[English] 日本語
- EMDB-0333: Helical RNA-bound Hantaan virus nucleocapsid -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 0333
TitleHelical RNA-bound Hantaan virus nucleocapsid
Map dataHelical RNA-bound Hantaan virus nucleocapsid structure
SampleRNA-bound Hantaan virus nucleocapsid:
Hantaan virus nucleoprotein / RNA / nucleic-acidNucleic acid / Nucleoprotein
Function / homologyHantavirus nucleocapsid protein / Hantavirus nucleocapsid protein / helical viral capsid / viral nucleocapsid / RNA binding / Nucleoprotein
Function and homology information
SourceHantaan orthohantavirus / Spodoptera frugiperda (fall armyworm) / Fall armyworm (fall armyworm)
Methodhelical reconstruction / cryo EM / 3.3 Å resolution
AuthorsArragain B / Reguera J / Desfosses A / Gutsche I / Schoehn G / Malet H
CitationJournal: Elife / Year: 2019
Title: High resolution cryo-EM structure of the helical RNA-bound Hantaan virus nucleocapsid reveals its assembly mechanisms.
Authors: Benoît Arragain / Juan Reguera / Ambroise Desfosses / Irina Gutsche / Guy Schoehn / Hélène Malet
Abstract: Negative-strand RNA viruses condense their genome into helical nucleocapsids that constitute essential templates for viral replication and transcription. The intrinsic flexibility of nucleocapsids ...Negative-strand RNA viruses condense their genome into helical nucleocapsids that constitute essential templates for viral replication and transcription. The intrinsic flexibility of nucleocapsids usually prevents their full-length structural characterisation at high resolution. Here, we describe purification of full-length recombinant metastable helical nucleocapsid of Hantaan virus ( family, order) and determine its structure at 3.3 Å resolution by cryo-electron microscopy. The structure reveals the mechanisms of helical multimerisation via sub-domain exchanges between protomers and highlights nucleotide positions in a continuous positively charged groove compatible with viral genome binding. It uncovers key sites for future structure-based design of antivirals that are currently lacking to counteract life-threatening hantavirus infections. The structure also suggests a model of nucleoprotein-polymerase interaction that would enable replication and transcription solely upon local disruption of the nucleocapsid.
Validation ReportPDB-ID: 6i2n

SummaryFull reportAbout validation report
DateDeposition: Nov 1, 2018 / Header (metadata) release: Dec 19, 2018 / Map release: Jan 23, 2019 / Last update: Jan 23, 2019

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6i2n
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_0333.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
1.07 Å/pix.
= 426.8 Å
400 pix
1.07 Å/pix.
= 426.8 Å
400 pix
1.07 Å/pix.
= 426.8 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Contour Level:0.025 (by author), 0.025 (movie #1):
Minimum - Maximum-0.06770787 - 0.12958607
Average (Standard dev.)0.000070503615 (0.0019500765)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 426.80002 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0671.0671.067
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z426.800426.800426.800
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0680.1300.000

Supplemental data

Sample components

Entire RNA-bound Hantaan virus nucleocapsid

EntireName: RNA-bound Hantaan virus nucleocapsid / Number of components: 5

Component #1: protein, RNA-bound Hantaan virus nucleocapsid

ProteinName: RNA-bound Hantaan virus nucleocapsid / Recombinant expression: No
MassTheoretical: 48.2 kDa

Component #2: protein, Hantaan virus nucleoprotein

ProteinName: Hantaan virus nucleoprotein / Recombinant expression: No
SourceSpecies: Hantaan orthohantavirus
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm) / Vector: pFastBac / Strain: SF21

Component #3: protein, RNA

ProteinName: RNA / Recombinant expression: No
SourceSpecies: Spodoptera frugiperda (fall armyworm)

Component #4: nucleic-acid, RNA (5'-R(P*UP*UP*U)-3')

Nucleic-acidName: RNA (5'-R(P*UP*UP*U)-3') / Class: RNA
Details: A poly-U has been built but the RNA corresponds to heterogeneous insect cell RNA that bind to nucleoproteins during expression.
Structure: OTHER / Synthetic: No
MassTheoretical: 0.87354 kDa
SourceSpecies: Fall armyworm (fall armyworm)

Component #5: protein, Nucleoprotein

ProteinName: Nucleoprotein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.262266 kDa
SourceSpecies: Hantaan orthohantavirus
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

Experimental details

Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 18.87 Å / Delta phi: -99.95 deg.
Sample solutionSpecimen conc.: 0.6 mg/ml / pH: 8
Support film30 mA
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 100 %
Details: 3 ul of sample were applied on the resulting glow-discharged grids and excess solution was blotted during 2.5 sec force 7.

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 4 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 46860.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Energy filter: GIF Quantum LS
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 4328 / Sampling size: 5 microns

Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: RELION / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF
Euler angles: Relion was used for helical symmetry search/refinement on the best segments (removing the ones with more than 20 degree angular tilt) with local CTF determination and CTF-refinement. Frames 3-18 were used.
FSC plot
(resolution estimation)

Atomic model buiding

Modeling #1Refinement space: REAL
Details: Fiber model was iteratively rebuilt and all-atom refined using stereochemical and NCS restraints
Input PDB model: 5FSG
Overall bvalue: 103
Output model

About Yorodumi


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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more


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.

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