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- PDB-6h9g: Influenza A nucleoprotein docked into 3D helical structure of the... -

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Basic information

Entry
Database: PDB / ID: 6h9g
TitleInfluenza A nucleoprotein docked into 3D helical structure of the wild type ribonucleoprotein complex obtained using cryoEM. Conformation 1.
Components
  • Nucleoprotein
  • Polypeptide loop
KeywordsVIRAL PROTEIN / Influenza A virus Ribonucleoprotein RNA binding protein
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
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 11 Å
AuthorsColoma, R. / Arranz, R. / de la Rosa-Trevin, J.M. / Sorzano, C.O.S. / Munier, S. / Carlero, D. / Naffakh, N. / Ortin, J. / Martin-Benito, J.
Funding support Spain, 2items
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, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Nucleoprotein
B: Polypeptide loop
C: Nucleoprotein
D: Polypeptide loop


Theoretical massNumber of molelcules
Total (without water)110,4434
Polymers110,4434
Non-polymers00
Water0
1
A: Nucleoprotein
B: Polypeptide loop


Theoretical massNumber of molelcules
Total (without water)55,2222
Polymers55,2222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
2
C: Nucleoprotein
D: Polypeptide loop


Theoretical massNumber of molelcules
Total (without water)55,2222
Polymers55,2222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Nucleoprotein / / Nucleocapsid protein / Protein N


Mass: 53114.328 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Influenza A virus (strain A/Wilson-Smith/1933 H1N1)
Cell line: COS1,MDCK / Strain: A/Wilson-Smith/1933 H1N1 / References: UniProt: Q1K9H2, UniProt: P15682*PLUS
#2: Protein/peptide Polypeptide loop


Mass: 2107.346 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Influenza A virus / Cell line: COS1,MDCK / Strain: A/WSN/33 / References: UniProt: P15682*PLUS

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Influenza A virus / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Influenza A virus / Strain: A/WSN/33
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 7.4 / Details: TN buffer (50 mM Tris-HCl, 150 mM KCl)
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM CPC / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 2 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 420
Image scansMovie frames/image: 69 / Used frames/image: 3-68

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Processing

EM software
IDNameVersionCategory
1Xmippparticle selection
2EPUimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
9SPIDERIHRSRinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -65.39 ° / Axial rise/subunit: 33.63 Å / Axial symmetry: D1
Particle selectionNum. of particles selected: 137461 / Details: Manual picking
3D reconstructionResolution: 11 Å / Resolution method: OTHER / Num. of particles: 2367 / Algorithm: BACK PROJECTION / Details: MonoRes Software Xmipp/SCIPION / Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 2IQH

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