[English] 日本語
Yorodumi
- EMDB-49196: LuIII VLP - Glycan [3's(LN)3] -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49196
TitleLuIII VLP - Glycan [3's(LN)3]
Map data
Sample
  • Virus: LuIII virus
    • Protein or peptide: Capsid protein VP1
KeywordsIcosahedron / Glycan / Receptor / Complex / VIRUS LIKE PARTICLE / VIRUS
Function / homology
Function and homology information


symbiont entry into host cell via permeabilization of host membrane / microtubule-dependent intracellular transport of viral material towards nucleus / T=1 icosahedral viral capsid / viral penetration into host nucleus / host cell / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / metal ion binding
Similarity search - Function
Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP1/VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Biological speciesLuIII virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsBusuttil KB / Bennett AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
CitationJournal: To Be Published
Title: Mapping the Sialic Acid Binding Sites of LuIII and H-1 Parvovirus
Authors: Busuttil KB / Bennett AB
History
DepositionFeb 12, 2025-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49196.png

Downloads & links

-
Map

FileDownload / File: emd_49196.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.05 Å/pix.
x 420 pix.
= 441.84 Å		1.05 Å/pix.
x 420 pix.
= 441.84 Å		1.05 Å/pix.
x 420 pix.
= 441.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.052 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-9.305889000000001 - 17.398050000000001
Average (Standard dev.)0.000000003458333 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-210-210-210
Dimensions420420420
Spacing420420420
CellA=B=C: 441.84003 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_49196_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_49196_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : LuIII virus

EntireName: LuIII virus
Components
  • Virus: LuIII virus
    • Protein or peptide: Capsid protein VP1

-
Supramolecule #1: LuIII virus

SupramoleculeName: LuIII virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 35339 / Sci species name: LuIII virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes

-
Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: LuIII virus
Molecular weightTheoretical: 62.239695 KDa
Recombinant expressionOrganism: Baculoviridae sp. (virus)
SequenceString: GGGVGVSTGS YDNQTHYKFL GDGWVEITAY STRMVHLNMP KSENYCRVRV HNTNDTGTAS HMAMDDAHEQ IWTPWSLVDA NAWGVWFQP SDWQYISNNM IHINLHSLDQ ELFNVVIKTV TEQNTGAEAI KVYNNDLTAA MMVALDSNNI LPYTPAIDNQ E TLGFYPWK ...String:
GGGVGVSTGS YDNQTHYKFL GDGWVEITAY STRMVHLNMP KSENYCRVRV HNTNDTGTAS HMAMDDAHEQ IWTPWSLVDA NAWGVWFQP SDWQYISNNM IHINLHSLDQ ELFNVVIKTV TEQNTGAEAI KVYNNDLTAA MMVALDSNNI LPYTPAIDNQ E TLGFYPWK PTIPSPYRYY FSCDRNLSVT YKDEAGTITD TMGLASGLNS QFFTIENTQR INLLRTGDEY ATGTYYFDTE PI RLTHTWQ TNRHLGQPPQ ITELPSSDTA NATLTARGYR SGLTQIQGRN DVTEATRVRP AQVGFCQPHD NFETSRAGPF KVP VVPADI TQGLDHDANG SLRYTYDKQH GQSWASQNNK DRYTWDAVNY DSGRWTNNCF IQSVPFTSEP NANQILTNRD NLAG KTDIH FTNAFNSYGP LTAFPHPAPI YPQGQIWDKE LDLEHKPRLH TQAPFVCKNN APGQLLVRLA PNLTDQYDPN SSNLS RIVT YGTFFWKGKL TLKAKMRPNA TWNPVFQISA TNQGTNDYMS IERWLPTATG NITNVPLLSR PVARNTY

UniProtKB: Capsid protein VP1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 75.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.11 µm / Nominal defocus min: 0.89 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

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

6b9q

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38079
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

+
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