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- EMDB-45158: SARS-CoV-2 Nucleocapsid dimer complexed to 24 bp RNA -

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Basic information

Entry
Database: EMDB / ID: EMD-45158
TitleSARS-CoV-2 Nucleocapsid dimer complexed to 24 bp RNA
Map data
Sample
  • Complex: SARS-CoV-2 Nucleocapsid dimer complexed to a 24 bp-RNA
    • Protein or peptide: SARS-CoV-2 Nucleocapsid complexed to a 24 bp-RNA
    • RNA: 24-bp RNA
KeywordsProtein / RNA / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2 / synthetic RNA (others)
Methodsingle particle reconstruction / negative staining / Resolution: 8.24 Å
AuthorsLanderas-Bueno S / Ollmann-Saphire E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIH R21 AI178427-01 United States
CitationJournal: To Be Published
Title: Structural stabilization of the intrinsically disordered SARS-CoV-2 N by binding to RNA sequences engineered from the viral genome
Authors: Landeras-Bueno S / Ollmann Saphire E
History
DepositionMay 31, 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_45158.png

Downloads & links

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Map

FileDownload / File: emd_45158.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.7 Å/pix.
x 256 pix.
= 435.2 Å		1.7 Å/pix.
x 256 pix.
= 435.2 Å		1.7 Å/pix.
x 256 pix.
= 435.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.416
Minimum - Maximum-0.19468032 - 1.0946211
Average (Standard dev.)0.001663685 (±0.03894703)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_45158_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45158_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 : SARS-CoV-2 Nucleocapsid dimer complexed to a 24 bp-RNA

EntireName: SARS-CoV-2 Nucleocapsid dimer complexed to a 24 bp-RNA
Components
  • Complex: SARS-CoV-2 Nucleocapsid dimer complexed to a 24 bp-RNA
    • Protein or peptide: SARS-CoV-2 Nucleocapsid complexed to a 24 bp-RNA
    • RNA: 24-bp RNA

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Supramolecule #1: SARS-CoV-2 Nucleocapsid dimer complexed to a 24 bp-RNA

SupramoleculeName: SARS-CoV-2 Nucleocapsid dimer complexed to a 24 bp-RNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: SARS-CoV-2 Nucleocapsid complexed to a 24 bp-RNA

MacromoleculeName: SARS-CoV-2 Nucleocapsid complexed to a 24 bp-RNA / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSDNGPQNQR NAPRITFGGP SDSTGSNQNG ERSGARSKQR RPQGLPNNTA SWFTALTQHG KEDLKFPRGQ GVPINTNSSP DDQIGYYRRA TRRIRGGDGK MKDLSPRWYF YYLGTGPEAG LPYGANKDGI IWVATEGALN TPKDHIGTRN PANNAAIVLQ LPQGTTLPKG ...String:
MSDNGPQNQR NAPRITFGGP SDSTGSNQNG ERSGARSKQR RPQGLPNNTA SWFTALTQHG KEDLKFPRGQ GVPINTNSSP DDQIGYYRRA TRRIRGGDGK MKDLSPRWYF YYLGTGPEAG LPYGANKDGI IWVATEGALN TPKDHIGTRN PANNAAIVLQ LPQGTTLPKG FYAEGSRGGS QASSRSSSRS RNSSRNSTPG SSRGTSPARM AGNGGDAALA LLLLDRLNQL ESKMSGKGQQ QQGQTVTKKS AAEASKKPRQ KRTATKAYNV TQAFGRRGPE QTQGNFGDQE LIRQGTDYKH WPQIAQFAPS ASAFFGMSRI GMEVTPSGTW LTYTGAIKLD DKDPNFKDQV ILLNKHIDAY KTFPPTEPKK DKKKKADETQ ALPQRQKKQQ TVTLLPAADL DDFSKQLQQS MSSADSTQ

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Macromolecule #2: 24-bp RNA

MacromoleculeName: 24-bp RNA / type: rna / ID: 2
Details: Engineered 24-bp RNA formed by two copies of the high-affinity binding sequence found in PDB 7ACS connected by a 10-bp RNA linker
Source (natural)Organism: synthetic RNA (others)
SequenceString:
CACUGACUUA ACGGUUACAC UGAC

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.02 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMHepesHepes
250.0 mMNaClsodium chloride

Details: 50 mM Hepes pH 7.5, 250mM NaCl
StainingType: NEGATIVE / Material: 0.75% uranyl acetate
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 2.15) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 48106
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2.15)

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