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- EMDB-44986: Structure of influenza A RNP, 4xNP local reconstruction, class 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-44986
TitleStructure of influenza A RNP, 4xNP local reconstruction, class 2
Map dataclass 2 sharpened map
Sample
  • Complex: Influenza A virus RNP complex
    • Protein or peptide: Nucleoprotein
    • RNA: viral RNA
KeywordsInfluenza / Ribonucleoprotein complex / nucleoprotein / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / ribonucleoprotein complex / symbiont entry into host cell / host cell nucleus / structural molecule activity / RNA binding
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Methodsubtomogram averaging / cryo EM / Resolution: 9.7 Å
AuthorsPeng R / Chang Y-W
Funding support United States, 1 items
OrganizationGrant numberCountry
David and Lucile Packard Foundation2019-69645 United States
CitationJournal: To Be Published
Title: Structure of influenza A RNP, 4xNP local reconstruction, class 2
Authors: Peng R / Chang Y-W
History
DepositionMay 22, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44986.png

Downloads & links

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Map

FileDownload / File: emd_44986.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationclass 2 sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.72 Å/pix.
x 64 pix.
= 174.08 Å		2.72 Å/pix.
x 64 pix.
= 174.08 Å		2.72 Å/pix.
x 64 pix.
= 174.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.34
Minimum - Maximum-0.22028628 - 1.2194566
Average (Standard dev.)0.06798159 (±0.14963031)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 174.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half 2

Fileemd_44986_half_map_1.map
Annotationhalf 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 1

Fileemd_44986_half_map_2.map
Annotationhalf 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Influenza A virus RNP complex

EntireName: Influenza A virus RNP complex
Components
  • Complex: Influenza A virus RNP complex
    • Protein or peptide: Nucleoprotein
    • RNA: viral RNA

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Supramolecule #1: Influenza A virus RNP complex

SupramoleculeName: Influenza A virus RNP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 3 MDa

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Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 56.454793 KDa
SequenceString: MATKGTKRSY EQMETDGERQ NATEIRASVG KMIDGIGRFY IQMCTELKLS DYEGRLIQNS LTIERMVLSA FDERRNKYLE EHPSAGKDP KKTGGPIYRR VDGKWRRELI LYDKEEIRRI WRQANNGDDA TAGLTHMMIW HSNLNDATYQ RTRALVRTGM D PRMCSLMQ ...String:
MATKGTKRSY EQMETDGERQ NATEIRASVG KMIDGIGRFY IQMCTELKLS DYEGRLIQNS LTIERMVLSA FDERRNKYLE EHPSAGKDP KKTGGPIYRR VDGKWRRELI LYDKEEIRRI WRQANNGDDA TAGLTHMMIW HSNLNDATYQ RTRALVRTGM D PRMCSLMQ GSTLPRRSGA AGAAVKGVGT MVMELIRMIK RGINDRNFWR GENGRRTRIA YERMCNILKG KFQTAAQRTM VD QVRESRN PGNAEFEDLI FLARSALILR GSVAHKSCLP ACVYGSAVAS GYDFEREGYS LVGIDPFRLL QNSQVYSLIR PNE NPAHKS QLVWMACHSA AFEDLRVSSF IRGTKVVPRG KLSTRGVQIA SNENMETMES STLELRSRYW AIRTRSGGNT NQQR ASSGQ ISIQPTFSVQ RNLPFDRPTI MAAFTGNTEG RTSDMRTEII RLMESARPED VSFQGRGVFE LSDEKATSPI VPSFD MSNE GSYFFGDNAE EYDN

UniProtKB: Nucleoprotein

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Macromolecule #2: viral RNA

MacromoleculeName: viral RNA / type: rna / ID: 2 / Number of copies: 2
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 18.32499 KDa
SequenceString:
UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: 1x PBS
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 1 / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 9.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number subtomograms used: 17357
ExtractionNumber tomograms: 289 / Number images used: 126276 / Software - Name: Warp (ver. 1.09)
CTF correctionSoftware - Name: Warp (ver. 1.09) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8pzq


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient

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