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- EMDB-49228: H-1 Parvovirus VLP - Glycan [s(Lex)2] -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-49228
TitleH-1 Parvovirus VLP - Glycan [s(Lex)2]
Map data
Sample
  • Virus: H-1 parvovirus
    • Protein or peptide: Major capsid protein
KeywordsIcosahedron / Virus / Glycan / Complex / Receptor / 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 VP1/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: 2.57 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) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49228.png

Downloads & links

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Map

FileDownload / File: emd_49228.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-7.772027 - 14.113636
Average (Standard dev.)0.000000001173426 (±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 °

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Supplemental data

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Half map: #2

Fileemd_49228_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49228_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : H-1 parvovirus

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

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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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: 2.2 µm / Nominal defocus min: 1.12 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cisTEM / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4g0r

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 30120
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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