[English] 日本語
Yorodumi
- EMDB-37443: NSs filament formation determines RVFV pathogenesis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-37443
TitleNSs filament formation determines RVFV pathogenesis
Map dataEM map
Sample
  • Complex: The self-assembly of RVFV NSs protein
    • Protein or peptide: Non-structural protein NS-S
KeywordsSelf-assembly / helical structure / VIRAL PROTEIN
Function / homologyPhlebovirus, non structural protein / Rift valley fever virus non structural protein-like / Rift valley fever virus non structural protein (NSs) like / Non-structural protein NS-S
Function and homology information
Biological speciesRift Valley fever virus
Methodhelical reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsLi H / Rao G / Cao S / Peng K
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303300 China
CitationJournal: Cell(Cambridge,Mass.) / Year: 2024
Title: Rift Valley fever virus coordinates the assembly of a programmable E3 ligase to promote viral replication
Authors: Li H / Zhang Y / Rao G / Zhang C / Guan Z / Huang Z / Li S / Lozach PY / Cao S / Peng K
History
DepositionSep 13, 2023-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_37443.png

Downloads & links

-
Map

FileDownload / File: emd_37443.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 256 pix.
= 243.2 Å		0.95 Å/pix.
x 256 pix.
= 243.2 Å		0.95 Å/pix.
x 256 pix.
= 243.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.81646717 - 1.4058331
Average (Standard dev.)0.005984196 (±0.0687474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 243.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: EM half map

Fileemd_37443_half_map_1.map
AnnotationEM half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: EM half map

Fileemd_37443_half_map_2.map
AnnotationEM half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : The self-assembly of RVFV NSs protein

EntireName: The self-assembly of RVFV NSs protein
Components
  • Complex: The self-assembly of RVFV NSs protein
    • Protein or peptide: Non-structural protein NS-S

-
Supramolecule #1: The self-assembly of RVFV NSs protein

SupramoleculeName: The self-assembly of RVFV NSs protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rift Valley fever virus

-
Macromolecule #1: Non-structural protein NS-S

MacromoleculeName: Non-structural protein NS-S / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rift Valley fever virus
Molecular weightTheoretical: 30.870221 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: HHHHHHGSGG DYFPVISVDL QSGRRVVSVE YIRGDGPPRI PYSMVGPCCV FLMHHRPSHE VRLRFSDFYN VGEFPYRVGL GDFASNVAP PPAKPFQRLI DLIGHMTLSD FTRFPNLKEA ISWPLGEPSL AFFDLSSTRV HRNDDIRRDQ IATLAMRSCK I TNDLEDSF ...String:
HHHHHHGSGG DYFPVISVDL QSGRRVVSVE YIRGDGPPRI PYSMVGPCCV FLMHHRPSHE VRLRFSDFYN VGEFPYRVGL GDFASNVAP PPAKPFQRLI DLIGHMTLSD FTRFPNLKEA ISWPLGEPSL AFFDLSSTRV HRNDDIRRDQ IATLAMRSCK I TNDLEDSF VGLHRMIVTE AILRGIDLCL LPGFDLMYEV AHVQCVRLLQ AAKEDISNAV VPNSALIALM EESLMLRSSL PS MMGRNNW IPVVPPIPDV EMESEEESDD DGFVEVD

UniProtKB: Non-structural protein NS-S

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 14.584 Å
Applied symmetry - Helical parameters - Δ&Phi: 83.437 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 617585
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
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