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Mm-cpn rls with ATP

by single particle reconstruction, at 6.7 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.28, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.28, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3izi, Surface level: 0.28, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5245
TitleMm-cpn rls with ATP
MapThis is the density map of Mm-cpn rls with ATP state
SampleMm-cpn rls with ATP
KeywordsMm-cpn, maripaludis, chaperonin
AuthorsDouglas NR, Reissmann S, Zhang J, Chen B, Jakana J, Kumar R, Chiu W, Frydman J
DateDeposition: 2010-10-29, Header release: 2011-01-24, Map release: 2011-01-24, Last update: 2011-07-08
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.28, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.28, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3izi, Surface level: 0.28, Made by UCSF CHIMERA

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

PDB-3izi

CiteFit

Cite: data citing same article

Fit: output model of fitting

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleCell, Vol. 144, Issue 2, Page 240-52, Year 2011
TitleDual action of ATP hydrolysis couples lid closure to substrate release into the group II chaperonin chamber.
AuthorsNicholai R Douglas, Stefanie Reissmann, Junjie Zhang, Bo Chen, Joanita Jakana, Ramya Kumar, Wah Chiu, Judith Frydman
Department of Biology, Stanford University, Stanford, CA 94305-5020, USA.
KeywordsAdenosine Triphosphatases (metabolism, 3.6.1.-), Adenosine Triphosphate (metabolism), Allosteric Regulation, Archaeal Proteins (chemistry), Binding Sites, Group II Chaperonins (chemistry, 3.6.1.-), Methanococcus (metabolism), Models, Molecular, Protein Folding
LinksPII: S0092-8674(10)01435-2, DOI: 10.1016/j.cell.2010.12.017, PubMed: 21241893, PMC: PMC3055171
Map
Fileemd_5245.map.gz ( map file in CCP4 format, 27649 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.33 A/pix
= 255.36 A
192 pix
1.33 A/pix
= 255.36 A
192 pix
1.33 A/pix
= 255.36 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.28 (by author), 0.28 (movie #1):
Minimum - Maximum: -0.365871 - 0.743929
Average (Standard dev.): 0.0168588 (0.0713206)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin-96-96-96
Limit959595
Spacing192192192
Unit CellA= B= C: 255.36 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.33 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.331.331.33
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z255.360255.360255.360
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.3660.7440.017
Annotation DetailsThis is the density map of Mm-cpn rls with ATP state
Supplement
Images
Images
Sample
NameMm-cpn rls with ATP
Number of Components2
Oligomeric State16-mer
Theoretical Mass0.9MDa
Experimental Mass0.9MDa
Component #1: protein - Mm-cpn
Scientific nameMethanococcus maripaludis chaperonin
Common NameMm-cpn
Theoretical Mass0.9 MDa
Experimental Mass0.9 MDa
Scientific Name of Speciesunidentified
NCBI taxonomy32644
Recombinant expressionYes
Experiment
Sample Preparation
Specimen Stateparticle
Vitrification
Cryogen NameETHANE
DetailsVitrification instrument: vitrobot
Humidity100
InstrumentFEI VITROBOT
Imaging
MicroscopeJEOL 3200FSC
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Illumination ModeFLOOD BEAM
Lens
Imaging ModeBRIGHT FIELD
Specimen Holder
HolderGatan side entry
ModelGATAN LIQUID NITROGEN
Camera
DetectorGENERIC GATAN (4k x 4k)
Image Acquisition
ScannerOTHER
Processing
Methodsingle particle reconstruction
3D reconstruction
SoftwareEMAN
Resolution By Author6.7 A
Resolution MethodFSC 0.5
Single Particle
Applied SymmetryD8 (2*8 fold dihedral)
Atomic Model Fitting
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-5245.xml (5.8 KB)
Map dataemd_5245.map.gz (25 MB)
Imagesemd_5245_1.jpg (166.2 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5245
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 26.1 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 26.1 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5.7 MB
Session file for UCSF-Chimera, 6.1 MB