[English] 日本語
Yorodumi
- EMDB-1603: 12 Angstrom resolution cryo-electron microscopy reconstruction of... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1603
Title12 Angstrom resolution cryo-electron microscopy reconstruction of a recombinant active ribonucleoprotein particle of influenza virus (9-fold symmetrized).
Map dataDensity map of a influenza virus recombinant active RNP refined with 9-fold symmetry. Density corresponding to the polymerase has been smeared out due to the symmetrization.
Sample
  • Sample: influenza virus ribonucleoprotein particle from INFLUENZA A VIRUS STRAIN A/VICTORIA/3/75 (H3N1 AFRICAN GREEN MONKEY
  • Protein or peptide: nucleoprotein
  • RNA: RNA
KeywordsInfluenza / RNA viruses / nucleoprotein / RNA
Function / homology
Function and homology information


cRNA Synthesis / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus ...cRNA Synthesis / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / vRNA Synthesis / Transport of Ribonucleoproteins into the Host Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / Viral Messenger RNA Synthesis / vRNP Assembly / helical viral capsid / Viral mRNA Translation / viral penetration into host nucleus / viral nucleocapsid / symbiont entry into host cell / ribonucleoprotein complex / host cell nucleus / structural molecule activity / RNA binding / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein
Similarity search - Domain/homology
Biological speciesInfluenza A virus (A/Victoria/3/1975(H3N2))
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 12.0 Å
AuthorsColoma R / Valpuesta JM / Arranz R / Carrascosa JL / Ortin J / Martin-Benito J
CitationJournal: PLoS Pathog / Year: 2009
Title: The structure of a biologically active influenza virus ribonucleoprotein complex.
Authors: Rocío Coloma / José M Valpuesta / Rocío Arranz / José L Carrascosa / Juan Ortín / Jaime Martín-Benito /
Abstract: The influenza viruses contain a segmented, single-stranded RNA genome of negative polarity. Each RNA segment is encapsidated by the nucleoprotein and the polymerase complex into ribonucleoprotein ...The influenza viruses contain a segmented, single-stranded RNA genome of negative polarity. Each RNA segment is encapsidated by the nucleoprotein and the polymerase complex into ribonucleoprotein particles (RNPs), which are responsible for virus transcription and replication. Despite their importance, information about the structure of these RNPs is scarce. We have determined the three-dimensional structure of a biologically active recombinant RNP by cryo-electron microscopy. The structure shows a nonameric nucleoprotein ring (at 12 Angstrom resolution) with two monomers connected to the polymerase complex (at 18 Angstrom resolution). Docking the atomic structures of the nucleoprotein and polymerase domains, as well as mutational analyses, has allowed us to define the interactions between the functional elements of the RNP and to propose the location of the viral RNA. Our results provide the first model for a functional negative-stranded RNA virus ribonucleoprotein complex. The structure reported here will serve as a framework to generate a quasi-atomic model of the molecular machine responsible for viral RNA synthesis and to test new models for virus RNA replication and transcription.
History
DepositionApr 15, 2009-
Header (metadata) releaseApr 23, 2009-
Map releaseJun 29, 2009-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-2wfs
  • Surface level: 3.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1603.png

Downloads & links

-
Map

FileDownload / File: emd_1603.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity map of a influenza virus recombinant active RNP refined with 9-fold symmetry. Density corresponding to the polymerase has been smeared out due to the symmetrization.
Voxel sizeX=Y=Z: 2.8 Å
Density
Contour LevelBy AUTHOR: 3.5 / Movie #1: 3.5
Minimum - Maximum-5.40916 - 14.1783
Average (Standard dev.)-0.000961337 (±0.885527)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 448 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z448.000448.000448.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-17-17-200
NX/NY/NZ123123401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-5.40914.178-0.001

-
Supplemental data

-
Sample components

-
Entire : influenza virus ribonucleoprotein particle from INFLUENZA A VIRUS...

EntireName: influenza virus ribonucleoprotein particle from INFLUENZA A VIRUS STRAIN A/VICTORIA/3/75 (H3N1 AFRICAN GREEN MONKEY
Components
  • Sample: influenza virus ribonucleoprotein particle from INFLUENZA A VIRUS STRAIN A/VICTORIA/3/75 (H3N1 AFRICAN GREEN MONKEY
  • Protein or peptide: nucleoprotein
  • RNA: RNA

-
Supramolecule #1000: influenza virus ribonucleoprotein particle from INFLUENZA A VIRUS...

SupramoleculeName: influenza virus ribonucleoprotein particle from INFLUENZA A VIRUS STRAIN A/VICTORIA/3/75 (H3N1 AFRICAN GREEN MONKEY
type: sample / ID: 1000
Oligomeric state: Nine monomers of nucleoprotein bound to a single stranded RNA
Number unique components: 2
Molecular weightTheoretical: 600 KDa

-
Macromolecule #1: nucleoprotein

MacromoleculeName: nucleoprotein / type: protein_or_peptide / ID: 1 / Name.synonym: nucleoprotein / Number of copies: 9 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Influenza A virus (A/Victoria/3/1975(H3N2)) / Location in cell: nucleus
Molecular weightTheoretical: 56 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)

-
Macromolecule #2: RNA

MacromoleculeName: RNA / type: rna / ID: 2 / Name.synonym: RNA / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No
Source (natural)Organism: Influenza A virus (A/Victoria/3/1975(H3N2))
Molecular weightTheoretical: 82 KDa

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Details: 50mM Tris-HCl,100mM KCl,5mM MgCl2,0.5% Igepal,150mM imidazole
StainingType: NEGATIVE
Details: Samples were applied to one side of a holey carbon grid, blotted and plunged into liquid ethane
VitrificationCryogen name: ETHANE / Instrument: LEICA PLUNGER / Details: Vitrification instrument: Leica plunger

-
Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingDigitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 159 / Details: downsampling factor 2. / Bits/pixel: 8
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Each plate
Final reconstructionApplied symmetry - Point group: C9 (9 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: spider / Number images used: 9571

-
Atomic model buiding 1

Initial modelPDB ID:

2iqh


Chain - Chain ID: A
SoftwareName: SITUS
DetailsPDBEntryID_givenInChain. Protocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Volumetric
Output model

PDB-2wfs:
Fitting of influenza virus NP structure into the 9-fold symmetryzed cryoEM reconstruction of an active RNP particle.

+
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