3D Electron Microscopy (3D-EM) Data Navigator [English / [日本語]]
Top Gallery List Statistics Shape search Viewer
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - EMDB-2333

This page is a legacy version and will be discarded in future. The new page is here.

Structural insights into the chaperone activity of Hsp40: DnaJ binds and remodels RepE

by single particle reconstruction, at 20 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 2.7, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 2.7, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 2333
TitleStructural insights into the chaperone activity of Hsp40: DnaJ binds and remodels RepE
Map3D Resonstruction of DnaJ:RepE(1-144) complex
SampleDnaJ:RepE(1-144) complex
KeywordsHsp40, DnaJ, RepE, chaperones, protein folding, electron microscopy
AuthorsCuellar J, Perales-Calvo J, Muga A, Valpuesta JM, Moro F
DateDeposition: 2013-03-15, Header release: 2013-04-17, Map release: 2013-04-24, Last update: 2013-12-25
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 2.7, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 2.7, Imaged by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

Cite: data citing same article

Similar-shape strucutres
Search for similar-shape assemblies throgh:
EMDB + EM entries in PDB
all of EMDB & PDB (Omokage search)
Article
Citation - Primary
ArticleJ. Biol. Chem., Vol. 288, Issue 21, Page 15065-15074, Year 2013
TitleStructural insights into the chaperone activity of the 40-kDa heat shock protein DnaJ: binding and remodeling of a native substrate.
AuthorsJorge Cuéllar, Judit Perales-Calvo, Arturo Muga, José María Valpuesta, Fernando Moro
Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología, CNB-CSIC, Darwin 3, 28049 Madrid, Spain.
KeywordsDnaJ protein, E coli, Escherichia coli (genetics), Escherichia coli Proteins (genetics), F Factor (genetics), HSP40 Heat-Shock Proteins (genetics), HSP70 Heat-Shock Proteins (genetics), Multiprotein Complexes (genetics), RepE protein, E coli, Repressor Proteins (genetics), dnaK protein, E coli (3.6.1.-)
LinksPubMed: 23580641, DOI: 10.1074/jbc.M112.430595, PMC: PMC3663527
Map
Fileemd_2333.map.gz ( map file in CCP4 format, 2001 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
80 pix
2.33 A/pix
= 186.4 A
80 pix
2.33 A/pix
= 186.4 A
80 pix
2.33 A/pix
= 186.4 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:2.7 (by author), 2.7 (movie #1):
Minimum - Maximum: -3.54815888 - 10.21153259
Average (Standard dev.): 0E-8 (0.99999994)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions808080
Origin-40-40-40
Limit393939
Spacing808080
Unit CellA= B= C: 186.4 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.33 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-27-15-36
NX/NY/NZ553173
MAP C/R/S123
start NC/NR/NS-40-40-40
NC/NR/NS808080
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-3.54810.212-0.000
Annotation Details3D Resonstruction of DnaJ:RepE(1-144) complex
Supplement
Images
Images
Sample
NameDnaJ:RepE(1-144) complex
Number of Components2
Oligomeric StateOne dimer of DnaJ binds to one dimer of RepE
Theoretical Mass0.115MDa
Mass-estimation MethodAnalytical ultracentrifugation (AU)
Experimental Mass0.115MDa
Component #1: protein - DnaJ
Scientific nameHsp40
Common NameDnaJ
Theoretical Mass0.08 MDa
Experimental Mass0.08 MDa
Oligomeric Detailsdimer
Number of Copies2
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
Recombinant expressionYes
Natural SourceCell Location: cytoplasm
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
LinksUni Prot: P08622
Component #2: protein - RepE(1-154)
Scientific nameShorter version of RepE (RepE 1-144)
Common NameRepE(1-154)
Theoretical Mass0.032 MDa
Experimental Mass0.032 MDa
Oligomeric Detailsdimer
Number of Copies2
Scientific Name of SpeciesEscherichia coli
NCBI taxonomy562
Recombinant expressionYes
Natural SourceCell Location: cytoplasm
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Experiment
Sample Preparation
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.
Specimen Stateparticle
Specimen Conc0.4 mg/ml
Specimen Support Details300 mesh Cu/Rh grid with thin carbon support and glow discharged
BufferDetails: 20mM Hepes pH 7.4, 50mM KCl, 5mM DTT and 0.1mM EDTA
pH: 7.4
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeJEOL 1200EXII
Date08-JUN-2011
DetailsAdditional details about microscope model:JEOL 1200EXII
Electron Gun
Electron SourceTUNGSTEN HAIRPIN
Accelerating Voltage100 kV
Electron Dose10 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 60000
AstigmatismObjective lens astigmatism was corrected at 100,000 times magnification
Nominal Cs5.6 mm
Imaging ModeBRIGHT FIELD
Specimen Holder
HolderStandard Jeol 1200 holder
ModelJEOL
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
#1
ScannerZEISS SCAI
Number of Digital Images270
Sampling Size14
Quant Bit Number8
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmiterative reconstruction after multi reference alignment
SoftwareEMAN, XMIPP
CTF CorrectionCTFFIND
Resolution By Author20 A
Resolution MethodFSC 0.5
Single Particle
Number of Class Averages75
Applied SymmetryC1 (asymmetric)
Number of Projections9623
DetailsThe particles were selected by manual picking
Download
Data from EMDB
Header (meta data in XML format)emd-2333.xml (8.6 KB)
Map dataemd_2333.map.gz (728.6 KB)
Imagesemd2333.jpg (32.5 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-2333
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 27.2 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.6 MB
Session file for UCSF-Chimera, 27.3 KB