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- EMDB-2289: Second 3D model of wild type MjHSP16.5 at room temperature by CryoEM. -

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Basic information

Entry
Database: EMDB / ID: 2289
TitleSecond 3D model of wild type MjHSP16.5 at room temperature by CryoEM.
Map dataSecond model for reconstruction of wild type MjHSP16.5 at room temperature
Samplewild type small heat shock protein (sHSP) HSP16.5 from Methanocaldococcus jannaschii (MjHSP16.5):
MjHSP16.5
KeywordsSmall heat shock protein / HSP16.5
Function / homologyAlpha crystallin/Hsp20 domain / HSP20-like chaperone / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / response to stress / protein stabilization / protein homooligomerization / protein-containing complex ...Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / response to stress / protein stabilization / protein homooligomerization / protein-containing complex / identical protein binding / cytoplasm / Small heat shock protein HSP16.5
Function and homology information
SourceMethanocaldococcus jannaschii (archaea)
Methodsingle particle reconstruction / cryo EM / 12 Å resolution
AuthorsRoy A Q / Yan Z / Andrew L / Ian W / Ehmke P / Fei S
CitationJournal: Philos. Trans. R. Soc. Lond., B, Biol. Sci. / Year: 2013
Title: Changes in the quaternary structure and function of MjHSP16.5 attributable to deletion of the IXI motif and introduction of the substitution, R107G, in the α-crystallin domain.
Authors: Roy A Quinlan / Yan Zhang / Andrew Lansbury / Ian Williamson / Ehmke Pohl / Fei Sun
DateDeposition: Jan 21, 2013 / Header (metadata) release: Feb 27, 2013 / Map release: Mar 13, 2013 / Last update: Jul 31, 2013

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.77
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.77
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_2289.map.gz (map file in CCP4 format, 65537 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
0.93 Å/pix.
= 238.848 Å
256 pix
0.93 Å/pix.
= 238.848 Å
256 pix
0.93 Å/pix.
= 238.848 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.933 Å
Density
Contour Level:1.77 (by author), 1.77 (movie #1):
Minimum - Maximum-5.24586439 - 7.56885481
Average (Standard dev.)0E-8 (0.97619569)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin-128-128-128
Limit127127127
Spacing256256256
CellA=B=C: 238.848 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9330.9330.933
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z238.848238.848238.848
α/β/γ90.00090.00090.000
start NX/NY/NZ-36-30-80
NX/NY/NZ7361161
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-5.2467.569-0.000

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Supplemental data

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Sample components

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Entire wild type small heat shock protein (sHSP) HSP16.5 from Methanocal...

EntireName: wild type small heat shock protein (sHSP) HSP16.5 from Methanocaldococcus jannaschii (MjHSP16.5)
Number of components: 1 / Oligomeric State: 24mer
MassTheoretical: 396 kDa / Experimental: 396 kDa

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Component #1: protein, MjHSP16.5

ProteinName: MjHSP16.5 / a.k.a: small heat shock protein (sHSP) from HSP16.5 / Oligomeric Details: 24mer / Recombinant expression: Yes / Number of Copies: 24
MassTheoretical: 16.5 kDa / Experimental: 16.5 kDa
SourceSpecies: Methanocaldococcus jannaschii (archaea)
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pET23b
Source (natural)Location in cell: cytoplasmic
External referencesInterPro: Alpha crystallin/Hsp20 domain, HSP20-like chaperone
UniProt: Small heat shock protein HSP16.5 / Gene Ontology: cytoplasm, response to stress

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.8 mg/ml / Buffer solution: 10mM HEPES, 100mM NaCl. / pH: 7.4
Support filmGIG holey grids (LifeTrust, China) were treated with a glow discharge machine (Master Plasmer)
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 93 K
Method: The samples were blotted for 2 s with blot force 2 at 100% humidity.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Sep 28, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 96000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 3000 nm
Specimen HolderHolder: liquid nitrogen cooled / Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 85 K
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1160 / Bit depth: 32
Details: Electron micrograph exposures were made with the automatic collection package Leginon.

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Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 193 / Applied symmetry: O (octahedral) / Number of projections: 4356
Details: The particles were selected using an automatic selection program Gautomatch developed in Fei Sun lab (to be published). Octahedron symmetry were imposed during 3D reconstructing.
3D reconstructionAlgorithm: projection matching / Software: EMAN1 / CTF correction: Each image
Details: The final reconstructed density map was further sharpened by application of an amplitude correction algorithm in the program BFACTOR.
Resolution: 12 Å / Resolution method: FSC 0.5

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