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Yorodumi- EMDB-3754: The cryo-EM structure of Tick-borne encephalitis virus complexed ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3754 | ||||||||||||
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Title | The cryo-EM structure of Tick-borne encephalitis virus complexed with Fab fragment of neutralizing antibody 19/1786 | ||||||||||||
Map data | Tick-borne encephalitis virus in complex with Fab fragment of neutralizing antibody 19/1786 | ||||||||||||
Sample |
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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 endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / 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 | Mus musculus (house mouse) / Tick-borne encephalitis virus (strain Hypr) / House mouse (house mouse) / Tick-borne encephalitis virus (strain HYPR) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
Authors | Fuzik T / Plevka P | ||||||||||||
Funding support | Czech Republic, Germany, 3 items
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Citation | Journal: Nat Commun / Year: 2018 Title: Structure of tick-borne encephalitis virus and its neutralization by a monoclonal antibody. Authors: Tibor Füzik / Petra Formanová / Daniel Růžek / Kentaro Yoshii / Matthias Niedrig / Pavel Plevka / Abstract: Tick-borne encephalitis virus (TBEV) causes 13,000 cases of human meningitis and encephalitis annually. However, the structure of the TBEV virion and its interactions with antibodies are unknown. ...Tick-borne encephalitis virus (TBEV) causes 13,000 cases of human meningitis and encephalitis annually. However, the structure of the TBEV virion and its interactions with antibodies are unknown. Here, we present cryo-EM structures of the native TBEV virion and its complex with Fab fragments of neutralizing antibody 19/1786. Flavivirus genome delivery depends on membrane fusion that is triggered at low pH. The virion structure indicates that the repulsive interactions of histidine side chains, which become protonated at low pH, may contribute to the disruption of heterotetramers of the TBEV envelope and membrane proteins and induce detachment of the envelope protein ectodomains from the virus membrane. The Fab fragments bind to 120 out of the 180 envelope glycoproteins of the TBEV virion. Unlike most of the previously studied flavivirus-neutralizing antibodies, the Fab fragments do not lock the E-proteins in the native-like arrangement, but interfere with the process of virus-induced membrane fusion. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3754.map.gz | 70.4 MB | EMDB map data format | |
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Header (meta data) | emd-3754-v30.xml emd-3754.xml | 20.8 KB 20.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3754_fsc.xml | 17.9 KB | Display | FSC data file |
Images | emd_3754.png | 322.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3754 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3754 | HTTPS FTP |
-Validation report
Summary document | emd_3754_validation.pdf.gz | 349.2 KB | Display | EMDB validaton report |
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Full document | emd_3754_full_validation.pdf.gz | 348.3 KB | Display | |
Data in XML | emd_3754_validation.xml.gz | 15.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3754 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3754 | HTTPS FTP |
-Related structure data
Related structure data | 5o6vMC 3752C 3755C 5o6aC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3754.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Tick-borne encephalitis virus in complex with Fab fragment of neutralizing antibody 19/1786 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.45 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Tick-borne encephalitis virus (strain HYPR) and Fab
Entire | Name: Tick-borne encephalitis virus (strain HYPR) and Fab |
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Components |
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-Supramolecule #1: Tick-borne encephalitis virus (strain HYPR) and Fab
Supramolecule | Name: Tick-borne encephalitis virus (strain HYPR) and Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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-Supramolecule #3: Mus musculus Fab
Supramolecule | Name: Mus musculus Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Supramolecule #2: Tick-borne encephalitis virus (strain HYPR)
Supramolecule | Name: Tick-borne encephalitis virus (strain HYPR) / type: virus / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 / NCBI-ID: 70733 Sci species name: Tick-borne encephalitis virus (strain HYPR) Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: Yes / Virus empty: No |
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-Macromolecule #1: Envelope protein
Macromolecule | Name: Envelope protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Tick-borne encephalitis virus (strain Hypr) |
Molecular weight | Theoretical: 53.667418 KDa |
Sequence | String: SRCTHLENRD FVTGTQGTTR VTLVLELGGC VTITAEGKPS MDVWLDAIYQ ENPAQTREYC LHAKLSDTKV AARCPTMGPA TLAEEHQGG TVCKRDQSDR GWGNHCGLFG KGSIVACVKA ACEAKKKATG HVYDANKIVY TVKVEPHTGD YVAANETHSG R KTASFTVS ...String: SRCTHLENRD FVTGTQGTTR VTLVLELGGC VTITAEGKPS MDVWLDAIYQ ENPAQTREYC LHAKLSDTKV AARCPTMGPA TLAEEHQGG TVCKRDQSDR GWGNHCGLFG KGSIVACVKA ACEAKKKATG HVYDANKIVY TVKVEPHTGD YVAANETHSG R KTASFTVS SEKTILTMGE YGDVSLLCRV ASGVDLAQTV ILELDKTVEH LPTAWQVHRD WFNDLALPWK HEGARNWNNA ER LVEFGAP HAVKMDVYNL GDQTGVLLKA LAGVPVAHIE GTKYHLKSGH VTCEVGLEKL KMKGLTYTMC DKTKFTWKRA PTD SGHDTV VMEVTFSGTK PCRIPVRAVA HGSPDVNVAM LITPNPTIEN NGGGFIEMQL PPGDNIIYVG ELSYQWFQKG SSIG RVFQK TKKGIERLTV IGEHAWDFGS AGGFLSSIGK ALHTVLGGAF NSIFGGVGFL PKLLLGVALA WLGLNMRNPT MSMSF LLAG VLVLAMTLGV GA |
-Macromolecule #2: Small envelope protein M
Macromolecule | Name: Small envelope protein M / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Tick-borne encephalitis virus (strain Hypr) |
Molecular weight | Theoretical: 8.339867 KDa |
Sequence | String: SVLIPSHAQG ELTGRGHKWL EGDSLRTHLT RVEGWVWKNR LLALAMVTVV WLTLESVVTR VAVLVVLLCL APVYA |
-Macromolecule #3: Fab 19/1786 - Heavy chain
Macromolecule | Name: Fab 19/1786 - Heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: House mouse (house mouse) |
Molecular weight | Theoretical: 22.730357 KDa |
Sequence | String: EVKLEESGGG LVQPGGSLKL SCAASGFTFS SYGMSWVRQT PDKRLELVAA TNSDGDSTYY PDSVKGRFTI SRDRAKNTLY LQMSSLKSE DTAMYYCTRV LYDYDGEFAY WGQGTLVTVS AAKTTPPSVY PLAPGSAAQT NSMVTLGCLV KGYFPEPVTV T WNSGSLSS ...String: EVKLEESGGG LVQPGGSLKL SCAASGFTFS SYGMSWVRQT PDKRLELVAA TNSDGDSTYY PDSVKGRFTI SRDRAKNTLY LQMSSLKSE DTAMYYCTRV LYDYDGEFAY WGQGTLVTVS AAKTTPPSVY PLAPGSAAQT NSMVTLGCLV KGYFPEPVTV T WNSGSLSS GVHTFPAVLQ SDLYTLSSSV TVPSKTWPSE TVTCNVAHPA SSTK |
-Macromolecule #4: Fab 19/1786 - Light chain
Macromolecule | Name: Fab 19/1786 - Light chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: House mouse (house mouse) |
Molecular weight | Theoretical: 22.84718 KDa |
Sequence | String: DIVMTQSQKF MSTSVGDRVT VTCKASQNVG TNVAWYQQKP GQSPKGLIYS ASYRYSGVPD RFIGSGSGTD FTLTISNVQS GDLAEYFCQ QYNNHPLTFG AGTKLELKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQDGV L NSWTDQDS ...String: DIVMTQSQKF MSTSVGDRVT VTCKASQNVG TNVAWYQQKP GQSPKGLIYS ASYRYSGVPD RFIGSGSGTD FTLTISNVQS GDLAEYFCQ QYNNHPLTFG AGTKLELKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQDGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 3 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: NITROGEN / Pretreatment - Pressure: 0.007 kPa | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV Details: Wait time: 10 s Blot time: 2 s Blot force: -2 Drain time: 0 s. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 1-7 / Number grids imaged: 1 / Number real images: 5426 / Average exposure time: 0.5 sec. / Average electron dose: 22.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 75000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Details | An initial model was generated based on the tick-borne encephalitis virus (TBEV) cryo-EM structure (PDB:5O6A) and a homology modle of the Fab 19/1786. The model was rigid-body fitted to the electron density map of the TBEV+Fab 19/1786 using the program Chimera. Subsequently, the structure was manually corrected using the program Coot, followed by real-space refinement in Phenix and reciprocal space refinement in Refmac5. |
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Refinement | Space: RECIPROCAL / Protocol: OTHER |
Output model | PDB-5o6v: |