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- EMDB-5391: 8-fold symmetric rATcpn-alpha in apo state -

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Basic information

Entry
Database: EMDB / ID: 5391
Title8-fold symmetric rATcpn-alpha in apo state
KeywordsGroup II chaperonin / thermosome
SamplerATcpn-alpha in apo state
SourceAcidianus tengchongensis / archaea
Map dataReconstruction of the 8-fold symmetric class of apo rATcpn-alpha
Methodsingle particle reconstruction, at 4.9 A resolution
AuthorsZhang K / Wang L / Liu YX / Wang X / Gao B / Hu ZJ / Ji G / Chan KY / Schulten K / Dong ZY / Sun F
CitationProtein Cell, 2013, 4, 432-444

Protein Cell, 2013, 4, 432-444 StrPapers
Flexible interwoven termini determine the thermal stability of thermosomes.
Kai Zhang / Li Wang / Yanxin Liu / Kwok-Yan Chan / Xiaoyun Pang / Klaus Schulten / Zhiyang Dong / Fei Sun

DateDeposition: Feb 7, 2012 / Header (metadata) release: Feb 16, 2012 / Map release: Aug 7, 2013 / Last update: Feb 7, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.3
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 3.3
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-3j1b
  • Surface level: 3.3
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_5391.map.gz (map file in CCP4 format, 93313 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
288 pix
0.93 A/pix
= 268.704 A
288 pix
0.93 A/pix
= 268.704 A
288 pix
0.93 A/pix
= 268.704 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 0.933 A
Density
Contour Level:3.3 (by author), 3.3 (movie #1):
Minimum - Maximum-7.62247181 - 13.75225735
Average (Standard dev.)0E-8 (1.2475096)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions288288288
Origin-144-144-144
Limit143143143
Spacing288288288
CellA=B=C: 268.704 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

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
D min/max/mean-7.62213.752-0.000

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Supplemental data

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Sample components

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Entire rATcpn-alpha in apo state

EntireName: rATcpn-alpha in apo state
Details: This sample contains about 90% 8-fold symmetric particles and about 10% 9-fold symmetric particles
Number of components: 1 / Oligomeric State: hexadecamer
MassTheoretical: 960 kDa / Experimental: 960 kDa

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Component #1: protein, Group II chaperonin alpha

ProteinName: Group II chaperonin alpha / a.k.a: rATcpn-alpha / Oligomeric Details: hexadecamer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 960 kDa / Experimental: 960 kDa
SourceSpecies: Acidianus tengchongensis / archaea / Strain: S5T
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: PET-23b

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 3 mg/ml
Buffer solution: 25 mM Tris-HCl, pH 7.5, 12 mM MgCl2, 50 mM KCl
pH: 7.5
Support film400-mesh GiGTM grid with holes of 2 um diameter and 2 um spacing
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 100 K / Humidity: 100 % / Method: Blot for 4 seconds before plunging

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN KRIOS / Date: Jul 23, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 96000 X (nominal), 96000 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 96,000 times magnification
Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 3500 nm
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3424 / Bit depth: 32

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 55460 / Applied symmetry: D8 (2*8 fold dihedral)
3D reconstructionSoftware: Spider,EMAN1.9 / CTF correction: The whole micrograph / Resolution: 4.9 A / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: flexible / Refinement space: REAL
Details: Protocol: Rigid body and Molecular Dynamics Flexible Fitting. symmetry-restrained MDFF
Input PDB model: 3KO1
Chain ID: A
Output model

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