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- PDB-2ymn: Organization of the Influenza Virus Replication Machinery -

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Basic information

Entry
Database: PDB / ID: 2ymn
TitleOrganization of the Influenza Virus Replication Machinery
ComponentsNUCLEOPROTEIN
KeywordsVIRAL PROTEIN / RNP / POLYMERASE
Function / homology
Function and homology information


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
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 20 Å
AuthorsMoeller, A. / Kirchdoerfer, R.N. / Potter, C.S. / Carragher, B. / Wilson, I.A.
CitationJournal: 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.
History
DepositionOct 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: em_image_scans / em_software
Item: _em_software.fitting_id / _em_software.image_processing_id / _em_software.name

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-2209
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: NUCLEOPROTEIN
B: NUCLEOPROTEIN
C: NUCLEOPROTEIN
D: NUCLEOPROTEIN
E: NUCLEOPROTEIN
F: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)338,7296
Polymers338,7296
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein
NUCLEOPROTEIN / / NUCLEOCAPSID PROTEIN / PROTEIN N


Mass: 56454.793 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: HELICAL ASSEMBLY OF NUCLEOPROTEINS WITHIN INFLUENZA RNP FILAMENT
Source: (gene. exp.) INFLUENZA A VIRUS (A/PUERTO RICO/8/1934(H1N1))
Cell line (production host): HEK 293T17 / Production host: HOMO SAPIENS (human) / References: UniProt: Q1I2B5, UniProt: Q1K9H2*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: INFLUENZA VIRUS RIBONUCLEOPROTEIN COMPLEX CENTRAL FILAMENT REGION
Type: VIRUS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 85, INSTRUMENT- FEI VITROBOT MARK II,

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI 20 / Date: Aug 27, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X
Image recordingElectron dose: 15 e/Å2 / Film or detector model: GENERIC CCD
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1CTFFIND3CTF correction
2UCSF Chimeramodel fitting
3Appion3D reconstruction
4IHRSR3D reconstruction
5IMAGIC3D reconstruction
6SPIDER3D reconstruction
7Xmipp3D reconstruction
CTF correctionDetails: WHOLEIMAGE
3D reconstructionMethod: IHRSR / Resolution: 20 Å / Num. of particles: 31573 / Nominal pixel size: 1.64 Å / Actual pixel size: 1.64 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2209.(DEPOSITION ID: 11133)
Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER / Space: REAL / Details: REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 2IQH
RefinementHighest resolution: 20 Å
Refinement stepCycle: LAST / Highest resolution: 20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18994 0 0 0 18994

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