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Yorodumi- EMDB-7564: Mouse norovirus model using the crystal structure of MNV P domain... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7564 | |||||||||
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Title | Mouse norovirus model using the crystal structure of MNV P domain and the Norwalkvirus shell domain | |||||||||
Map data | mouse norovirus (MNV-1) in PBS, pH 7.2 | |||||||||
Sample | mouse norovirus model != Murine norovirus 1 mouse norovirus model
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Keywords | norovirus / mouse / VIRUS | |||||||||
Function / homology | Function and homology information T=3 icosahedral viral capsid / host cell cytoplasm / virus-mediated perturbation of host defense response / identical protein binding Similarity search - Function | |||||||||
Biological species | Murine norovirus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.0 Å | |||||||||
Authors | Smith TJ | |||||||||
Citation | Journal: J Virol / Year: 2010 Title: High-resolution cryo-electron microscopy structures of murine norovirus 1 and rabbit hemorrhagic disease virus reveal marked flexibility in the receptor binding domains. Authors: Umesh Katpally / Neil R Voss / Tommaso Cavazza / Stefan Taube / John R Rubin / Vivienne L Young / Jeanne Stuckey / Vernon K Ward / Herbert W Virgin / Christiane E Wobus / Thomas J Smith / Abstract: Our previous structural studies on intact, infectious murine norovirus 1 (MNV-1) virions demonstrated that the receptor binding protruding (P) domains are lifted off the inner shell of the virus. ...Our previous structural studies on intact, infectious murine norovirus 1 (MNV-1) virions demonstrated that the receptor binding protruding (P) domains are lifted off the inner shell of the virus. Here, the three-dimensional (3D) reconstructions of recombinant rabbit hemorrhagic disease virus (rRHDV) virus-like particles (VLPs) and intact MNV-1 were determined to approximately 8-A resolution. rRHDV also has a raised P domain, and therefore, this conformation is independent of infectivity and genus. The atomic structure of the MNV-1 P domain was used to interpret the MNV-1 reconstruction. Connections between the P and shell domains and between the floating P domains were modeled. This observed P-domain flexibility likely facilitates virus-host receptor interactions. | |||||||||
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_7564.map.gz | 169.9 MB | EMDB map data format | |
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Header (meta data) | emd-7564-v30.xml emd-7564.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | emd_7564.png | 325 KB | ||
Filedesc metadata | emd-7564.cif.gz | 5.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7564 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7564 | HTTPS FTP |
-Validation report
Summary document | emd_7564_validation.pdf.gz | 633.4 KB | Display | EMDB validaton report |
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Full document | emd_7564_full_validation.pdf.gz | 632.9 KB | Display | |
Data in XML | emd_7564_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | emd_7564_validation.cif.gz | 8.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7564 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7564 | HTTPS FTP |
-Related structure data
Related structure data | 6crjMC 6c6qC 6c74C 6e47C 6e48C M: atomic model generated by this map C: citing same article (ref.) |
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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_7564.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | mouse norovirus (MNV-1) in PBS, pH 7.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.5599 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 : mouse norovirus model
Entire | Name: mouse norovirus model |
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Components |
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-Supramolecule #1: Murine norovirus 1
Supramolecule | Name: Murine norovirus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all Details: chimera of Norwalk virus shell domain and MNV P domain NCBI-ID: 223997 / Sci species name: Murine norovirus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Mus (mice) |
-Macromolecule #1: Norwalk virus, MNV-1 capsid protein chimera
Macromolecule | Name: Norwalk virus, MNV-1 capsid protein chimera / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Murine norovirus 1 |
Molecular weight | Theoretical: 57.127523 KDa |
Recombinant expression | Organism: Mus abbotti (Abbott's mouse) |
Sequence | String: SSVDGASGAG QLVPEVNASD PLAMDPVAGS STAVATAGQV NPIDPWIINN FVQAPQGEFT ISPNNTPGDV LFDLSLGPHL NPFLLHLSQ MYNGWVGNMR VRIMLAGNAF TAGKIIVSCI PPGFGSHNLT IAQATLFPHV IADVRTLDPI EVPLEDVRNV L FHNNDRNQ ...String: SSVDGASGAG QLVPEVNASD PLAMDPVAGS STAVATAGQV NPIDPWIINN FVQAPQGEFT ISPNNTPGDV LFDLSLGPHL NPFLLHLSQ MYNGWVGNMR VRIMLAGNAF TAGKIIVSCI PPGFGSHNLT IAQATLFPHV IADVRTLDPI EVPLEDVRNV L FHNNDRNQ QTMRLVCMLY TPLRTGGGTG DSFVVAGRVM TCPSPDFNFL FLVPAAAAAA RMVDLPVIQP RLCTHARWPA PV YGLLVDP SLPSNPQWQN GRVHVDGTLL GTTPISGSWV SCFAAEAAYE FQSGTGEVAT FTLIEQDGSA YVPGDRAAPL GYP DFSGQL EIEVQTETTK TGDKLKVTTF EMILGPTTNA DQAPYQGRVF ASVTAAASLD LVDGRVRAVP RSIYGFQDTI PEYN DGLLV PLAPPIGPFL PGEVLLRFRT YMRQIDTADA AAEAIDCALP QEFVSWFASN AFTVQSEALL LRYRNTLTGQ LLFEC KLYN EGYIALSYSG SGPLTFPTDG IFEVVSWVPR LYQLASVGSL ATGRMLK UniProtKB: Capsid protein VP1, Capsid protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 / Details: PBS |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: FEI EAGLE (2k x 2k) / Average electron dose: 10.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 20425 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-6crj: |