelope protein / precursor membrane protein / chaperone / flavivirus maturation / trans-golgi acid pH
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
ACETATE ION / Genome polyprotein
Similarity search - Component
Biological speciesTick-borne encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsVaney, M.C. / Dellarole, M. / 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: Nature / Year: 1995
Title: The envelope glycoprotein from tick-borne encephalitis virus at 2 A resolution.
Authors: Rey, F.A. / Heinz, F.X. / Mandl, C. / Kunz, C. / Harrison, S.C.
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
D: Genome polyprotein
A: Envelope protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,23012
Polymers61,3432
Non-polymers88710
Water39622
1
D: Genome polyprotein
A: Envelope protein E
hetero molecules

D: Genome polyprotein
A: Envelope protein E
hetero molecules


  • defined by author&software
  • Evidence: The hetero-tetramer structure (pr/E)2 is a crystallographic hetero-dimer related by a two-fold axis. This assemby is the one that it is presented at the surface of the immature flavivirus virion at acidic pH.
  • 124 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)124,46024
Polymers122,6874
Non-polymers1,77320
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation19_444-x-1/4,-z-1/4,-y-1/41
Buried area12540 Å2
ΔGint-249 kcal/mol
Surface area42600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.320, 164.320, 164.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Genome polyprotein


Mass: 13703.804 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: For purification, at the C-terminal of pr (chain D), an enterokinase site with a dstrep-tag sequence is added: GPFEDDDDKAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK.
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 Envelope protein E


Mass: 47639.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: For purification, at the C-terminal of E (chain A), an enterokinase site with a dstrep-tag sequence is added: GPFEDDDDKAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.01 Å3/Da / Density % sol: 59.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6
Details: 0.2M (NH4)SO4, 0.1M Na acetate pH 4.6, 28% (v/v) PEG MME 550, 2.8% (v/v) tert-Butanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.07197 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07197 Å / Relative weight: 1
ReflectionResolution: 2.7→49.56 Å / Num. obs: 21401 / % possible obs: 100 % / Redundancy: 32.9 % / Biso Wilson estimate: 101.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.244 / Rpim(I) all: 0.043 / Rrim(I) all: 0.248 / Net I/σ(I): 13.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.7-2.83304.82515170.3320.894.908100
12.17-49.5623.40.0593030.9980.0130.0698.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSFeb 5 2021data reduction
Aimless0.5.28data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SVB, 3C5X

1svb

3c5x


Resolution: 2.7→49.54 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 0.386 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.403 / SU Rfree Blow DPI: 0.28 / SU Rfree Cruickshank DPI: 0.28
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1071 5 %RANDOM
Rwork0.188 ---
obs0.191 21399 99.9 %-
Displacement parametersBiso max: 178.58 Å2 / Biso mean: 85.14 Å2 / Biso min: 33.51 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: final / Resolution: 2.7→49.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 0 48 22 3728
Biso mean--134.39 63.69 -
Num. residues----480
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1285SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes90HARMONIC2
X-RAY DIFFRACTIONt_gen_planes552HARMONIC5
X-RAY DIFFRACTIONt_it3795HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion495SEMIHARMONIC5
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_contact3902SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3795HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5160HARMONIC21.26
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion19.3
LS refinement shellResolution: 2.7→2.83 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.3128 139 5.03 %
Rwork0.2507 2622 -
all0.2538 2761 -
obs--99.6 %
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)
13.13061.505-1.85564.5677-1.07523.73740.03770.1281-0.29710.4933-0.22180.43530.5442-0.32360.18410.2316-0.1520.1213-0.2134-0.0438-0.1457-29.0711-24.9148-59.5819
25.8221.9465-0.08233.50780.42522.26240.1956-0.41380.45580.5442-0.11630.11550.02750.1307-0.07930.0005-0.10070.0268-0.08650.0014-0.1576-31.923642.3835-21.6047
35.0831-2.9104-2.38313.00932.08771.56510.17720.54420.4218-0.0763-0.0594-0.39030.0096-0.2446-0.1178-0.1545-0.0044-0.0016-0.15940.0499-0.1118-32.217818.1674-39.6972
40-0.2419-0.17493.99282.32241.945-0.0155-0.0561-0.12280.0688-0.33360.39690.198-0.54420.349-0.049-0.08970.03510.1385-0.152-0.0525-34.4819-6.5751-60.3076
56.04962.370.09974.38780.58474.86880.3326-0.47510.16410.5442-0.121-0.40010.4025-0.1666-0.2116-0.0349-0.027-0.0871-0.1648-0.0804-0.062-12.424352.9467-12.6033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{D|1:80}D1 - 80
2X-RAY DIFFRACTION2{A|1:48}A1 - 48
5X-RAY DIFFRACTION3{A|49:61}A49 - 61
9X-RAY DIFFRACTION4{A|62:124}A62 - 124
11X-RAY DIFFRACTION5{A|302:400}A302 - 400
3X-RAY DIFFRACTION2{A|137:192}A137 - 192
4X-RAY DIFFRACTION2{A|285:301}A285 - 301
6X-RAY DIFFRACTION3{A|125:136}A125 - 136
7X-RAY DIFFRACTION3{A|193:225}A193 - 225
8X-RAY DIFFRACTION3{A|260:284}A260 - 284
10X-RAY DIFFRACTION4{A|226:259}A226 - 259

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