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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.
KeywordsSmall heat shock protein / HSP16.5
Samplewild type small heat shock protein (sHSP) HSP16.5 from Methanocaldococcus jannaschii (MjHSP16.5)
SourceMethanocaldococcus jannaschii / archaea / メタノカルドコッカス・ジャナスキイ
Map dataSecond model for reconstruction of wild type MjHSP16.5 at room temperature
Methodsingle particle reconstruction, at 12 Å resolution
AuthorsRoy A Q / Yan Z / Andrew L / Ian W / Ehmke P / Fei S
CitationPhilos. Trans. R. Soc. Lond., B, Biol. Sci., 2013, 368, 20120327-20120327

Philos. Trans. R. Soc. Lond., B, Biol. Sci., 2013, 368, 20120327-20120327 Yorodumi Papers
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.
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
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Supplemental images

Downloads & links

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Map

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

Image control

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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 package.

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 / メタノカルドコッカス・ジャナスキイ
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pET23b
Source (natural)Location in cell: cytoplasmic
External referencesInterPro: InterPro: 002068, InterPro: 008978 / UniProt: UniProt: Q57733 / Gene Ontology: GO: 0005737, GO: 0006950

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Experimental details

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Sample preparation

Specimen stateparticle
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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