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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0333
TitleHelical RNA-bound Hantaan virus nucleocapsid
Map dataHelical RNA-bound Hantaan virus nucleocapsid structure
Sample
  • Complex: RNA-bound Hantaan virus nucleocapsid
    • Complex: Hantaan virus nucleoprotein
      • Protein or peptide: Nucleoprotein
    • Complex: RNA
      • RNA: RNA (5'-R(P*UP*UP*U)-3')
KeywordsNucleoprotein / Nucleocapsid / RNA-binding / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated suppression of host apoptosis / helical viral capsid / viral nucleocapsid / endonuclease activity / host cell Golgi apparatus / Hydrolases; Acting on ester bonds / host cell perinuclear region of cytoplasm / ribonucleoprotein complex / RNA binding
Similarity search - Function
Hantavirus nucleocapsid protein / Hantavirus nucleocapsid protein
Similarity search - Domain/homology
Biological speciesHantaan orthohantavirus / Spodoptera frugiperda (fall armyworm)
Methodhelical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsArragain B / Reguera J
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.
History
DepositionNov 1, 2018-
Header (metadata) releaseDec 19, 2018-
Map releaseJan 23, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • 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:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0333.png

Downloads & links

-
Map

FileDownload / File: emd_0333.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical RNA-bound Hantaan virus nucleocapsid structure
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 426.8 Å		1.07 Å/pix.
x 400 pix.
= 426.8 Å		1.07 Å/pix.
x 400 pix.
= 426.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.06770787 - 0.12958607
Average (Standard dev.)0.000070503615 (±0.0019500765)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 426.80002 Å
α=β=γ: 90.0 °

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
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0680.1300.000

-
Supplemental data

-
Half map: Half map 2

Fileemd_0333_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1

Fileemd_0333_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : RNA-bound Hantaan virus nucleocapsid

EntireName: RNA-bound Hantaan virus nucleocapsid
Components
  • Complex: RNA-bound Hantaan virus nucleocapsid
    • Complex: Hantaan virus nucleoprotein
      • Protein or peptide: Nucleoprotein
    • Complex: RNA
      • RNA: RNA (5'-R(P*UP*UP*U)-3')

-
Supramolecule #1: RNA-bound Hantaan virus nucleocapsid

SupramoleculeName: RNA-bound Hantaan virus nucleocapsid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 48.2 KDa

-
Supramolecule #2: Hantaan virus nucleoprotein

SupramoleculeName: Hantaan virus nucleoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Hantaan orthohantavirus

-
Supramolecule #3: RNA

SupramoleculeName: RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Spodoptera frugiperda (fall armyworm)

-
Macromolecule #1: RNA (5'-R(P*UP*UP*U)-3')

MacromoleculeName: RNA (5'-R(P*UP*UP*U)-3') / type: rna / ID: 1
Details: A poly-U has been built but the RNA corresponds to heterogeneous insect cell RNA that bind to nucleoproteins during expression.
Number of copies: 1
Source (natural)Organism: Spodoptera frugiperda (fall armyworm)
Molecular weightTheoretical: 873.54 Da
SequenceString:
UUU

-
Macromolecule #2: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hantaan orthohantavirus
Molecular weightTheoretical: 48.262266 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GMATMEELQR EINAHEGQLV IARQKVRDAE KQYEKDPDEL NKRTLTDREG VAVSIQAKID ELKRQLADRI ATGKNLGKEQ DPTGVEPGD HLKERSMLSY GNVLDLNHLD IDEPTGQTAD WLSIIVYLTS FVVPILLKAL YMLTTRGRQT TKDNKGTRIR F KDDSSFED ...String:
GMATMEELQR EINAHEGQLV IARQKVRDAE KQYEKDPDEL NKRTLTDREG VAVSIQAKID ELKRQLADRI ATGKNLGKEQ DPTGVEPGD HLKERSMLSY GNVLDLNHLD IDEPTGQTAD WLSIIVYLTS FVVPILLKAL YMLTTRGRQT TKDNKGTRIR F KDDSSFED VNGIRKPKHL YVSLPNAQSS MKAEEITPGR YRTAVCGLYP AQIKARQMIS PVMSVIGFLA LAKDWSDRIE QW LIEPCKL LPDTAAVSLL GGPATNRDYL RQRQVALGNM ETKESKAIRQ HAEAAGCSMI EDIESPSSIW VFAGAPDRCP PTC LFIAGI AELGAFFSIL QDMRNTIMAS KTVGTSEEKL RKKSSFYQSY LRRTQSMGIQ LGQRIIVLFM VAWGKEAVDN FHLG DDMDP ELRTLAQSLI DVKVKEISNQ EPLKL

UniProtKB: Nucleoprotein

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration0.6 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris-HCl
300.0 mMSodium chlorideNaCl
10.0 mMMagnesium chlorideMgCl2
2.0 mMBeta-mercapto-ethanol
20.0 mMImidazole
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Details: 30 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV
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

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3840 pixel / Digitization - Dimensions - Height: 3712 pixel / Digitization - Frames/image: 3-18 / Number grids imaged: 1 / Number real images: 4328 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.5 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 46860 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 18.87 Å
Applied symmetry - Helical parameters - Δ&Phi: -99.95 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 105665
Segment selectionNumber selected: 168709 / Software - Name: RELION (ver. 2.1) / Software - details: manual picking
Details: Straight HTNV-NC were manually picked and computationally cut with an inter-box distance of 38 A along the helical axis into overlapping boxes of 400*400 pixels, resulting in 168,709 ...Details: Straight HTNV-NC were manually picked and computationally cut with an inter-box distance of 38 A along the helical axis into overlapping boxes of 400*400 pixels, resulting in 168,709 extracted segments. 2D classification was used to eliminate bad quality filaments.
Startup modelType of model: OTHER
Details: 130 A diameter featureless cylinder to which helical symmetry was applied.
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.1)
Details: 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 1

Initial modelPDB ID:

5fsg


Chain - Residue range: 113-429 / Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsFiber model was iteratively rebuilt and all-atom refined using stereochemical and NCS restraints
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 103
Output model

PDB-6i2n:
Helical RNA-bound Hantaan virus nucleocapsid

+
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