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- EMDB-64333: Cryo-EM structure of the SFTSV NP-RNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-64333
TitleCryo-EM structure of the SFTSV NP-RNA complex
Map data
Sample
  • Complex: SFTSV NP-RNA
    • Protein or peptide: Nucleoprotein
    • RNA: RNA (28-MER)
KeywordsSFTSV / N protein / RNP complex / NUCLEAR PROTEIN/RNA / NUCLEAR PROTEIN-RNA complex
Function / homology
Function and homology information


viral nucleocapsid / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / ribonucleoprotein complex / host cell nucleus / RNA binding
Similarity search - Function
Nucleocapsid, Phlebovirus/Tenuivirus / Nucleocapsid, Phlebovirus / Tenuivirus/Phlebovirus nucleocapsid protein
Similarity search - Domain/homology
Biological speciesSFTS virus HB29 / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.98 Å
AuthorsWang Y / Wu H / Deng Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of SFTSV N-RNA complex
Authors: Wu H / Deng Z
History
DepositionApr 23, 2025-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64333.png

Downloads & links

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Map

FileDownload / File: emd_64333.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 240 pix.
= 228. Å		0.95 Å/pix.
x 240 pix.
= 228. Å		0.95 Å/pix.
x 240 pix.
= 228. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.129
Minimum - Maximum-0.92532486 - 1.1959955
Average (Standard dev.)-0.00015617872 (±0.034247175)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 228.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64333_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64333_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SFTSV NP-RNA

EntireName: SFTSV NP-RNA
Components
  • Complex: SFTSV NP-RNA
    • Protein or peptide: Nucleoprotein
    • RNA: RNA (28-MER)

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Supramolecule #1: SFTSV NP-RNA

SupramoleculeName: SFTSV NP-RNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: SFTS virus HB29

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Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: SFTS virus HB29
Molecular weightTheoretical: 27.017234 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSEWSRIAVE FGEQQLNLTE LEDFARELAY EGLDPALIIK KLKETGGDDW VKDTKFIIVF ALTRGNKIVK ASGKMSNSGS KRLMALQEK YGLVERAETR LSITPVRVAQ SLPTWTCAAA AALKEYLPVG PAVMNLKVEN YPPEMMCMAF GSLIPTAGVS E ATTKTLME ...String:
MSEWSRIAVE FGEQQLNLTE LEDFARELAY EGLDPALIIK KLKETGGDDW VKDTKFIIVF ALTRGNKIVK ASGKMSNSGS KRLMALQEK YGLVERAETR LSITPVRVAQ SLPTWTCAAA AALKEYLPVG PAVMNLKVEN YPPEMMCMAF GSLIPTAGVS E ATTKTLME AYSLWQDAFT KTINVKMRGA SKTEVYNSFR DPLHAAVNSV FFPNDVRVKW LKAKGILGPD GVPSRAAEVA AA AYRNL

UniProtKB: Nucleoprotein

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Macromolecule #2: RNA (28-MER)

MacromoleculeName: RNA (28-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.527686 KDa
SequenceString:
UUUUUUUUUU UUUUUUUUUU UUUUUUUU

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 63930
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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