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- PDB-4bbl: Cryo-electron microscopy reconstruction of the helical part of in... -

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Basic information

Entry
Database: PDB / ID: 4bbl
TitleCryo-electron microscopy reconstruction of the helical part of influenza A virus ribonucleoprotein isolated from virions.
Components
  • NUCLEOPROTEIN
  • RNA
KeywordsNUCLEAR PROTEIN / NUCLEOCAPSID
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
RNA / RNA (> 10) / RNA (> 100) / Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesINFLUENZA A VIRUS
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 18 Å
Model type detailsP ATOMS ONLY, CHAIN Y, Z
AuthorsArranz, R. / Coloma, R. / Chichon, F.J. / Conesa, J.J. / Carrascosa, J.L. / Valpuesta, J.M. / Ortin, J. / Martin-Benito, J.
CitationJournal: Science / Year: 2012
Title: The structure of native influenza virion ribonucleoproteins.
Authors: Rocío Arranz / Rocío Coloma / Francisco Javier Chichón / José Javier Conesa / José L Carrascosa / José M Valpuesta / Juan Ortín / Jaime Martín-Benito /
Abstract: The influenza viruses cause annual epidemics of respiratory disease and occasional pandemics, which constitute a major public-health issue. The segmented negative-stranded RNAs are associated with ...The influenza viruses cause annual epidemics of respiratory disease and occasional pandemics, which constitute a major public-health issue. The segmented negative-stranded RNAs are associated with the polymerase complex and nucleoprotein (NP), forming ribonucleoproteins (RNPs), which are responsible for virus transcription and replication. We describe the structure of native RNPs derived from virions. They show a double-helical conformation in which two NP strands of opposite polarity are associated with each other along the helix. Both strands are connected by a short loop at one end of the particle and interact with the polymerase complex at the other end. This structure will be relevant for unraveling the mechanisms of nuclear import of parental virus RNPs, their transcription and replication, and the encapsidation of progeny RNPs into virions.
History
DepositionSep 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Sep 16, 2015Group: Source and taxonomy / Structure summary
Revision 1.3Aug 23, 2017Group: Data collection / Category: 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-2205
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NUCLEOPROTEIN
B: NUCLEOPROTEIN
C: NUCLEOPROTEIN
D: NUCLEOPROTEIN
E: NUCLEOPROTEIN
F: NUCLEOPROTEIN
G: NUCLEOPROTEIN
H: NUCLEOPROTEIN
I: NUCLEOPROTEIN
J: NUCLEOPROTEIN
K: NUCLEOPROTEIN
L: NUCLEOPROTEIN
M: NUCLEOPROTEIN
N: NUCLEOPROTEIN
O: NUCLEOPROTEIN
P: NUCLEOPROTEIN
Q: NUCLEOPROTEIN
R: NUCLEOPROTEIN
S: NUCLEOPROTEIN
T: NUCLEOPROTEIN
U: NUCLEOPROTEIN
V: NUCLEOPROTEIN
W: NUCLEOPROTEIN
X: NUCLEOPROTEIN
Y: RNA
Z: RNA


Theoretical massNumber of molelcules
Total (without water)1,551,85326
Polymers1,551,85326
Non-polymers00
Water0
1


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

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Components

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


Mass: 56806.047 Da / Num. of mol.: 24 / Fragment: RESIDUES 8-498
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/WSN/33 (H1N1)
Description: CRYOEM MAP FROM A/WSN/33 STRAND (H1N1). DOCKED PDB ID 2IQH.
Cell line (production host): MDCK / Production host: CANIS LUPUS FAMILIARIS (dog) / References: UniProt: P15682, UniProt: Q1K9H2*PLUS
#2: RNA chain RNA / / Coordinate model: P atoms only


Mass: 94253.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/WSN/33 (H1N1)
Description: CRYOEM MAP FROM A/WSN/33 STRAND (H1N1). DOCKED PDB ID 2IQH.
Cell line (production host): MDCK / Production host: CANIS LUPUS FAMILIARIS (dog)

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: NATIVE INFLUENZA A VIRUS RIBONUCLEOPROTEIN (STRAIN A WSN 33, H1N1)
Type: COMPLEX / Details: MICROGRAPHS SELECTED BY CTF QUALITY.
Buffer solutionName: 50MM TRIS-HCL,100MM KCL, 5MM MGCL2,0.5% IGEPAL,150MM IMIDAZOLE
pH: 8
Details: 50MM TRIS-HCL,100MM KCL, 5MM MGCL2,0.5% IGEPAL,150MM IMIDAZOLE
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: LEICA EM CPC / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- LEICA EM CPC, METHOD- BLOT FOR 2 SECONDS BEFORE PLUNGING,

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jan 1, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 65000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.26 mm
Image recordingFilm or detector model: FEI EAGLE (4k x 4k)
Image scansNum. digital images: 559
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1Situsmodel fitting
2UCSF Chimeramodel fitting
3IHRSR3D reconstruction
4SPIDER3D reconstruction
5Xmipp3D reconstruction
CTF correctionDetails: EACH PLATE
3D reconstructionMethod: ITERATIVE HELICAL REAL SPACE RECONSTRUCTION PROTOCOL
Resolution: 18 Å / Num. of particles: 876 / Nominal pixel size: 4.42 Å / Actual pixel size: 4.42 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2205.(DEPOSITION ID: 10953).
Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: VOLUMETRIC / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 2IQH
RefinementHighest resolution: 18 Å
Refinement stepCycle: LAST / Highest resolution: 18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms78285 616 0 0 78901

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