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- PDB-7qrf: Structure of the dimeric complex between precursor membrane ectod... -

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Basic information

Entry
Database: PDB / ID: 7qrf
TitleStructure of the dimeric complex between precursor membrane ectodomain (prM) and envelope protein ectodomain (E) from tick-borne encephalitis virus
Components
  • Envelope protein E
  • Genome polyprotein
  • Unknown peptide
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 / 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: 2.28 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: 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
A: Envelope protein E
C: Unknown peptide
D: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,54913
Polymers63,6023
Non-polymers94710
Water1,33374
1
A: Envelope protein E
C: Unknown peptide
D: Genome polyprotein
hetero molecules

A: Envelope protein E
C: Unknown peptide
D: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,09926
Polymers127,2056
Non-polymers1,89420
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)155.730, 155.730, 161.880
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-603-

HOH

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Components

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Protein , 2 types, 2 molecules AD

#1: Protein Envelope protein E /


Mass: 47867.855 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 3) 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 3) 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).
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: 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

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Protein/peptide , 1 types, 1 molecules C

#2: Protein/peptide Unknown peptide


Mass: 443.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This peptide should be part of the M ectodomain but we were unable to attribute the true sequence.
Source: (gene. exp.) Tick-borne encephalitis virus (WESTERN SUBTYPE)
Strain: NEUDOERFL / Plasmid: PT389 / Cell (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly)

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Non-polymers , 4 types, 84 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 3.5
Details: 0.2M Li(SO4), 0.1M Na citrate pH 3.5, 28% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.28→49 Å / Num. obs: 28985 / % possible obs: 95 % / Redundancy: 19.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.023 / Rrim(I) all: 0.099 / Net I/σ(I): 19.8
Reflection shellResolution: 2.28→2.435 Å / Rmerge(I) obs: 2.623 / Num. unique obs: 1449 / CC1/2: 0.323 / Rpim(I) all: 0.891 / Rrim(I) all: 2.699

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Processing

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

1svb

3c5x


Resolution: 2.28→28.42 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.217 / SU Rfree Blow DPI: 0.18 / SU Rfree Cruickshank DPI: 0.183
Details: The BUSTER refinement was done against the STARANISO corrected intensity from anisotropy. This is the reason why, in the last shell of resolution, the completness is 7% while the working ...Details: The BUSTER refinement was done against the STARANISO corrected intensity from anisotropy. This is the reason why, in the last shell of resolution, the completness is 7% while the working Rfactor is higher than the free Rfactor. All the refinement stastitics introduced here are from the STARANISO statistics output.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1487 5.13 %RANDOM
Rwork0.181 ---
obs0.183 28965 84 %-
Displacement parametersBiso max: 178.25 Å2 / Biso mean: 80.83 Å2 / Biso min: 44.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.0434 Å20 Å20 Å2
2--1.0434 Å20 Å2
3----2.0868 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 2.28→28.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3562 0 53 74 3689
Biso mean--95.3 66.1 -
Num. residues----467
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1263SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes87HARMONIC2
X-RAY DIFFRACTIONt_gen_planes527HARMONIC5
X-RAY DIFFRACTIONt_it3683HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion482SEMIHARMONIC5
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_contact3861SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3683HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4974HARMONIC21.16
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion17.16
LS refinement shellResolution: 2.28→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.1972 16 6.84 %
Rwork0.2401 218 -
all0.2375 234 -
obs--6.99 %
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)
14.74040.6381-1.58332.7994-0.19534.15950.2909-0.37380.571-0.0081-0.0488-0.2988-0.74350.1992-0.24210.15930.0970.1801-0.2394-0.0715-0.0412-5.222241.0406101.283
24.8493-3.02450.64265.13420.06924.41380.3870.4215-0.1228-0.27-0.1589-0.16450.23390.5435-0.2281-0.11730.02880.07920.1093-0.024-0.075919.23171.673338.1871
31.3117-0.10511.04210.73550.73618.31550.17520.0608-0.053-0.08390.1981-0.02520.19160.0962-0.3733-0.17880.01520.0315-0.1782-0.0196-0.16547.506715.566462.8568
42.0151-0.7727-1.65050.60490.98383.70060.170.17520.2678-0.0450.0789-0.0535-0.426-0.3506-0.2488-0.04490.16180.1375-0.10780.045-0.1357-9.075528.04387.695
57.6373-1.1366-1.23752.2284-0.70166.86870.11260.4029-0.2936-0.4305-0.1660.15090.6441-0.02720.05340.06580.26050.06240.116-0.1156-0.031140.1169-12.108638.5986
6-2.52051.45521.98522.52051.422300.082-0.41060.00650.20110.0186-0.04430.0208-0.0686-0.10070.11060.0873-0.0556-0.3413-0.20760.28660.524551.6612102.054
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{D|0:81}D0 - 81
2X-RAY DIFFRACTION2{A|-2:48}A-2 - 48
3X-RAY DIFFRACTION2{A|137:192}A137 - 192
4X-RAY DIFFRACTION2{A|285:301}A285 - 301
5X-RAY DIFFRACTION3{A|49:61}A49 - 61
6X-RAY DIFFRACTION3{A|125:136}A125 - 136
7X-RAY DIFFRACTION3{A|193:225}A193 - 225
8X-RAY DIFFRACTION3{A|260:284}A260 - 284
9X-RAY DIFFRACTION4{A|62:124}A62 - 124
10X-RAY DIFFRACTION4{A|226:259}A226 - 259
11X-RAY DIFFRACTION5{A|302:395}A302 - 395
12X-RAY DIFFRACTION6{C|1:5}C1 - 5

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