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Yorodumi- PDB-7qrg: Structure of the post-fusion complex between precursor membrane e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qrg | ||||||||||||
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Title | Structure of the post-fusion complex between precursor membrane ectodomain (prM) and envelope ectodomain protein (E) from tick-borne encephalitis virus | ||||||||||||
Components |
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Keywords | VIRAL 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 / 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 | ||||||||||||
Biological species | Tick-borne encephalitis virus | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||||||||
Authors | Vaney, M.C. / Rouvinski, A. / Rey, F.A. | ||||||||||||
Funding support | France, 3items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qrg.cif.gz | 191.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qrg.ent.gz | 151.6 KB | Display | PDB format |
PDBx/mmJSON format | 7qrg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qrg_validation.pdf.gz | 424.3 KB | Display | wwPDB validaton report |
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Full document | 7qrg_full_validation.pdf.gz | 425.1 KB | Display | |
Data in XML | 7qrg_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 7qrg_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/7qrg ftp://data.pdbj.org/pub/pdb/validation_reports/qr/7qrg | HTTPS FTP |
-Related structure data
Related structure data | 7qreC 7qrfC 1urzS 3c5xS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | ||||
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#2: Protein | 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 | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.33 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Displacement parameters | Biso max: 241.56 Å2 / Biso mean: 79.9 Å2 / Biso min: 33.62 Å2
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Refine analyze | Luzzati coordinate error obs: 0.5 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→48.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.99 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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