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Yorodumi- EMDB-16426: CryoEM structure of the Hendra henipavirus nucleocapsid sauronoid... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16426 | |||||||||
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Title | CryoEM structure of the Hendra henipavirus nucleocapsid sauronoid assembly multimer | |||||||||
Map data | Hendra henipavirus nucleoprotein sauronoid EM density postprocessed map | |||||||||
Sample |
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Keywords | Nucleoprotein / RNA-binding protein / Sauronoid / VIRAL PROTEIN | |||||||||
Function / homology | Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein / helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / structural molecule activity / RNA binding / Nucleocapsid Function and homology information | |||||||||
Biological species | Hendra henipavirus / Escherichia coli BL21(DE3) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.485 Å | |||||||||
Authors | Passchier TC / Maskell DP / Edwards TA / Barr JN | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: Sci Rep / Year: 2024 Title: The cryoEM structure of the Hendra henipavirus nucleoprotein reveals insights into paramyxoviral nucleocapsid architectures. Authors: Tim C Passchier / Joshua B R White / Daniel P Maskell / Matthew J Byrne / Neil A Ranson / Thomas A Edwards / John N Barr / Abstract: We report the first cryoEM structure of the Hendra henipavirus nucleoprotein in complex with RNA, at 3.5 Å resolution, derived from single particle analysis of a double homotetradecameric RNA-bound ...We report the first cryoEM structure of the Hendra henipavirus nucleoprotein in complex with RNA, at 3.5 Å resolution, derived from single particle analysis of a double homotetradecameric RNA-bound N protein ring assembly exhibiting D14 symmetry. The structure of the HeV N protein adopts the common bi-lobed paramyxoviral N protein fold; the N-terminal and C-terminal globular domains are bisected by an RNA binding cleft containing six RNA nucleotides and are flanked by the N-terminal and C-terminal arms, respectively. In common with other paramyxoviral nucleocapsids, the lateral interface between adjacent N and N protomers involves electrostatic and hydrophobic interactions mediated primarily through the N-terminal arm and globular domains with minor contribution from the C-terminal arm. However, the HeV N multimeric assembly uniquely identifies an additional protomer-protomer contact between the N N-terminus and N C-terminal arm linker. The model presented here broadens the understanding of RNA-bound paramyxoviral nucleocapsid architectures and provides a platform for further insight into the molecular biology of HeV, as well as the development of antiviral interventions. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16426.map.gz | 16.3 MB | EMDB map data format | |
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Header (meta data) | emd-16426-v30.xml emd-16426.xml | 17.8 KB 17.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16426_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_16426.png | 117.6 KB | ||
Masks | emd_16426_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-16426.cif.gz | 6.2 KB | ||
Others | emd_16426_half_map_1.map.gz emd_16426_half_map_2.map.gz | 138.3 MB 138.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16426 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16426 | HTTPS FTP |
-Validation report
Summary document | emd_16426_validation.pdf.gz | 848.8 KB | Display | EMDB validaton report |
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Full document | emd_16426_full_validation.pdf.gz | 848.4 KB | Display | |
Data in XML | emd_16426_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | emd_16426_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16426 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16426 | HTTPS FTP |
-Related structure data
Related structure data | 8c4hMC 8cbwMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16426.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Hendra henipavirus nucleoprotein sauronoid EM density postprocessed map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16426_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Hendra henipavirus nucleoprotein sauronoid EM density half map 2
File | emd_16426_half_map_1.map | ||||||||||||
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Annotation | Hendra henipavirus nucleoprotein sauronoid EM density half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Hendra henipavirus nucleoprotein sauronoid EM density half map 1
File | emd_16426_half_map_2.map | ||||||||||||
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Annotation | Hendra henipavirus nucleoprotein sauronoid EM density half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Sauronoid assembly of Hendra henipavirus nucleoprotein
Entire | Name: Sauronoid assembly of Hendra henipavirus nucleoprotein |
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Components |
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-Supramolecule #1: Sauronoid assembly of Hendra henipavirus nucleoprotein
Supramolecule | Name: Sauronoid assembly of Hendra henipavirus nucleoprotein type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Recombinantly expressed Hendra henipavirus nucleoprotein forming sauronoid complexes. |
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Source (natural) | Organism: Hendra henipavirus |
Molecular weight | Theoretical: 1.691779 MDa |
-Macromolecule #1: Nucleocapsid
Macromolecule | Name: Nucleocapsid / type: protein_or_peptide / ID: 1 / Number of copies: 28 / Enantiomer: LEVO |
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Source (natural) | Organism: Hendra henipavirus |
Molecular weight | Theoretical: 58.54132 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSDIFDEAAS FRSYQSKLGR DGRASAATAT LTTKIRIFVP ATNSPELRWE LTLFALDVIR SPSAAESMKI GAAFTLISMY SERPGALIR SLLNDPDIEA VIIDVGSMLN GIPVMERRGD KAQEEMEGLM RILKTARESS KGKTPFVDSR AYGLRITDMS T LVSAVITI ...String: MSDIFDEAAS FRSYQSKLGR DGRASAATAT LTTKIRIFVP ATNSPELRWE LTLFALDVIR SPSAAESMKI GAAFTLISMY SERPGALIR SLLNDPDIEA VIIDVGSMLN GIPVMERRGD KAQEEMEGLM RILKTARESS KGKTPFVDSR AYGLRITDMS T LVSAVITI EAQIWILIAK AVTAPDTAEE SETRRWAKYV QQKRVNPFFA LTQQWLTEMR NLLSQSLSVR KFMVEILMEV KK GGSAKGR AVEIISDIGN YVEETGMAGF FATIRFGLET RYPALALNEF QSDLNTIKGL MLLYREIGPR APYMVLLEES IQT KFAPGG YPLLWSFAMG VATTIDRSMG ALNINRGYLE PMYFRLGQKS ARHHAGGIDQ NMANKLGLNS DQVAELAAAV QETS VGRQD NNMQAREAKF AAGGVLVGGG EQDIDEEEEP IEHSGRQSVT FKREMSMSSL ADSVPSSSVS TSGGTRLTNS LLNLR SRLA AKAIKESTAQ SSSERNPPNN RPQADSGRKD DQEPKPAQND LDFVRADV UniProtKB: Nucleocapsid |
-Macromolecule #2: RNA (84-MER)
Macromolecule | Name: RNA (84-MER) / type: rna / ID: 2 / Number of copies: 2 |
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Source (natural) | Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: Rosetta 2 |
Molecular weight | Theoretical: 25.672984 KDa |
Sequence | String: UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUU |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 281 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 / Number grids imaged: 1 / Number real images: 3548 / Average exposure time: 1.5 sec. / Average electron dose: 59.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.7000000000000001 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 |