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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: Nat Commun / Year: 2025
Title: Structural stabilization of the intrinsically disordered SARS-CoV-2 N by binding to RNA sequences engineered from the viral genome fragment.
Authors: Sara Landeras-Bueno / Chitra Hariharan / Ruben Diaz Avalos / Andrew S Norris / Dalton T Snyder / Kathryn M Hastie / Stephanie Harkins / Michelle Zandonatti / Roshan R Rajamanickam / Eduardo ...Authors: Sara Landeras-Bueno / Chitra Hariharan / Ruben Diaz Avalos / Andrew S Norris / Dalton T Snyder / Kathryn M Hastie / Stephanie Harkins / Michelle Zandonatti / Roshan R Rajamanickam / Eduardo Olmedillas / Robyn Miller / Sujan Shresta / Vicki H Wysocki / Erica Ollmann Saphire /
Abstract: The nucleocapsid N is one of four structural proteins of the coronaviruses. Its essential role in genome encapsidation makes it a critical therapeutic target for COVID-19 and related diseases. ...The nucleocapsid N is one of four structural proteins of the coronaviruses. Its essential role in genome encapsidation makes it a critical therapeutic target for COVID-19 and related diseases. However, the inherent disorder of full-length N hampers its structural analysis. Here, we describe a stepwise method using viral-derived RNAs to stabilize SARS-CoV-2 N for EM analysis. We identify pieces of RNA from the SARS-CoV-2 genome that promote the formation of structurally homogeneous N dimers, intermediates of assembly, and filamentous capsid-like structures. Building on these results, we engineer a symmetric RNA to stabilize N protein dimers, the building block of high-order assemblies, for EM studies. We combine domain-specific monoclonal antibodies against N with chemical cross-linking mass spectrometry to validate the spatial arrangement of the N domains within the dimer. Additionally, our cryo-EM analysis reveals novel antigenic sites on the N protein. Our findings provide insights into N protein´s architectural and antigenic principles, which can guide design of pan-coronavirus therapeutics.
History
DepositionMay 31, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 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

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Slices (1/2)
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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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