|Entry||Database: EMDB / ID: EMD-2213|
|Title||Organization of the Influenza Virus Replication Machinery|
|Sample||influenza virus polymerase|
|Keywords||Influenza / RNP / Polymerase|
|Biological species||Influenza A virus (A/Puerto Rico/8/1934(H1N1))|
|Method||single particle reconstruction / cryo EM / Resolution: 13 Å|
|Authors||Moeller A / Kirchdoerfer RN / Potter CS / Carragher B / Wilson IA|
|Citation||Journal: Science / Year: 2012|
Title: Organization of the influenza virus replication machinery.
Authors: Arne Moeller / Robert N Kirchdoerfer / Clinton S Potter / Bridget Carragher / Ian A Wilson /
Abstract: Influenza virus ribonucleoprotein complexes (RNPs) are central to the viral life cycle and in adaptation to new host species. RNPs are composed of the viral genome, viral polymerase, and many copies ...Influenza virus ribonucleoprotein complexes (RNPs) are central to the viral life cycle and in adaptation to new host species. RNPs are composed of the viral genome, viral polymerase, and many copies of the viral nucleoprotein. In vitro cell expression of all RNP protein components with four of the eight influenza virus gene segments enabled structural determination of native influenza virus RNPs by means of cryogenic electron microscopy (cryo-EM). The cryo-EM structure reveals the architecture and organization of the native RNP, defining the attributes of its largely helical structure and how polymerase interacts with nucleoprotein and the viral genome. Observations of branched-RNP structures in negative-stain electron microscopy and their putative identification as replication intermediates suggest a mechanism for viral replication by a second polymerase on the RNP template.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_2213.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 2.18 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire influenza virus polymerase
|Entire||Name: influenza virus polymerase / Number of components: 3|
-Component #1: protein, influenza virus polymerase
|Protein||Name: influenza virus polymerase / Recombinant expression: Yes|
|Source||Species: Influenza A virus (A/Puerto Rico/8/1934(H1N1))|
|Source (engineered)||Expression System: Homo sapiens (human)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 85 %|
-Electron microscopy imaging
|Imaging||Microscope: FEI TECNAI 20 / Date: Mar 11, 2011|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 100000 X (nominal) / Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: GATAN LIQUID NITROGEN|
|Camera||Detector: GENERIC CCD|
|Image acquisition||Number of digital images: 1878|
|Processing||Method: single particle reconstruction / Number of projections: 16958 / Applied symmetry: C1 (asymmetric)|
|3D reconstruction||Software: XMIPP, IMAGIC, SPIDER, APPION, CTFFIND3 / CTF correction: wholeimage / Resolution: 13 Å / Resolution method: FSC 0.5|
-Aug 12, 2020. New: Covid-19 info
New: Covid-19 info
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info
+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. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
+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. See below links for details.
- 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.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
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.
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