[English] 日本語
Yorodumi
- EMDB-39616: Semliki Forest virus virion -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-39616
TitleSemliki Forest virus virion
Map data
Sample
  • Organelle or cellular component: Semliki Forest virus viron
    • Protein or peptide: Spike glycoprotein E1
    • Protein or peptide: Spike glycoprotein E2
    • Protein or peptide: Spike glycoprotein E3
    • Protein or peptide: capsid protein
KeywordsSemliki Forest virus virion / VLDLR / VIRAL PROTEIN
Function / homology:
Function and homology information
Biological speciesSemliki Forest virus 4
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsZheng T / Wang J / Yang D
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Semliki Forest virus viron
Authors: Zheng T
History
DepositionMar 29, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_39616.png

Downloads & links

-
Map

FileDownload / File: emd_39616.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.8532582 - 1.2640104
Average (Standard dev.)0.0034815024 (±0.048515532)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_39616_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_39616_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Semliki Forest virus viron

EntireName: Semliki Forest virus viron
Components
  • Organelle or cellular component: Semliki Forest virus viron
    • Protein or peptide: Spike glycoprotein E1
    • Protein or peptide: Spike glycoprotein E2
    • Protein or peptide: Spike glycoprotein E3
    • Protein or peptide: capsid protein

-
Supramolecule #1: Semliki Forest virus viron

SupramoleculeName: Semliki Forest virus viron / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Semliki Forest virus 4

-
Macromolecule #1: Spike glycoprotein E1

MacromoleculeName: Spike glycoprotein E1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Semliki Forest virus 4
Molecular weightTheoretical: 47.489766 KDa
SequenceString: YEHSTVMPNV VGFPYKAHIE RPGYSPLTLQ MQVVETSLEP TLNLEYITCE YKTVVPSPYV KCCGASECST KEKPDYQCKV YTGVYPFMW GGAYCFCDSE NTQLSEAYVD RSDVCRHDHA SAYKAHTASL KAKVRVMYGN VNQTVDVYVN GDHAVTIGGT Q FIFGPLSS ...String:
YEHSTVMPNV VGFPYKAHIE RPGYSPLTLQ MQVVETSLEP TLNLEYITCE YKTVVPSPYV KCCGASECST KEKPDYQCKV YTGVYPFMW GGAYCFCDSE NTQLSEAYVD RSDVCRHDHA SAYKAHTASL KAKVRVMYGN VNQTVDVYVN GDHAVTIGGT Q FIFGPLSS AWTPFDNKIV VYKDEVFNQD FPPYGSGQPG RFGDIQSRTV ESNDLYANTA LKLARPSPGM VHVPYTQTPS GF KYWLKEK GTALNTKAPF GCQIKTNPVR AMNCAVGNIP VSMNLPDSAF TRIVEAPTII DLTCTVATCT HSSDFGGVLT LTY KTDKNG DCSVHSHSNV ATLQEATAKV KTAGKVTLHF STASASPSFV VSLCSARATC SASCEPPKDH IVPYAASHSN VVFP DMSGT ALSWVQKISG GLGAFAIGAI LVLVVVTCIG LRR

UniProtKB: UNIPROTKB: A0A0E3T652

-
Macromolecule #2: Spike glycoprotein E2

MacromoleculeName: Spike glycoprotein E2 / type: protein_or_peptide / ID: 2
Details: Molecular name is based on https://www.ebi.ac.uk/interpro/protein/UniProt/A0A0E3T652/ as Uniprot Reference A0A0E3T652 and author provided name are both Structural polyprotein.
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Semliki Forest virus 4
Molecular weightTheoretical: 46.468867 KDa
SequenceString: HFNVYKATRP YIAYCADCGA GHSCHSPVAI EAVRSEATDG MLKIQFSAQI GIDKSDNHDY TKIRYADGHA IENAVRSSLK VATSGDCFV HGTMGHFILA KCPPGEFLQV SIQDTRNAVR ACRIQYHHDP QPVGREKFTI RPHYGKEIPC TTYQQTTAKT V EEIDMHMP ...String:
HFNVYKATRP YIAYCADCGA GHSCHSPVAI EAVRSEATDG MLKIQFSAQI GIDKSDNHDY TKIRYADGHA IENAVRSSLK VATSGDCFV HGTMGHFILA KCPPGEFLQV SIQDTRNAVR ACRIQYHHDP QPVGREKFTI RPHYGKEIPC TTYQQTTAKT V EEIDMHMP PDTPDRTLLS QQSGNVKITV GGKKVKYNCT CGTGNVGTTN SDMTINTCLI EQCHVSVTDH KKWQFNSPFV PR ADEPARK GKVHIPFPLD NITCRVPMAR EPTVIHGKRE VTLHLHPDHP TLFSYRTLGE DPQYHEEWVT AAVERTIPVP VDG MEYHWG NNDPVRLWSQ LTTEGKPHGW PHQIVQYYYG LYPAATVSAV VGMSLLALIS IFASCYMLVA ARSKCLTPYA LTPG AAVPW TLGILCCAPR AHA

UniProtKB: UNIPROTKB: A0A0E3T652

-
Macromolecule #3: Spike glycoprotein E3

MacromoleculeName: Spike glycoprotein E3 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Semliki Forest virus 4
Molecular weightTheoretical: 5.848729 KDa
SequenceString:
MCVLANATFP CFQPPCVPCC YENNAEATLR MLEDNVDRPG YYDLLQAALT CR

UniProtKB: UNIPROTKB: A0A0E3T652

-
Macromolecule #4: capsid protein

MacromoleculeName: capsid protein / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Semliki Forest virus 4
Molecular weightTheoretical: 17.791299 KDa
SequenceString:
KRERMCMKIE NDCIFEVKHE GKVTGYACLV GDKVMKPAHV KGVIDNADLA KLAFKKSSKY DLECAQIPVH MRSDASKYTH EKPEGHYNW HHGAVQYSGG RFTIPTGAGK PGDSGRPIFD NKGRVVAIVL GGANEGSRTA LSVVTWNKDM VTRVTPEGSE E W

UniProtKB: UNIPROTKB: A0A0E3T652

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

-
Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15328
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8yvy:
Semliki Forest virus virion

+
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