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Lidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state

by single particle reconstruction, at 8 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.075, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.075, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3j02, Surface level: 0.075, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5258
TitleLidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state
MapThis is the density map of lidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state.
SampleLidless D386A Mm-cpn variant
KeywordsMm-cpn, Chaperonin, ATP-bound
AuthorsZhang J, Ma B, DiMaio F, Douglas NR, Joachimiak L, Baker D, Frydman J, Levitt M, Chiu W
DateDeposition: 2011-02-10, Header release: 2011-05-11, Map release: 2011-05-11, Last update: 2014-05-07
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.075, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.075, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3j02, Surface level: 0.075, Image by UCSF CHIMERA

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

PDB-3j02

CiteFit

Cite: data citing same article

Fit: output model of fitting

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Article
Citation - Primary
ArticleStructure, Vol. 19, Issue 5, Page 633-9, Year 2011
TitleCryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure.
AuthorsJunjie Zhang, Boxue Ma, Frank DiMaio, Nicholai R Douglas, Lukasz A Joachimiak, David Baker, Judith Frydman, Michael Levitt, Wah Chiu
KeywordsAdenosine Triphosphate (metabolism), Binding Sites, Cryoelectron Microscopy (methods), Group II Chaperonins (chemistry, 3.6.1.-), Hydrolysis, Methanococcus (chemistry), Models, Molecular, Protein Binding, Protein Conformation, Protein Folding, Protein Subunits (chemistry)
LinksPII: S0969-2126(11)00102-X, DOI: 10.1016/j.str.2011.03.005, PubMed: 21565698, PMC: PMC3705922
Map
Fileemd_5258.map.gz ( map file in CCP4 format, 54001 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
1.42 A/pix
= 340.8 A
240 pix
1.42 A/pix
= 340.8 A
240 pix
1.42 A/pix
= 340.8 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.02 (by emdb), 0.075 (movie #1):
Minimum - Maximum: -0.12193819 - 0.23173273
Average (Standard dev.): 0.00300522 (0.01658083)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin-120-120-120
Limit119119119
Spacing240240240
Unit CellA= B= C: 340.8 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.42 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.421.421.42
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z340.800340.800340.800
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
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-0.1220.2320.003
Annotation DetailsThis is the density map of lidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state.
Supplement
Images
Images
Sample
NameLidless D386A Mm-cpn variant
Number of Components1
Theoretical Mass1MDa
Experimental Mass1MDa
Component #1: protein - Mm-cpn
Scientific nameMethanococcus maripaludis chaperonin
Common NameMm-cpn
Theoretical Mass1 MDa
Experimental Mass1 MDa
Detailsincubated with 1mM ATP
Oligomeric Details16-mer
Number of Copies1
Scientific Name of SpeciesMethanococcus maripaludis
NCBI taxonomy39152
Recombinant expressionYes
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Experiment
Sample Preparation
Specimen Stateparticle
Vitrification
Cryogen NameETHANE
DetailsVitrification instrument: vitrobot
Humidity100
InstrumentFEI VITROBOT
Imaging
MicroscopeJEOL 2200FS
Date08-SEP-2009
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 80000, Calibrated: 112000
Imaging ModeBRIGHT FIELD
Defocus1000 nm - 2500 nm
Energy FilterEnergy Filter: in-column omega energy filter , Energy Window: 0-10 eV
Specimen Holder
HolderGatan side entry
ModelGATAN LIQUID NITROGEN
Camera
DetectorGENERIC GATAN (4k x 4k)
Image Acquisition
#1
Number of Digital Images64
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmprojection matching
SoftwareEMAN
CTF CorrectionEach CCD image
Resolution By Author8 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections12761
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-5258.xml (6.8 KB)
Map dataemd_5258.map.gz (3.2 MB)
Imagesemd_5258_1.png (219.5 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5258
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 26.5 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, 26.6 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.7 MB
Session file for UCSF-Chimera, 5.8 MB