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8-fold symmetric rATcpn-alpha in apo state

by single particle reconstruction, at 4.9 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 3.3, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 3.3, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3j1b, Surface level: 3.3, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5391
Title8-fold symmetric rATcpn-alpha in apo state
MapReconstruction of the 8-fold symmetric class of apo rATcpn-alpha
SamplerATcpn-alpha in apo state
KeywordsGroup II chaperonin, thermosome
AuthorsZhang K, Wang L, Liu YX, Wang X, Gao B, Hu ZJ, Ji G, Chan KY, Schulten K, Dong ZY, Sun F
DateDeposition: 2012-02-07, Header release: 2012-02-16, Map release: 2013-08-07, Last update: 2013-08-07
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 3.3, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 3.3, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3j1b, Surface level: 3.3, Image by UCSF CHIMERA

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

PDB-3j1b

CiteFit

Cite: data citing same article

Fit: output model of fitting

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Article
Citation - Primary
ArticleProtein Cell, Vol. 4, Issue 6, Page 432-44, Year 2013
TitleFlexible interwoven termini determine the thermal stability of thermosomes.
AuthorsKai Zhang, Li Wang, Yanxin Liu, Kwok-Yan Chan, Xiaoyun Pang, Klaus Schulten, Zhiyang Dong, Fei Sun
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
KeywordsAcidianus (metabolism), Adenosine Triphosphate (metabolism), Amino Acid Sequence, Cryoelectron Microscopy, Hydrogen-Ion Concentration, Molecular Sequence Data, Mutation, Nucleotides (metabolism), Protein Binding, Protein Folding, Protein Stability, Protein Structure, Quaternary, Sequence Alignment, Static Electricity, Temperature, Thermosomes (chemistry, 3.6.1.-)
LinksDOI: 10.1007/s13238-013-3026-9, PubMed: 23709365, PMC: PMC3740188
Map
Fileemd_5391.map.gz ( map file in CCP4 format, 93313 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
288 pix
0.933 A/pix
= 268.704 A
288 pix
0.933 A/pix
= 268.704 A
288 pix
0.933 A/pix
= 268.704 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:3.3 (by author), 3.3 (movie #1):
Minimum - Maximum: -7.62247181 - 13.75225735
Average (Standard dev.): 0E-8 (1.2475096)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions288288288
Origin-144-144-144
Limit143143143
Spacing288288288
Unit CellA= B= C: 268.704 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 0.933 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z0.9330.9330.933
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z268.704268.704268.704
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-144-144-144
NC/NR/NS288288288
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-7.62213.752-0.000
Annotation DetailsReconstruction of the 8-fold symmetric class of apo rATcpn-alpha
Supplement
Images
Images
Sample
NamerATcpn-alpha in apo state
Number of Components1
Oligomeric Statehexadecamer
Theoretical Mass0.96MDa
DetailsThis sample contains about 90% 8-fold symmetric particles and about 10% 9-fold symmetric particles
Experimental Mass0.96MDa
Component #1: protein - rATcpn-alpha
Scientific nameGroup II chaperonin alpha
Common NamerATcpn-alpha
Theoretical Mass0.96 MDa
Experimental Mass0.96 MDa
Oligomeric Detailshexadecamer
Number of Copies1
Scientific Name of SpeciesAcidianus tengchongensis
Common Name of SpeciesArchaea
NCBI taxonomy146920
StrainS5T
Recombinant expressionYes
Engineered SourceVector: PET-23b
NCBI taxonomy: 562
Expression system: Escherichia coli
Experiment
Sample Preparation
Specimen Conc3 mg/ml
Specimen Support Details400-mesh GiGTM grid with holes of 2 um diameter and 2 um spacing
Specimen Stateparticle
BufferDetails: 25 mM Tris-HCl, pH 7.5, 12 mM MgCl2, 50 mM KCl
pH: 7.5
Vitrification
MethodBlot for 4 seconds before plunging
Cryogen NameETHANE
Humidity100
InstrumentFEI VITROBOT MARK IV
Temperature100 Kelvin
Imaging
MicroscopeFEI TITAN KRIOS
Date23-JUL-2010
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 96000, Calibrated: 96000
AstigmatismObjective lens astigmatism was corrected at 96,000 times magnification
Nominal Cs2.7 mm
Imaging ModeBRIGHT FIELD
Defocus1500 nm - 3500 nm
Specimen Holder
ModelGATAN LIQUID NITROGEN
Camera
DetectorGATAN ULTRASCAN 4000 (4k x 4k)
Image Acquisition
#1
Number of Digital Images3424
Quant Bit Number32
Processing
Methodsingle particle reconstruction
3D reconstruction
SoftwareSpider,EMAN1.9
CTF CorrectionThe whole micrograph
Resolution By Author4.9 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections55460
Applied SymmetryD8 (2*8 fold dihedral)
Atomic Model Fitting
Model #0
DetailsProtocol: Rigid body and Molecular Dynamics Flexible Fitting. symmetry-restrained MDFF
SoftwareChimera
Refinement Protocolflexible
Refinement SpaceREAL
PDB Entry ID3KO1
PDB Chain IDA
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-5391.xml (7.8 KB)
Map dataemd_5391.map.gz (82.4 MB)
Imagesemd_5391_1.png (306.4 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5391
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.5 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 26.6 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5.8 MB
Session file for UCSF-Chimera, 6.3 MB