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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

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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
Verna and Marrs McLean Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA.
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
NX/NY/NZ
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