[English] 日本語
Yorodumi
- EMDB-49205: H-1 Parvovirus VLP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49205
TitleH-1 Parvovirus VLP
Map data
Sample
  • Virus: H-1 parvovirus
    • Protein or peptide: Major capsid protein
KeywordsIcosahedron / Virus / Capsid / Cryo-EM / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


symbiont entry into host cell via permeabilization of host membrane / T=1 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / structural molecule activity
Similarity search - Function
Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Major capsid protein
Similarity search - Component
Biological speciesH-1 parvovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsBusuttil KB / Bennett AB / McKenna R
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 13, 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_49205.png

Downloads & links

-
Map

FileDownload / File: emd_49205.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. Å		1.05 Å/pix.
x 420 pix.
= 441. Å		1.05 Å/pix.
x 420 pix.
= 441. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-8.865178999999999 - 16.720006999999999
Average (Standard dev.)0.000000001813024 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-210-210-210
Dimensions420420420
Spacing420420420
CellA=B=C: 440.99997 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_49205_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_49205_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : H-1 parvovirus

EntireName: H-1 parvovirus
Components
  • Virus: H-1 parvovirus
    • Protein or peptide: Major capsid protein

-
Supramolecule #1: H-1 parvovirus

SupramoleculeName: H-1 parvovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10799 / Sci species name: H-1 parvovirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes

-
Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: H-1 parvovirus
Molecular weightTheoretical: 62.413285 KDa
Recombinant expressionOrganism: Baculoviridae sp. (virus)
SequenceString: GGGGIGVSTG TYDNQTTYKF LGDGWVEITA HASRLLHLGM PPSENYCRVT VHNNQTTGHG TKVKGNMAYD DTHQQIWTPW SLVDANAWG VWFQPSDWQF IQNSMESLNL DSLSQELFNV VVKTVTEQQG AGQDAIKVYN NDLTACMMVA LDSNNILPYT P AAQTSETL ...String:
GGGGIGVSTG TYDNQTTYKF LGDGWVEITA HASRLLHLGM PPSENYCRVT VHNNQTTGHG TKVKGNMAYD DTHQQIWTPW SLVDANAWG VWFQPSDWQF IQNSMESLNL DSLSQELFNV VVKTVTEQQG AGQDAIKVYN NDLTACMMVA LDSNNILPYT P AAQTSETL GFYPWKPTAP APYRYYFFMP RQLSVTSSNS AEGTQITDTI GEPQALNSQF FTIENTLPIT LLRTGDEFTT GT YIFNTDP LKLTHTWQTN RHLGMPPRIT DLPTSDTATA SLTANGDRFG STQTQNVNYV TEALRTRPAQ IGFMQPHDNF EAN RGGPFK VPVVPLDITA GEDHDANGAI RFNYGKQHGE DWAKQGAAPE RYTWDAIDSA AGRDTARCFV QSAPISIPPN QNQI LQRED AIAGRTNMHY TNVFNSYGPL SAFPHPDPIY PNGQIWDKEL DLEHKPRLHV TAPFVCKNNP PGQLFVRLGP NLTDQ FDPN STTVSRIVTY STFYWKGILK FKAKLRPNLT WNPVYQATTD SVANSYMNVK KWLPSATGNM HSDPLICRPV PHMTY

UniProtKB: Major capsid protein

-
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: 2.89 µm / Nominal defocus min: 0.81 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

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

4g0r

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32893
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