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- EMDB-32017: Small heat shock protein (48-mer) from Synechococcus phage S-ShM2 -

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Basic information

Entry
Database: EMDB / ID: EMD-32017
TitleSmall heat shock protein (48-mer) from Synechococcus phage S-ShM2
Map dataSmall heat shock protein (48-mer) from Synechococcus phage S-ShM2
Sample
  • Complex: Small heat shock protein (48-mer) from Synechococcus phage S-ShM2
Function / homologyHsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Heat shock protein
Function and homology information
Biological speciesSynechococcus phage S-ShM2 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsBiswas S / Garg P / Dutta S / Suguna K
Funding support India, 4 items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)EMR/2016/005407 India
Department of Science & Technology (DST, India)BT/PR25580/BRB/10/1619/2017 India
Department of Biotechnology (DBT, India)BT/INF/22/SP22844/2017 India
Department of Science & Technology (DST, India)SR/FST/LSII-039/2015 India
CitationJournal: Sci Rep / Year: 2021
Title: Multiple nanocages of a cyanophage small heat shock protein with icosahedral and octahedral symmetries.
Authors: Sreeparna Biswas / Priyanka Garg / Somnath Dutta / Kaza Suguna /
Abstract: The structures of a cyanophage small heat shock protein (sHSP) were determined as octahedrons of 24-mers and 48-mers and as icosahedrons of 60-mers. An N-terminal deletion construct of an 18 kDa ...The structures of a cyanophage small heat shock protein (sHSP) were determined as octahedrons of 24-mers and 48-mers and as icosahedrons of 60-mers. An N-terminal deletion construct of an 18 kDa sHSP of Synechococcus sp. phage S-ShM2 crystallized as a 24-mer and its structure was determined at a resolution of 7 Å. The negative stain electron microscopy (EM) images showed that the full-length protein is a mixture of a major population of larger and a minor population of smaller cage-like particles. Their structures have been determined by electron cryomicroscopy 3D image reconstruction at a resolution of 8 Å. The larger particles are 60-mers with icosahedral symmetry and the smaller ones are 48-mers with octahedral symmetry. These structures are the first of the viral/phage origin and the 60-mer is the largest and the first icosahedral assembly to be reported for sHSPs.
History
DepositionSep 30, 2021-
Header (metadata) releaseNov 24, 2021-
Map releaseNov 24, 2021-
UpdateMar 2, 2022-
Current statusMar 2, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0092
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0092
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32017.png

Downloads & links

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Map

FileDownload / File: emd_32017.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSmall heat shock protein (48-mer) from Synechococcus phage S-ShM2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 264 pix.
= 316.8 Å		1.2 Å/pix.
x 264 pix.
= 316.8 Å		1.2 Å/pix.
x 264 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0092 / Movie #1: 0.0092
Minimum - Maximum-0.00823852 - 0.027148647
Average (Standard dev.)-0.000100544545 (±0.0025057776)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions264264264
Spacing264264264
CellA=B=C: 316.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21.21.2
M x/y/z264264264
origin x/y/z0.0000.0000.000
length x/y/z316.800316.800316.800
α/β/γ90.00090.00090.000
start NX/NY/NZ535455
NX/NY/NZ134138134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS264264264
D min/max/mean-0.0080.027-0.000

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Supplemental data

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Sample components

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Entire : Small heat shock protein (48-mer) from Synechococcus phage S-ShM2

EntireName: Small heat shock protein (48-mer) from Synechococcus phage S-ShM2
Components
  • Complex: Small heat shock protein (48-mer) from Synechococcus phage S-ShM2

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Supramolecule #1: Small heat shock protein (48-mer) from Synechococcus phage S-ShM2

SupramoleculeName: Small heat shock protein (48-mer) from Synechococcus phage S-ShM2
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Synechococcus phage S-ShM2 (virus)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15258
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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