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Visualizing the ATPase cycle in a protein disaggregating machine: structural basis for substrate binding by ClpB.

by single particle reconstruction, at 16.7 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.880175, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.880175, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1242
TitleVisualizing the ATPase cycle in a protein disaggregating machine: structural basis for substrate binding by ClpB.
Mapvolume file of TClpB ADP bound state
SampleClpB
AuthorsTsai F
DateDeposition: 2006-07-12, Header release: 2006-07-12, Map release: 2007-03-27, Last update: 2011-05-26
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.880175, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.880175, Made by UCSF CHIMERA

Supplemental images

1242.gif
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

EMDB-1241
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EMDB-1243
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EMDB-1244
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Cite: data citing same article

Similar strucutres (beta)

Diagram

EMDB-1241

EMDB-1283

EMDB-1711

EMDB-5371
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleMol. Cell, Vol. 25, Issue 2, Page 261-71, Year 2007
TitleVisualizing the ATPase cycle in a protein disaggregating machine: structural basis for substrate binding by ClpB.
AuthorsSukyeong Lee, Jae-Mun Choi, Francis T F Tsai
Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
KeywordsAdenine Nucleotides (metabolism), Adenosine Triphosphatases (chemistry, 3.6.1.-), Bacterial Proteins (chemistry), ClpB protein, E coli, Cryoelectron Microscopy, Enzyme Activation, Escherichia coli Proteins (chemistry), Heat-Shock Proteins (chemistry), Image Processing, Computer-Assisted, Models, Molecular, Protein Structure, Quaternary, Protein Structure, Tertiary, Substrate Specificity, Thermus thermophilus (genetics)
LinksPII: S1097-2765(07)00003-2, DOI: 10.1016/j.molcel.2007.01.002, PubMed: 17244533, PMC: PMC1855157
Map
FileEMD-1242.map ( map file in CCP4 format, 5620 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:0.92, 0.880175 (movie #1):
Minimum - Maximum: -0.208361 - 3.91959
Average (Standard dev.): 0.100174 (0.390358)
Data Typefloat (32-bit)
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 112 112 112
Origin : -56 -56 -56
Limit : 55 55 55
Spacing : 112 112 112
Unit CellA = 243.04 A , B = 243.04 A , C = 243.04 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 2.17 A , Y = 2.17 A , Z = 2.17 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.172.172.17
M x/y/z112112112
origin x/y/z0.0000.0000.000
length x/y/z243.040243.040243.040
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-56-56-56
NC/NR/NS112112112
start NC,NX/NR,NY/NS,NZ-56-56-56
NC,NX/NR,NY/NS,NZ112112112
D min/max/mean-0.2083.9200.100
Annotation Detailsvolume file of TClpB ADP bound state
Supplement
Images
Images

1242.gif
Sample
NameClpB
Oligomeric Statehomohexamer
Number of Components1
Experimental Mass0.6 MDa
Theoretical Mass0.6 MDa
Component #1: protein - ClpB
Scientific nameClpB
Theoretical Mass0.1 MDa
Experimental Mass0.1 MDa
Oligomeric Detailshexamer
Number of Copies6
Scientific Name of SpeciesThermus thermophilus (NCBI Taxonomy: 274)
Recombinant expressionYes
Natural SourceCell: E.Coli
Cell Location: cytoplasm
Engineered SourceVector: pET15b
Exp System: Escherichia coli (NCBI Taxonomy: 562)
Experiment
Sample Preparation
Specimen Conc0.03 mg/ml
Specimen Support Details400 mesh copper grid
Specimen Stateparticle
BufferDetails: 50mM MOPS, 150 mM KCl, 5mM MgCl2
pH: 7.5
Vitrification
Cryogen NameETHANE
Humidity37
InstrumentREICHERT-JUNG PLUNGER
DetailsVitrification instrument: Reichert plunger
Imaging
MicroscopeJEOL 2010F
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose15 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 6900 X,
Astigmatismobjective lens astigmatism was corrected at 400,000x magnification
Nominal Cs1.0 mm
Imaging ModeBRIGHT FIELD
Defocus1400 nm - 3200 nm
Specimen Holder
HolderEucentric ( GATAN LIQUID NITROGEN )
Temperature90 Kelvin
Camera
DetectorGatan 4kx4k CCD camera
Image Acquisition
Number of Digital Images46
Quant Bit Number16
Processing
Methodsingle particle reconstruction
3 D reconstruction
Algorithmprojection matching
SoftwareEMAN
CTF Correctioneach CCD frame
Resolution By Author16.7
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Projections17270
Download
Data from EMDB
Header (meta data in XML format)emd-1242.xml (6.9 KB)
Map dataemd_1242.map.gz (942.7 KB)
Images1242.gif (20.2 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1242
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 19.8 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.5 MB
Session file for UCSF-Chimera, 19.9 KB