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Lidless Mm-cpn in the open state

by single particle reconstruction, at 8 A resolution

Movie

Orientation:

#1: Surface view. , Surface level: 1.05, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1.05, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3iyf, Surface level: 1.05, Image by UCSF CHIMERA

#4: Surface view with fitted model, atomic models: PDB-3iyf, Surface level: 1.05, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5140
TitleLidless Mm-cpn in the open state
MapThis is a map of the lidless Mm-cpn in the nucleotide-free open state.
SampleLidless Mm-cpn
KeywordsGroup II chaperonin, Protein Folding, Mm-cpn, Single Particle Reconstruction, Methanococcus maripaludis, Chaperone
AuthorsZhang J, Baker ML, Schroeder G, Douglas NR, Reissmann S, Jakana J, Dougherty M, Fu CJ, Levitt M, Ludtke SJ, Frydman J, Chiu W
DateDeposition: 2009-10-23, Header release: 2010-02-04, Map release: 2010-02-04, Last update: 2011-07-08
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view. , Surface level: 1.05, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1.05, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3iyf, Surface level: 1.05, Image by UCSF CHIMERA

#4: Surface view with fitted model, atomic models: PDB-3iyf, Surface level: 1.05, Image by UCSF CHIMERA

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

PDB-3iyf

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
ArticleNature, Vol. 463, Issue 7279, Page 379-83, Year 2010
TitleMechanism of folding chamber closure in a group II chaperonin.
AuthorsJunjie Zhang, Matthew L Baker, Gunnar F Schröder, Nicholai R Douglas, Stefanie Reissmann, Joanita Jakana, Matthew Dougherty, Caroline J Fu, Michael Levitt, Steven J Ludtke, Judith Frydman, Wah Chiu
Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.
KeywordsAdenosine Triphosphate (chemistry), Allosteric Regulation, Binding Sites, Cryoelectron Microscopy, Group II Chaperonins (chemistry, 3.6.1.-), Hydrolysis (drug effects), Methanococcus (chemistry), Models, Molecular, Protein Binding, Protein Conformation (drug effects), Protein Folding, Protein Subunits (chemistry), Structure-Activity Relationship
LinksDOI: 10.1038/nature08701, PubMed: 20090755, PMC: PMC2834796
Map
Fileemd_5140.map.gz ( map file in CCP4 format, 54001 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
1.33 A/pix
= 319.2 A
240 pix
1.33 A/pix
= 319.2 A
240 pix
1.33 A/pix
= 319.2 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.95 (by author), 1.05 (movie #1):
Minimum - Maximum: -1.7838 - 2.47715
Average (Standard dev.): 0.0335325 (0.191107)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin-120-120-120
Limit119119119
Spacing240240240
Unit CellA= B= C: 319.2 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/z240240240
origin x/y/z0.0000.0000.000
length x/y/z319.200319.200319.200
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-120-120-120
NC/NR/NS240240240
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-1.7842.4770.034
Annotation DetailsThis is a map of the lidless Mm-cpn in the nucleotide-free open state.
Supplement
Images
Images
Sample
NameLidless Mm-cpn
Number of Components1
Oligomeric State16-mer
Theoretical Mass0.96MDa
Experimental Mass0.96MDa
Component #1: protein - Lidless Mm-cpn
Scientific nameLidless Methanococcus maripaludis chaperonin
Common NameLidless Mm-cpn
Theoretical Mass0.96 MDa
Experimental Mass0.96 MDa
Oligomeric Details16-mer
Number of Copies16
Scientific Name of SpeciesMethanococcus maripaludis
NCBI taxonomy39152
Recombinant expressionYes
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Experiment
Sample Preparation
Specimen Stateparticle
Vitrification
Method1 blot 3 seconds
Cryogen NameETHANE
DetailsVitrification instrument: Vitrobot
Humidity100
InstrumentFEI VITROBOT
Imaging
MicroscopeJEOL 3200FSC
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 80000, Calibrated: 112000
Astigmatismobjective lens astigmatism was corrected at 100,000 times magnification
Nominal Cs4.1 mm
Imaging ModeBRIGHT FIELD
Defocus1000 nm - 3000 nm
Energy FilterEnergy Filter: in column omega filter , Energy Window: 0-10 eV
Specimen Holder
Holderside-entry
ModelJEOL 3200FSC CRYOHOLDER
Temperature100 K
Camera
DetectorGENERIC GATAN (4k x 4k)
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmProjection-match
SoftwareEMAN
CTF CorrectionEach micrograph
Resolution By Author8 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-5140.xml (7 KB)
Map dataemd_5140.map.gz (10.4 MB)
Imagesemd_5140_1.png (219.6 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5140
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.4 MB
Session file for UCSF-Chimera, 25.1 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, 26.5 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 6.2 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.7 MB
Session file for UCSF-Chimera, 1.5 MB