+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9576 | |||||||||
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Title | Cryo-EM structure of T=3 Penaeus vannamei nodavirus | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Nodaviridae / shrimp nodavirus / VIRUS LIKE PARTICLE | |||||||||
Function / homology | Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / Viral coat protein subunit / viral capsid / structural molecule activity / metal ion binding / Capsid protein Function and homology information | |||||||||
Biological species | Penaeus vannamei nodavirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Chen NC / Miyazaki N | |||||||||
Funding support | Taiwan, 1 items
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Citation | Journal: Commun Biol / Year: 2019 Title: The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism. Authors: Nai-Chi Chen / Masato Yoshimura / Naoyuki Miyazaki / Hong-Hsiang Guan / Phimonphan Chuankhayan / Chien-Chih Lin / Shao-Kang Chen / Pei-Ju Lin / Yen-Chieh Huang / Kenji Iwasaki / Atsushi ...Authors: Nai-Chi Chen / Masato Yoshimura / Naoyuki Miyazaki / Hong-Hsiang Guan / Phimonphan Chuankhayan / Chien-Chih Lin / Shao-Kang Chen / Pei-Ju Lin / Yen-Chieh Huang / Kenji Iwasaki / Atsushi Nakagawa / Sunney I Chan / Chun-Jung Chen / Abstract: Shrimp nodaviruses, including (PvNV) and nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity ...Shrimp nodaviruses, including (PvNV) and nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity during infections. Here, we show cryo-EM structures of = 3 and = 1 PvNV-like particles (PvNV-LPs), crystal structures of the protrusion-domains (P-domains) of PvNV and MrNV, and the crystal structure of the ∆N-ARM-PvNV shell-domain (S-domain) in = 1 subviral particles. The capsid protein of PvNV reveals five domains: the P-domain with a new jelly-roll structure forming cuboid-like spikes; the jelly-roll S-domain with two calcium ions; the linker between the S- and P-domains exhibiting new cross and parallel conformations; the N-arm interacting with nucleotides organized along icosahedral two-fold axes; and a disordered region comprising the basic -terminal arginine-rich motif (N-ARM) interacting with RNA. The N-ARM controls = 3 and = 1 assemblies. Increasing the /-termini flexibility leads to particle polymorphism. Linker flexibility may influence the dimeric-spike arrangement. | |||||||||
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_9576.map.gz | 79.4 MB | EMDB map data format | |
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Header (meta data) | emd-9576-v30.xml emd-9576.xml | 13.8 KB 13.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9576_fsc.xml | 18.1 KB | Display | FSC data file |
Images | emd_9576.png | 230.5 KB | ||
Filedesc metadata | emd-9576.cif.gz | 6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9576 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9576 | HTTPS FTP |
-Validation report
Summary document | emd_9576_validation.pdf.gz | 558.7 KB | Display | EMDB validaton report |
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Full document | emd_9576_full_validation.pdf.gz | 558.2 KB | Display | |
Data in XML | emd_9576_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | emd_9576_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9576 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9576 | HTTPS FTP |
-Related structure data
Related structure data | 6ab6MC 6999C 5ykuC 5ykvC 5ykxC 5ykzC 5yl0C 5yl1C 6ab5C 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_9576.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.12 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 : Penaeus vannamei nodavirus
Entire | Name: Penaeus vannamei nodavirus |
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Components |
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-Supramolecule #1: Penaeus vannamei nodavirus
Supramolecule | Name: Penaeus vannamei nodavirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 430911 / Sci species name: Penaeus vannamei nodavirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Litopenaeus vannamei (Pacific white shrimp) |
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Penaeus vannamei nodavirus |
Molecular weight | Theoretical: 40.262168 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKRKPNSNQN NNNNRGNGNG LRRVRGGRVS RRRVVINQSN QSMPVTSNGA PLQALTSYSR PNVNKISRLG PDSDFLTSVV AKASTSIVT PADRILVKQP LSASSFPGTR ITGLSSYWER YKWLSAVARY VPAVPNTVAC QFVMYIDTDP LDDPSNISDD N QIVRQAVS ...String: MKRKPNSNQN NNNNRGNGNG LRRVRGGRVS RRRVVINQSN QSMPVTSNGA PLQALTSYSR PNVNKISRLG PDSDFLTSVV AKASTSIVT PADRILVKQP LSASSFPGTR ITGLSSYWER YKWLSAVARY VPAVPNTVAC QFVMYIDTDP LDDPSNISDD N QIVRQAVS QAGSNQFNFN TSKTVPLIVR ADNQYYYTGV DKQNLRFSLQ GILYIIQVTD LINFNGELIT QDLTCGSLFL DW LVNFSIP QINPTSLTDV RVDKAVNFIK PEVSGVAEIQ TVTGLSPSTS YLLTPAFLEQ NFQSEAGIYI LSATPVEGEG TIS INMDPT VTTVSGFIKV KTDTFGTFDL SVVLTTASKK QTTGFNIIAA TS UniProtKB: Capsid protein |
-Macromolecule #2: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 6 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 2806 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.75 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |