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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

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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
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