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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
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-62-62-62
NX/NY/NZ125125125
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