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- EMDB-2333: Structural insights into the chaperone activity of Hsp40: DnaJ bi... -

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Basic information

Entry
Database: EMDB / ID: 2333
TitleStructural insights into the chaperone activity of Hsp40: DnaJ binds and remodels RepE
Map data3D Resonstruction of DnaJ:RepE(1-144) complex
SampleDnaJ:RepE(1-144) complex:
Hsp40Chaperone DnaJ / Shorter version of RepE (RepE 1-144)
KeywordsHsp40 / DnaJ / RepE / chaperones / protein folding / electron microscopy
Function / homologyChaperone DnaJ, C-terminal / DnaJ domain, conserved site / Zinc finger CR-type profile. / dnaJ domain profile. / Nt-dnaJ domain signature. / DnaJ domain / DnaJ C terminal domain / DnaJ central domain / Heat shock protein DnaJ, cysteine-rich domain / DnaJ domain ...Chaperone DnaJ, C-terminal / DnaJ domain, conserved site / Zinc finger CR-type profile. / dnaJ domain profile. / Nt-dnaJ domain signature. / DnaJ domain / DnaJ C terminal domain / DnaJ central domain / Heat shock protein DnaJ, cysteine-rich domain / DnaJ domain / Chaperone J-domain superfamily / HSP40/DnaJ peptide-binding / Chaperone DnaJ / Heat shock protein DnaJ, cysteine-rich domain superfamily / sigma factor antagonist activity / protein disulfide isomerase activity / chaperone cofactor-dependent protein refolding / heat shock protein binding / protein disulfide oxidoreductase activity / protein-containing complex assembly / protein folding / unfolded protein binding / chaperone binding / response to heat / protein refolding / DNA replication / viral process / protein-containing complex / zinc ion binding / membrane / ATP binding / cytosol / cytoplasm / Chaperone protein DnaJ
Function and homology information
SourceEscherichia coli (E. coli)
Methodsingle particle reconstruction / negative staining / 20 Å resolution
AuthorsCuellar J / Perales-Calvo J / Muga A / Valpuesta JM / Moro F
CitationJournal: J. Biol. Chem. / Year: 2013
Title: Structural insights into the chaperone activity of the 40-kDa heat shock protein DnaJ: binding and remodeling of a native substrate.
Authors: Jorge Cuéllar / Judit Perales-Calvo / Arturo Muga / José María Valpuesta / Fernando Moro
DateDeposition: Mar 15, 2013 / Header (metadata) release: Apr 17, 2013 / Map release: Apr 24, 2013 / Last update: Dec 25, 2013

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_2333.map.gz (map file in CCP4 format, 2001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
80 pix
2.33 Å/pix.
= 186.4 Å
80 pix
2.33 Å/pix.
= 186.4 Å
80 pix
2.33 Å/pix.
= 186.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.33 Å
Density
Contour Level:2.7 (by author), 2.7 (movie #1):
Minimum - Maximum-3.54815888 - 10.21153259
Average (Standard dev.)0E-8 (0.99999994)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions808080
Origin-40-40-40
Limit393939
Spacing808080
CellA=B=C: 186.4 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.332.332.33
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z186.400186.400186.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-27-15-36
NX/NY/NZ553173
MAP C/R/S123
start NC/NR/NS-40-40-40
NC/NR/NS808080
D min/max/mean-3.54810.212-0.000

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Supplemental data

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Sample components

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Entire DnaJ:RepE(1-144) complex

EntireName: DnaJ:RepE(1-144) complex / Number of components: 2
Oligomeric State: One dimer of DnaJ binds to one dimer of RepE
MassTheoretical: 115 kDa / Experimental: 115 kDa / Measured by: Analytical ultracentrifugation (AU)

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Component #1: protein, Hsp40

ProteinName: Hsp40Chaperone DnaJ / a.k.a: DnaJChaperone DnaJ / Oligomeric Details: dimer / Number of Copies: 2 / Recombinant expression: Yes
MassTheoretical: 80 kDa / Experimental: 80 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)
Source (natural)Location in cell: cytoplasm
External referencesUniProt: Chaperone protein DnaJ

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Component #2: protein, Shorter version of RepE (RepE 1-144)

ProteinName: Shorter version of RepE (RepE 1-144) / a.k.a: RepE(1-154) / Oligomeric Details: dimer / Recombinant expression: Yes / Number of Copies: 2
MassTheoretical: 32 kDa / Experimental: 32 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)
Source (natural)Location in cell: cytoplasm

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionSpecimen conc.: 0.4 mg/ml
Buffer solution: 20mM Hepes pH 7.4, 50mM KCl, 5mM DTT and 0.1mM EDTA
pH: 7.4
Support film300 mesh Cu/Rh grid with thin carbon support and glow discharged
StainingSamples (either DnaJ:RepE, DnaJ:RepE1-144 or DnaJ:RepE54 complexes) were diluted 1:100 in 20mM Hepes pH 7.4, 50mM KCl, 5mM DTT and 0.1mM EDTA buffer, applied onto carbon-coated copper grids and stained with 2% uranyl acetate.
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: JEOL 1200EXII / Date: Jun 8, 2011
Details: Additional details about microscope model:JEOL 1200EXII
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 100 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 60000 X (nominal)
Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Cs: 5.6 mm / Imaging mode: BRIGHT FIELD
Specimen HolderHolder: Standard Jeol 1200 holder / Model: JEOL
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 270 / Scanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 8

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Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 75 / Applied symmetry: C1 (asymmetric) / Number of projections: 9623 / Details: The particles were selected by manual picking
3D reconstructionAlgorithm: iterative reconstruction after multi reference alignment
Software: EMAN, XMIPP / CTF correction: CTFFIND / Resolution: 20 Å / Resolution method: FSC 0.5

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