[English] 日本語
Yorodumi
- EMDB-49803: Cryo-EM structure of the Nipah Virus nucleocapsid complex -

+
Open data


ID or keywords:

Loading...

-
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: Commun Biol / Year: 2026
Title: Structural insights into the Nipah virus nucleocapsid assembly.
Authors: Ge Yang / Dmytro Kompaniiets / Dong Wang / Bin Liu /
Abstract: Nipah virus (NiV), a lethal zoonotic henipavirus, poses a major public health threat. Its nucleoprotein (N) safeguards the genome by forming a nucleocapsid, which, together with the RNA-dependent RNA ...Nipah virus (NiV), a lethal zoonotic henipavirus, poses a major public health threat. Its nucleoprotein (N) safeguards the genome by forming a nucleocapsid, which, together with the RNA-dependent RNA polymerase (L) and phosphoprotein (P), constitutes the ribonucleoprotein complex. Here, we report a 2.96 Å cryo-EM structure of the NiV nucleocapsid co-expressed with L and P. The structure, resolved under C1 symmetry without imposing helical or other symmetry restraints, reveals irregular helical packing and axis bending that likely reflect the physiological nucleocapsid. Detailed analysis defines N-N and N-RNA interfaces, including critical salt bridges and hydrogen bonds, and uncovers a previously unrecognized loop-mediated contact bridging adjacent turns. Functional validation by site-directed mutagenesis and minigenome assays establishes their potential role of these interactions in nucleocapsid stability. Collectively, these integrated structural and functional insights refine our understanding of NiV nucleocapsid assembly and highlight structural vulnerabilities that could be targeted for antiviral development.
History
DepositionMar 19, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49803.png

Downloads & links

-
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 °

-
Supplemental data

-
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)

-
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)

-
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)

-
Sample components

-
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)

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more