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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6999 | |||||||||
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Title | Cryo-EM structure of T=1 Penaeus vannamei nodavirus | |||||||||
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![]() | 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![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Chen NC / Miyazaki N | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 21.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.4 KB 13.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.4 KB | Display | ![]() |
Images | ![]() | 88.7 KB | ||
Filedesc metadata | ![]() | 5.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 509.3 KB | Display | ![]() |
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Full document | ![]() | 508.9 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ab5MC ![]() 9576C ![]() 5ykuC ![]() 5ykvC ![]() 5ykxC ![]() 5ykzC ![]() 5yl0C ![]() 5yl1C ![]() 6ab6C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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Sample components
-Entire : Penaeus vannamei nodavirus
Entire | Name: ![]() |
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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: all / 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: ![]() |
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 40.262168 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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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: ![]() |
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 |