[English] 日本語
Yorodumi
- EMDB-0175: Helical part of the influenza A virus ribonucleoprotein. Conforma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0175
TitleHelical part of the influenza A virus ribonucleoprotein. Conformation 1.
Map dataHelical part of influenza A virus ribonucleoprotein (vRNP)
Sample
  • Complex: Influenza A virus
    • Protein or peptide: Nucleoprotein
    • Protein or peptide: Polypeptide loop
Function / homology
Function and homology information


negative stranded viral RNA replication / helical viral capsid / viral penetration into host nucleus / viral nucleocapsid / symbiont entry into host cell / ribonucleoprotein complex / host cell nucleus / structural molecule activity / RNA binding / identical protein binding
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein
Similarity search - Domain/homology
Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesInfluenza A virus / Influenza A virus (strain A/WS/1933 H1N1)
Methodhelical reconstruction / cryo EM / Resolution: 11.0 Å
AuthorsColoma R / Arranz R / de la Rosa-Trevin JM / Sorzano COS / Munier S / Carlero D / Naffakh N / Ortin J / Martin-Benito J
Funding support Spain, 2 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU2017-90018-R Spain
Spanish Ministry of Science, Innovation, and UniversitiesBFU2011-25090/BMC Spain
CitationJournal: Nat Microbiol / Year: 2020
Title: Structural insights into influenza A virus ribonucleoproteins reveal a processive helical track as transcription mechanism.
Authors: Rocío Coloma / Rocío Arranz / José M de la Rosa-Trevín / Carlos O S Sorzano / Sandie Munier / Diego Carlero / Nadia Naffakh / Juan Ortín / Jaime Martín-Benito /
Abstract: The influenza virus genome consists of eight viral ribonucleoproteins (vRNPs), each consisting of a copy of the polymerase, one of the genomic RNA segments and multiple copies of the nucleoprotein ...The influenza virus genome consists of eight viral ribonucleoproteins (vRNPs), each consisting of a copy of the polymerase, one of the genomic RNA segments and multiple copies of the nucleoprotein arranged in a double helical conformation. vRNPs are macromolecular machines responsible for messenger RNA synthesis and genome replication, that is, the formation of progeny vRNPs. Here, we describe the structural basis of the transcription process. The mechanism, which we call the 'processive helical track', is based on the extreme flexibility of the helical part of the vRNP that permits a sliding movement between both antiparallel nucleoprotein-RNA strands, thereby allowing the polymerase to move over the genome while bound to both RNA ends. Accordingly, we demonstrate that blocking this movement leads to inhibition of vRNP transcriptional activity. This mechanism also reveals a critical role of the nucleoprotein in maintaining the double helical structure throughout the copying process to make the RNA template accessible to the polymerase.
History
DepositionAug 3, 2018-
Header (metadata) releaseFeb 12, 2020-
Map releaseFeb 12, 2020-
UpdateMay 6, 2020-
Current statusMay 6, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6h9g
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6h9g
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0175.png

Downloads & links

-
Map

FileDownload / File: emd_0175.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical part of influenza A virus ribonucleoprotein (vRNP)
Voxel sizeX=Y=Z: 2.26 Å
Density
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.050032586 - 0.08805794
Average (Standard dev.)0.0034064166 (±0.018405953)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 271.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.262.262.26
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z271.200271.200271.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS120120120
D min/max/mean-0.0500.0880.003

-
Supplemental data

-
Additional map: MonoRes 3D Resolution map. colorkey 0.01,0.05 0.02,0.95 7.00...

Fileemd_0175_additional.map
AnnotationMonoRes 3D Resolution map. colorkey 0.01,0.05 0.02,0.95 7.00 #000080 " " #0018ff 12.0 #004cff " " #0080ff " " #00e4f8 16.0 #29ffce " " #a4ff53 21.0 #ceff29 " " #bb0000 30.0 #800000
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Influenza A virus

EntireName: Influenza A virus
Components
  • Complex: Influenza A virus
    • Protein or peptide: Nucleoprotein
    • Protein or peptide: Polypeptide loop

-
Supramolecule #1: Influenza A virus

SupramoleculeName: Influenza A virus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Influenza A virus / Strain: A/WSN/33

-
Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (strain A/WS/1933 H1N1) / Strain: A/Wilson-Smith/1933 H1N1
Molecular weightTheoretical: 53.114328 KDa
SequenceString: NATEIRASVG KMIDGIGRFY IQMCTELKLS DYEGRLIQNS LTIERMVLSA FDERRNKYLE EHPSAGKDPK KTGGPIYRRV DGKWRRELI LYDKEEIRRI WRQANNGDDA TAGLTHMMIW HSNLNDATYQ RTRALVRTGM DPRMCSLMQG STLPRRSGAA G AAVKGVGT ...String:
NATEIRASVG KMIDGIGRFY IQMCTELKLS DYEGRLIQNS LTIERMVLSA FDERRNKYLE EHPSAGKDPK KTGGPIYRRV DGKWRRELI LYDKEEIRRI WRQANNGDDA TAGLTHMMIW HSNLNDATYQ RTRALVRTGM DPRMCSLMQG STLPRRSGAA G AAVKGVGT MVMELIRMIK RGINDRNFWR GENGRRTRIA YERMCNILKG KFQTAAQRTM VDQVRESRNP GNAEFEDLIF LA RSALILR GSVAHKSCLP ACVYGSAVAS GYDFEREGYS LVGIDPFRLL QNSQVYSLIR PNENPAHKSQ LVWMACHSAA FED LRVSSF IRGTKVVPRG KLSTRGVQIA SNENMETMES STLELRSRYW AIRTRSGGNT NQQRASSGQI SIQPTFSVQR NLPF DRPTI MAAFTGNTEG RTSDMRTEII RLMESARPED VSFQGRGVFE LSDEKATSPI VPSFDMSNEG SYFF

-
Macromolecule #2: Polypeptide loop

MacromoleculeName: Polypeptide loop / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus / Strain: A/WSN/33
Molecular weightTheoretical: 2.107346 KDa
SequenceString:
SSGQISIQPT FSVQRNLPF

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
Sample preparation

BufferpH: 7.4 / Details: TN buffer (50 mM Tris-HCl, 150 mM KCl)
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 3-68 / Number real images: 420 / Average electron dose: 2.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Segment selectionNumber selected: 137461 / Software - Name: Xmipp / Details: Manual picking
CTF correctionSoftware - Name: CTFFIND
Startup modelType of model: OTHER
Details: Initial model created using Iterative Helical Real Space Reconstruction
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION
Final reconstructionApplied symmetry - Helical parameters - Δz: 33.63 Å
Applied symmetry - Helical parameters - Δ&Phi: -65.39 °
Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: OTHER / Software - Name: RELION / Details: MonoRes Software Xmipp/SCIPION / Number images used: 2367

-
Atomic model buiding 1

Initial modelPDB ID:

2iqh

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6h9g:
Influenza A nucleoprotein docked into 3D helical structure of the wild type ribonucleoprotein complex obtained using cryoEM. Conformation 1.

+
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