[English] 日本語
Yorodumi
- EMDB-0141: Cryo-EM structure of in vitro assembled Measles virus N into nucl... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 0141
TitleCryo-EM structure of in vitro assembled Measles virus N into nucleocapsid-like particles (NCLPs) bound to polyA RNA hexamers.
Map dataCryo-EM map of in vitro assembled Measles virus N into nucleocapsid-like particles (NCLPs) bound to polyA RNA hexamers.
SampleMeasles virus Nucleoprotein assembled into nucleocapsid-like particles (NCLPs) bound to polyA RNA hexamers.:
Measles virus Nucleoprotein / polyA RNA / NucleocapsidCapsid / nucleic-acidNucleic acid
Function / homologyParamyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein / helical viral capsid / viral nucleocapsid / host cell cytoplasm / structural molecule activity / RNA binding / Nucleocapsid
Function and homology information
SourceMeasles virus / synthetic construct (others) / Measles morbillivirus
Methodhelical reconstruction / cryo EM / 3.3 Å resolution
AuthorsDesfosses A / Milles S / Ringkjobing Jensen M / Guseva S / Colletier J / Maurin D / Schoehn G / Gutsche I / Ruigrok R / Blackledge M
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Assembly and cryo-EM structures of RNA-specific measles virus nucleocapsids provide mechanistic insight into paramyxoviral replication.
Authors: Ambroise Desfosses / Sigrid Milles / Malene Ringkjøbing Jensen / Serafima Guseva / Jacques-Philippe Colletier / Damien Maurin / Guy Schoehn / Irina Gutsche / Rob W H Ruigrok / Martin Blackledge
Validation ReportPDB-ID: 6h5q

SummaryFull reportAbout validation report
DateDeposition: Jul 25, 2018 / Header (metadata) release: Aug 8, 2018 / Map release: Mar 13, 2019 / Last update: Mar 13, 2019

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6h5q
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6h5q
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_0141.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
0.82 Å/pix.
= 261.12 Å
320 pix
0.82 Å/pix.
= 261.12 Å
320 pix
0.82 Å/pix.
= 261.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.816 Å
Density
Contour Level:0.02 (by author), 0.02 (movie #1):
Minimum - Maximum-0.0512 - 0.08295685
Average (Standard dev.)0.00043131955 (0.0054542553)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin-160.0-160.0-160.0
Limit159.0159.0159.0
Spacing320320320
CellA=B=C: 261.12 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8160.8160.816
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z261.120261.120261.120
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-0.0510.0830.000

-
Supplemental data

-
Sample components

+
Entire Measles virus Nucleoprotein assembled into nucleocapsid-like part...

EntireName: Measles virus Nucleoprotein assembled into nucleocapsid-like particles (NCLPs) bound to polyA RNA hexamers.
Number of components: 5

+
Component #1: protein, Measles virus Nucleoprotein assembled into nucleocapsid-...

ProteinName: Measles virus Nucleoprotein assembled into nucleocapsid-like particles (NCLPs) bound to polyA RNA hexamers.
Recombinant expression: No

+
Component #2: protein, Measles virus Nucleoprotein

ProteinName: Measles virus Nucleoprotein / Recombinant expression: No
SourceSpecies: Measles virus
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

+
Component #3: protein, polyA RNA

ProteinName: polyA RNA / Recombinant expression: No
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: synthetic construct (others)

+
Component #4: protein, Nucleocapsid

ProteinName: NucleocapsidCapsid / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.425863 kDa
SourceSpecies: Measles morbillivirus
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

+
Component #5: nucleic-acid, RNA (5'-R(*AP*AP*AP*AP*AP*A)-3')

Nucleic-acidName: RNA (5'-R(*AP*AP*AP*AP*AP*A)-3') / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAAAAA
MassTheoretical: 1.930277 kDa
SourceSpecies: synthetic construct (others)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 3.920265781 Å / Delta phi: -29.17105583 deg.
Sample solutionSpecimen conc.: 1 mg/ml
Buffer solution: 50 mM Na-phosphate pH 6, 150 mM NaCl, 2 mM DTT
pH: 6
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 293.15 K / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 3 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 23000.0 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 0.8 - 3.0 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 186 / Sampling size: 5 microns

-
Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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 PDBe / 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

-
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.

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