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- EMDB-49803: Cryo-EM structure of the Nipah Virus nucleocapsid complex -

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Basic information

Entry
Database: EMDB / ID: EMD-49803
TitleCryo-EM structure of the Nipah Virus nucleocapsid complex
Map dataCryoEM structure of the Nipah virus nucleocapsid complex
Sample
  • Complex: The Nipah Virus nucleocapsid complex
    • Protein or peptide: Nucleoprotein
    • RNA: RNA (84-MER)
KeywordsNipah virus / nucleocapsid (N) protein / ribonucleoprotein (RNP) complex / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


negative stranded viral RNA transcription / negative stranded viral RNA replication / helical viral capsid / viral nucleocapsid / molecular adaptor activity / host cell cytoplasm / ribonucleoprotein complex / structural molecule activity / RNA binding
Similarity search - Function
Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein
Similarity search - Domain/homology
Biological speciesHenipavirus nipahense
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsLiu B / Yang G / Wang D
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of the Nipah Virus nucleocapsid complex
Authors: Liu B / Yang G
History
DepositionMar 19, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49803.png

Downloads & links

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Map

FileDownload / File: emd_49803.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure of the Nipah virus nucleocapsid complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 540 pix.
= 478.08 Å		0.89 Å/pix.
x 540 pix.
= 478.08 Å		0.89 Å/pix.
x 540 pix.
= 478.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88533 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.23957899 - 0.5678514
Average (Standard dev.)0.00045947498 (±0.011619445)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 478.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: CryoEM structure of the Nipah virus nucleocapsid complex...

Fileemd_49803_additional_1.map
AnnotationCryoEM structure of the Nipah virus nucleocapsid complex - sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_49803_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_49803_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The Nipah Virus nucleocapsid complex

EntireName: The Nipah Virus nucleocapsid complex
Components
  • Complex: The Nipah Virus nucleocapsid complex
    • Protein or peptide: Nucleoprotein
    • RNA: RNA (84-MER)

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Supramolecule #1: The Nipah Virus nucleocapsid complex

SupramoleculeName: The Nipah Virus nucleocapsid complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 1.01 MDa

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Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 58.231898 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSDIFEEAAS FRSYQSKLGR DGRASAATAT LTTKIRIFVP ATNSPELRWE LTLFALDVIR SPSAAESMKV GAAFTLISMY SERPGALIR SLLNDPDIEA VIIDVGSMVN GIPVMERRGD KAQEEMEGLM RILKTARDSS KGKTPFVDSR AYGLRITDMS T LVSAVITI ...String:
MSDIFEEAAS FRSYQSKLGR DGRASAATAT LTTKIRIFVP ATNSPELRWE LTLFALDVIR SPSAAESMKV GAAFTLISMY SERPGALIR SLLNDPDIEA VIIDVGSMVN GIPVMERRGD KAQEEMEGLM RILKTARDSS KGKTPFVDSR AYGLRITDMS T LVSAVITI EAQIWILIAK AVTAPDTAEE SETRRWAKYV QQKRVNPFFA LTQQWLTEMR NLLSQSLSVR KFMVEILIEV KK GGSAKGR AVEIISDIGN YVEETGMAGF FATIRFGLET RYPALALNEF QSDLNTIKSL MLLYREIGPR APYMVLLEES IQT KFAPGG YPLLWSFAMG VATTIDRSMG ALNINRGYLE PMYFRLGQKS ARHHAGGIDQ NMANRLGLSS DQVAELAAAV QETS AGRQE SNVQAREAKF AAGGVLIGGS DQDIDEGEEP IEQSGRQSVT FKREMSISSL ANSVPSSSVS TSGGTRLTNS LLNLR SRLA AKAAKEAASS NATDDPAISN RTQGESEKKN NQDLKPAQND LDFVRADV

UniProtKB: Nucleoprotein

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Macromolecule #2: RNA (84-MER)

MacromoleculeName: RNA (84-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 25.672984 KDa
SequenceString:
UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUU

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 63.0 K / Max: 77.0 K
Specialist opticsEnergy filter - Slit width: 20 eV
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 6267 / Average exposure time: 1.7 sec. / Average electron dose: 50.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
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

Particle selectionNumber selected: 1326637
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 138389
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Overall B value: 55.4
Output model

PDB-9nuf:
Cryo-EM structure of the Nipah Virus nucleocapsid complex

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