[English] 日本語
Yorodumi
- EMDB-33027: SFTSV 3 fold hexmer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-33027
TitleSFTSV 3 fold hexmer
Map dataSFTSV 3 fold hexamer
Sample
  • Virus: severe fever with thrombocytopenia syndrome virus
    • Protein or peptide: Envelopment polyprotein
    • Protein or peptide: Envelopment polyprotein
KeywordsVirus / Glycoproteins / prefusion / heterodimer / VIRAL PROTEIN
Function / homology
Function and homology information


host cell Golgi membrane / host cell endoplasmic reticulum membrane / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G2, fusion domain / Phlebovirus glycoprotein G2, C-terminal domain / Phlebovirus glycoprotein G2 fusion domain / Phlebovirus glycoprotein G2 C-terminal domain
Similarity search - Domain/homology
Envelopment polyprotein / Envelopment polyprotein
Similarity search - Component
Biological speciesSevere fever with thrombocytopenia syndrome virus / severe fever with thrombocytopenia syndrome virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsSun Z / Lou Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U20A20135 China
CitationJournal: Protein Cell / Year: 2023
Title: Architecture of severe fever with thrombocytopenia syndrome virus.
Authors: Zixian Sun / Jing Cheng / Yuan Bai / Lin Cao / Daoxin Xie / Fei Deng / Xinzheng Zhang / Zihe Rao / Zhiyong Lou /
History
DepositionMar 8, 2022-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_33027.png

Downloads & links

-
Map

FileDownload / File: emd_33027.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSFTSV 3 fold hexamer
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.030617097 - 0.047257878
Average (Standard dev.)0.0007220792 (±0.004166354)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 414.72003 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half1 map

Fileemd_33027_half_map_1.map
Annotationhalf1_map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half2 map

Fileemd_33027_half_map_2.map
Annotationhalf2_map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : severe fever with thrombocytopenia syndrome virus

EntireName: severe fever with thrombocytopenia syndrome virus
Components
  • Virus: severe fever with thrombocytopenia syndrome virus
    • Protein or peptide: Envelopment polyprotein
    • Protein or peptide: Envelopment polyprotein

-
Supramolecule #1: severe fever with thrombocytopenia syndrome virus

SupramoleculeName: severe fever with thrombocytopenia syndrome virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1003835
Sci species name: severe fever with thrombocytopenia syndrome virus
Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

-
Macromolecule #1: Envelopment polyprotein

MacromoleculeName: Envelopment polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe fever with thrombocytopenia syndrome virus
Molecular weightTheoretical: 61.745293 KDa
SequenceString: MMKVIWFSSL VCLVIQCSGD SGPIICAGPI HSNKSAGIPH LLGYSEKICQ IDRLIHVSSW LRNHSQFQGY VGQRGGRSQV SYYPAENSY SRWSGLLSPC DADWLGMLVV KKAKGSDMIV PGPSYKGKVL FERPTFDGYV GWGCGSGKSR TESGELCSSD S GTSSGLLP ...String:
MMKVIWFSSL VCLVIQCSGD SGPIICAGPI HSNKSAGIPH LLGYSEKICQ IDRLIHVSSW LRNHSQFQGY VGQRGGRSQV SYYPAENSY SRWSGLLSPC DADWLGMLVV KKAKGSDMIV PGPSYKGKVL FERPTFDGYV GWGCGSGKSR TESGELCSSD S GTSSGLLP SDRVLWIGDV ACQPMTPIPE ETFLELKSFS QSEFPDICKI DGIVFNQCEG ESLPQPFDVA WMDVGHSHKI IM REHKTKW VQESSSKDFV CYKEGTGPCS ESEEKACKTS GSCRGDMQFC KVAGCEHGEE ASEAKCRCSL VHKPGEVVVS YGG MRVRPK CYGFSRMMAT MEVNPPEQRI GQCTGCHLEC INGGVRLITL TSELKSATVC ASHFCSSATS GKKSTEIHFH SGSL VGKAA IHVKGALVDG TEFTFEGSCM FPDGCNAVDC TFCREFLKNP QCYPAKKWLF IIIVILLGYA GLMLLTNVLK AIGVW GSWV IAPVKLMFAI MKKLMRTVSC LVGKLMDRGR QVIHEEIGEN GEGNQDDVRI EMARPRRVRH WMYSPVILTI LAIGLA EG

UniProtKB: Envelopment polyprotein

-
Macromolecule #2: Envelopment polyprotein

MacromoleculeName: Envelopment polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe fever with thrombocytopenia syndrome virus
Molecular weightTheoretical: 54.927797 KDa
SequenceString: CDEMVHADSK LVSCRQGSGN MKECVTTGRA LLPAVNPGQE ACLHFTAPGS PDSKCLKIKV KRINLKCKKS SSYFVPDARS RCTSVRRCR WAGDCQSGCP PHFTSNSFSD DWAGKMDRAG LGFSGCSDGC GGAACGCFNA APSCIFWRKW VENPHGIIWK V SPCAAWVP ...String:
CDEMVHADSK LVSCRQGSGN MKECVTTGRA LLPAVNPGQE ACLHFTAPGS PDSKCLKIKV KRINLKCKKS SSYFVPDARS RCTSVRRCR WAGDCQSGCP PHFTSNSFSD DWAGKMDRAG LGFSGCSDGC GGAACGCFNA APSCIFWRKW VENPHGIIWK V SPCAAWVP SAVIELTMPS GEVRTFHPMS GIPTQVFKGV SVTYLGSDME VSGLTDLCEI EELKSKKLAL APCNQAGMGV VG KVGEIQC SSEESARTIK KDGCIWNADL VGIELRVDDA VCYSKITSVE AVANYSAIPT TIGGLRFERS HDSQGKISGS PLD ITAIRG SFSVNYRGLR LSLSEITATC TGEVTNVSGC YSCMTGAKVS IKLHSSKNST AHVRCKGDET AFSVLEGVHS YTVS LSFDH AVVDEQCQLN CGGHESQVTL KGNLIFLDVP KFVDGSYMQT YHSTVPTGAN IPSPTDWLNA LFGNGLSRWI LGVIG VLLG GLALFFLIMF LFKLGTKQVF RSRTKLA

UniProtKB: Envelopment polyprotein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridMaterial: GOLD
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 2.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.38 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5y10


Details: 5y10, 5g47, 4hjc, 3n43
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45407

+
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