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Yorodumi- EMDB-30129: Helical stem of the cleaved double-headed nucleocapsids of sendai... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30129 | |||||||||
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Title | Helical stem of the cleaved double-headed nucleocapsids of sendai virus | |||||||||
Map data | helical stem of cleaved double-headed nucleocapsids | |||||||||
Sample |
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Keywords | nucleocapsid / Sendai virus / NUCLEAR PROTEIN / NUCLEAR PROTEIN-RNA complex | |||||||||
Function / homology | Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein / helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / structural molecule activity / RNA binding / Nucleoprotein Function and homology information | |||||||||
Biological species | Murine respirovirus / Sendai virus (strain Ohita) / synthetic construct (others) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Shen Q / Shan H / Zhang N | |||||||||
Funding support | China, 1 items
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Citation | Journal: Commun Biol / Year: 2021 Title: Structure and assembly of double-headed Sendai virus nucleocapsids. Authors: Na Zhang / Hong Shan / Mingdong Liu / Tianhao Li / Rui Luo / Liuyan Yang / Lei Qi / Xiaofeng Chu / Xin Su / Rui Wang / Yunhui Liu / Wenzhi Sun / Qing-Tao Shen / Abstract: Paramyxoviruses, including the mumps virus, measles virus, Nipah virus and Sendai virus (SeV), have non-segmented single-stranded negative-sense RNA genomes which are encapsidated by nucleoproteins ...Paramyxoviruses, including the mumps virus, measles virus, Nipah virus and Sendai virus (SeV), have non-segmented single-stranded negative-sense RNA genomes which are encapsidated by nucleoproteins into helical nucleocapsids. Here, we reported a double-headed SeV nucleocapsid assembled in a tail-to-tail manner, and resolved its helical stems and clam-shaped joint at the respective resolutions of 2.9 and 3.9 Å, via cryo-electron microscopy. Our structures offer important insights into the mechanism of the helical polymerization, in particular via an unnoticed exchange of a N-terminal hole formed by three loops of nucleoproteins, and unveil the clam-shaped joint in a hyper-closed state for nucleocapsid dimerization. Direct visualization of the loop from the disordered C-terminal tail provides structural evidence that C-terminal tail is correlated to the curvature of nucleocapsid and links nucleocapsid condensation and genome replication and transcription with different assembly forms. | |||||||||
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_30129.map.gz | 332.8 MB | EMDB map data format | |
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Header (meta data) | emd-30129-v30.xml emd-30129.xml | 10.7 KB 10.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30129_fsc.xml | 18.6 KB | Display | FSC data file |
Images | emd_30129.png | 230.9 KB | ||
Filedesc metadata | emd-30129.cif.gz | 5.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30129 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30129 | HTTPS FTP |
-Validation report
Summary document | emd_30129_validation.pdf.gz | 632.8 KB | Display | EMDB validaton report |
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Full document | emd_30129_full_validation.pdf.gz | 632.4 KB | Display | |
Data in XML | emd_30129_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | emd_30129_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30129 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30129 | HTTPS FTP |
-Related structure data
Related structure data | 6m7dMC 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_30129.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | helical stem of cleaved double-headed nucleocapsids | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.52 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 : cleaved double-headed nucleocapsid of sendai virus
Entire | Name: cleaved double-headed nucleocapsid of sendai virus |
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Components |
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-Supramolecule #1: cleaved double-headed nucleocapsid of sendai virus
Supramolecule | Name: cleaved double-headed nucleocapsid of sendai virus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Murine respirovirus |
-Macromolecule #1: Nucleoprotein
Macromolecule | Name: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Sendai virus (strain Ohita) / Strain: Ohita |
Molecular weight | Theoretical: 57.20002 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MAGLLSTFDT FSSRRSESIN KSGGGAVIPG QRSTVSVFVL GPSVTDDADK LSIATTFLAH SLDTDKQHSQ RGGFLVSLLA MAYSSPELY LTTNGVNADV KYVIYNIEKD PKRTKTDGFI VKTRDMEYER TTEWLFGPMV NKSPLFQGQR DAADPDTLLQ I YGYPACLG ...String: MAGLLSTFDT FSSRRSESIN KSGGGAVIPG QRSTVSVFVL GPSVTDDADK LSIATTFLAH SLDTDKQHSQ RGGFLVSLLA MAYSSPELY LTTNGVNADV KYVIYNIEKD PKRTKTDGFI VKTRDMEYER TTEWLFGPMV NKSPLFQGQR DAADPDTLLQ I YGYPACLG AIIVQVWIVL VKAITSSAGL RKGFFNRLEA FRQDGTVKGA LVFTGETVEG IGSVMRSQQS LVSLMVETLV TM NTARSDL TTLEKNIQIV GNYIRDAGLA SFMNTIKYGV ETKMAALTLS NLRPDINKLR SLIDTYLSKG PRAPFICILK DPV HGEFAP GNYPALWSYA MGVAVVQNKA MQQYVTGRTY LDMEMFLLGQ AVAKDAESKI SSALEDELGV TDTAKERLRH HLAN LSGGD GAYHKPTGGG AIEVALDNAD IDLEPEAHTD QDARGWGGDS GDRWARSMGS GHFITLHGAE RLEEETNDED VSDIE RRIA RRLAERRQED ATTHEDEGRN NGVDHDEEDD AAAAAGMGGI UniProtKB: Nucleoprotein |
-Macromolecule #2: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
Macromolecule | Name: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 1.792037 KDa |
Sequence | String: UUUUUU |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 1 mg/mL | ||||||
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Buffer | pH: 7.4 / Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 0.068 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |