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- EMDB-7302: Atomic resolution structure of human bufavirus 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-7302
TitleAtomic resolution structure of human bufavirus 3
Map dataAtomic resolution structure of human bufavirus 3
Sample
  • Virus: Bufavirus-3
    • Protein or peptide: VP2
Keywordsparvovirus / protoparvovirus / Bufavirus / VIRUS LIKE PARTICLE
Function / homologyParvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / T=1 icosahedral viral capsid / structural molecule activity / VP2
Function and homology information
Biological speciesBufavirus-3
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsMietzsch M / Agbandje-McKenna M
CitationJournal: Viruses / Year: 2018
Title: Atomic Resolution Structures of Human Bufaviruses Determined by Cryo-Electron Microscopy.
Authors: Maria Ilyas / Mario Mietzsch / Shweta Kailasan / Elina Väisänen / Mengxiao Luo / Paul Chipman / J Kennon Smith / Justin Kurian / Duncan Sousa / Robert McKenna / Maria Söderlund-Venermo / ...Authors: Maria Ilyas / Mario Mietzsch / Shweta Kailasan / Elina Väisänen / Mengxiao Luo / Paul Chipman / J Kennon Smith / Justin Kurian / Duncan Sousa / Robert McKenna / Maria Söderlund-Venermo / Mavis Agbandje-McKenna /
Abstract: Bufavirus strain 1 (BuV1), a member of the genus of the , was first isolated from fecal samples of children with acute diarrhea in Burkina Faso. Since this initial discovery, BuVs have been isolated ...Bufavirus strain 1 (BuV1), a member of the genus of the , was first isolated from fecal samples of children with acute diarrhea in Burkina Faso. Since this initial discovery, BuVs have been isolated in several countries, including Finland, the Netherlands, and Bhutan, in pediatric patients exhibiting similar symptoms. Towards their characterization, the structures of virus-like particles of BuV1, BuV2, and BuV3, the current known genotypes, have been determined by cryo-electron microscopy and image reconstruction to 2.84, 3.79, and 3.25 Å, respectively. The BuVs, 65-73% identical in amino acid sequence, conserve the major viral protein, VP2, structure and general capsid surface features of parvoviruses. These include a core β-barrel (βB-βI), α-helix A, and large surface loops inserted between these elements in VP2. The capsid contains depressions at the icosahedral 2-fold and around the 5-fold axes, and has three separated protrusions surrounding the 3-fold axes. Structure comparison among the BuVs and to available parvovirus structures revealed capsid surface variations and capsid 3-fold protrusions that depart from the single pinwheel arrangement of the animal protoparvoviruses. These structures provide a platform to begin the molecular characterization of these potentially pathogenic viruses.
History
DepositionDec 15, 2017-
Header (metadata) releaseJan 24, 2018-
Map releaseJan 24, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6bx1
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6bx1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7302.png

Downloads & links

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Map

FileDownload / File: emd_7302.map.gz / Format: CCP4 / Size: 176.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAtomic resolution structure of human bufavirus 3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.06 Å/pix.
x 359 pix.
= 380.54 Å		1.06 Å/pix.
x 359 pix.
= 380.54 Å		1.06 Å/pix.
x 359 pix.
= 380.54 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-8.38461 - 15.309699999999999
Average (Standard dev.)0.00000000110841 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-179-179-179
Dimensions359359359
Spacing359359359
CellA=B=C: 380.53998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z359359359
origin x/y/z0.0000.0000.000
length x/y/z380.540380.540380.540
α/β/γ90.00090.00090.000
start NX/NY/NZ-179-179-179
NX/NY/NZ359359359
MAP C/R/S213
start NC/NR/NS-179-179-179
NC/NR/NS359359359
D min/max/mean-8.38515.3100.000

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Supplemental data

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Sample components

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Entire : Bufavirus-3

EntireName: Bufavirus-3
Components
  • Virus: Bufavirus-3
    • Protein or peptide: VP2

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Supramolecule #1: Bufavirus-3

SupramoleculeName: Bufavirus-3 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1391667 / Sci species name: Bufavirus-3 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4 MDa
Virus shellShell ID: 1 / Name: BuV3 capsid

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Macromolecule #1: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Bufavirus-3
Molecular weightTheoretical: 61.565652 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SGVGHSTGNY NNRTIFHYHG DEVTIICHAT RHIHLNMSPT EEYKIYDTNH GPEFPNTGDQ TQQGRNTVND SYHAKVETPW YLINPNSWG IWFNPADFQQ LITTCTHVTI ETLTQEIDNI VIKTVSKQGS GAEETTQYNN DLTALLEVAL DKSNMLPWVA D NMYLNSLG ...String:
SGVGHSTGNY NNRTIFHYHG DEVTIICHAT RHIHLNMSPT EEYKIYDTNH GPEFPNTGDQ TQQGRNTVND SYHAKVETPW YLINPNSWG IWFNPADFQQ LITTCTHVTI ETLTQEIDNI VIKTVSKQGS GAEETTQYNN DLTALLEVAL DKSNMLPWVA D NMYLNSLG YIPWRPCKLT QFCYHTNFYN TINLLEGTQQ NQWSQIKEGI QYDNLQFTPI ETSAEIDLLR TGDSWTSGTY HF KCKPTQL FYHWQSTRHI GAPHPTTSPE QEGQKGQIIQ DTNGWQWGDR DNPISASTTV KDFHIGYSWP EWRWHYSTGG PSI NPGSAF SQTPWGSEVG GTRLTQGASE KAIFDYNHGE AEPGHRDQWW QNNAQQTGQT NWAIKNAHQS ELRNATASRE TFWT QDYHN TFGPYTAVDD VGIQYPWGAM WGKQPDTTHK PMMSAHAPFT CQNGPPGQLL VKLAPNYTDS LNNEGLQTNR IVTFA TFWW TGRCTFKAKL RTPRQFNAYQ LPGIPSGTNP KKFVPDAIGR FELPFMPGRA MPNYTY

UniProtKB: VP2

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Frames/image: 2-20 / Number real images: 689 / 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 / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6543
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Auto3DEM (ver. 4.05.2) / Number images used: 5234
Initial angle assignmentType: COMMON LINE / Software - Name: Auto3DEM (ver. 4.05.2)
Final angle assignmentType: NOT APPLICABLE / Software - Name: Auto3DEM (ver. 4.05.2)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT / Target criteria: Correlation coefficient
Output model

PDB-6bx1:
Atomic resolution structure of human bufavirus 3

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