[English] 日本語
Yorodumi
- EMDB-11847: Organisation of a helical Bunyamwera virus ribonucleoprotein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11847
TitleOrganisation of a helical Bunyamwera virus ribonucleoprotein
Map data
Sample
  • Complex: Native ribonucleoprotein extracted from Bunyamwera virus
    • Protein or peptide: Nucleoprotein
Keywordshelix / ribonucleoprotein / nucleocapsid / virus / VIRAL PROTEIN
Function / homology
Function and homology information


helical viral capsid / viral nucleocapsid / ribonucleoprotein complex / symbiont-mediated suppression of host gene expression / RNA binding
Similarity search - Function
Bunyavirus nucleocapsid (N) protein / Bunyavirus nucleocapsid (N) , C-terminal domain / Bunyavirus nucleocapsid (N) , N-terminal domain / Bunyavirus nucleocapsid (N) protein
Similarity search - Domain/homology
Biological speciesBunyamwera virus
Methodsingle particle reconstruction / cryo EM / Resolution: 13.0 Å
AuthorsHopkins FR / Fontana J
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: mBio / Year: 2022
Title: The Native Orthobunyavirus Ribonucleoprotein Possesses a Helical Architecture.
Authors: Francis R Hopkins / Beatriz Álvarez-Rodríguez / George R Heath / Kyriakoulla Panayi / Samantha Hover / Thomas A Edwards / John N Barr / Juan Fontana /
Abstract: The order is the largest group of negative-sense RNA viruses, containing many lethal human pathogens for which approved anti-infective measures are not available. The bunyavirus genome consists of ...The order is the largest group of negative-sense RNA viruses, containing many lethal human pathogens for which approved anti-infective measures are not available. The bunyavirus genome consists of multiple negative-sense RNA segments enwrapped by the virus-encoded nucleocapsid protein (NP), which together with the viral polymerase form ribonucleoproteins (RNPs). RNPs represent substrates for RNA synthesis and virion assembly, which require inherent flexibility, consistent with the appearance of RNPs spilled from virions. These observations have resulted in conflicting models describing the overall RNP architecture. Here, we purified RNPs from Bunyamwera virus (BUNV), the prototypical orthobunyavirus. The lengths of purified RNPs imaged by negative staining resulted in 3 populations of RNPs, suggesting that RNPs possess a consistent method of condensation. Employing microscopy approaches, we conclusively show that the NP portion of BUNV RNPs is helical. Furthermore, we present a pseudo-atomic model for this portion based on a cryo-electron microscopy average at 13 Å resolution, which allowed us to fit the BUNV NP crystal structure by molecular dynamics. This model was confirmed by NP mutagenesis using a mini-genome system. The model shows that adjacent NP monomers in the RNP chain interact laterally through flexible N- and C-terminal arms only, with no longitudinal helix-stabilizing interactions, thus providing a potential model for the molecular basis for RNP flexibility. Excessive RNase treatment disrupts native RNPs, suggesting that RNA was key in maintaining the RNP structure. Overall, this work will inform studies on bunyaviral RNP assembly, packaging, and RNA replication, and aid in future antiviral strategies. Bunyaviruses are emerging RNA viruses that cause significant disease and economic burden and for which vaccines or therapies approved for humans are not available. The bunyavirus genome is wrapped up by the nucleoprotein (NP) and interacts with the viral polymerase, forming a ribonucleoprotein (RNP). This is the only form of the genome active for viral replication and assembly. However, until now how NPs are organized within an RNP was not known for any orthobunyavirus. Here, we purified RNPs from the prototypical orthobunyavirus, Bunyamwera virus, and employed microscopy approaches to show that the NP portion of the RNP was helical. We then combined our helical average with the known structure of an NP monomer, generating a pseudo-atomic model of this region. This arrangement allowed the RNPs to be highly flexible, which was critical for several stages of the viral replication cycle, such as segment circularization.
History
DepositionOct 15, 2020-
Header (metadata) releaseMay 4, 2022-
Map releaseMay 4, 2022-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_11847.png

Downloads & links

-
Map

FileDownload / File: emd_11847.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.28 Å/pix.
x 64 pix.
= 273.92 Å		4.28 Å/pix.
x 64 pix.
= 273.92 Å		4.28 Å/pix.
x 64 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.28 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.056
Minimum - Maximum-0.05011415 - 0.14635378
Average (Standard dev.)0.0025318959 (±0.017285418)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-63
Dimensions646464
Spacing646464
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Native ribonucleoprotein extracted from Bunyamwera virus

EntireName: Native ribonucleoprotein extracted from Bunyamwera virus
Components
  • Complex: Native ribonucleoprotein extracted from Bunyamwera virus
    • Protein or peptide: Nucleoprotein

-
Supramolecule #1: Native ribonucleoprotein extracted from Bunyamwera virus

SupramoleculeName: Native ribonucleoprotein extracted from Bunyamwera virus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bunyamwera virus

-
Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Bunyamwera virus
Molecular weightTheoretical: 26.69876 KDa
SequenceString: MIELEFHDVA ANTSSTFDPE VAYANFKRVH TTGLSYDHIR IFYIKGREIK TSLAKRSEWE VTLNLGGWKI TVYNTNFPGN RNNPVPDDG LTLHRLSGFL ARYLLEKMLK VSEPEKLIIK SKIINPLAEK NGITWNDGEE VYLSFFPGSE MFLGTFRFYP L AIGIYKVQ ...String:
MIELEFHDVA ANTSSTFDPE VAYANFKRVH TTGLSYDHIR IFYIKGREIK TSLAKRSEWE VTLNLGGWKI TVYNTNFPGN RNNPVPDDG LTLHRLSGFL ARYLLEKMLK VSEPEKLIIK SKIINPLAEK NGITWNDGEE VYLSFFPGSE MFLGTFRFYP L AIGIYKVQ RKEMEPKYLE KTMRQRYMGL EAATWTVSKL TEVQSALTVV SSLGWKKTNV SAAARDFLAK FGINM

UniProtKB: Nucleoprotein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: NITROGEN / Instrument: FEI VITROBOT MARK II

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 9.0 sec. / Average electron dose: 51.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER
Details: Previously generated sub-tomogram average of the same sample
Final reconstructionResolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5077
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

3zla


Chain - Chain ID: B / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-7aoy:
Helical arrangement of Bunyamwera virus nucleocapsid protein within a native ribonucleoprotein

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more