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- EMDB-5140: Lidless Mm-cpn in the open state -

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Open data


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Basic information

Entry
Database: EMDB / ID: 5140
TitleLidless Mm-cpn in the open state
KeywordsGroup II chaperonin / Protein Folding / Mm-cpn / Single Particle Reconstruction / Methanococcus maripaludis / Chaperone
SampleLidless Mm-cpn
SourceMethanococcus maripaludis / archaea / メタノコッカス・マリパルディス
Map dataThis is a map of the lidless Mm-cpn in the nucleotide-free open state.
Methodsingle particle reconstruction, at 8 A resolution
AuthorsZhang J / Baker ML / Schroeder G / Douglas NR / Reissmann S / Jakana J / Dougherty M / Fu CJ / Levitt M / Ludtke SJ / Frydman J / Chiu W
CitationNature, 2010, 463, 379-383

Nature, 2010, 463, 379-383 StrPapers
Mechanism of folding chamber closure in a group II chaperonin.
Junjie Zhang / Matthew L Baker / Gunnar F Schröder / Nicholai R Douglas / Stefanie Reissmann / Joanita Jakana / Matthew Dougherty / Caroline J Fu / Michael Levitt / Steven J Ludtke / Judith Frydman / Wah Chiu

DateDeposition: Oct 23, 2009 / Header (metadata) release: Feb 4, 2010 / Map release: Feb 4, 2010 / Last update: Oct 23, 2009

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Structure visualization

Movie
  • Colored surface
  • Surface level: 1.05
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.05
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-3iyf
  • Surface level: 1.05
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-3iyf
  • Surface level: 1.05
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_5140.map.gz (map file in CCP4 format, 54001 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
1.33 A/pix
= 319.2 A
240 pix
1.33 A/pix
= 319.2 A
240 pix
1.33 A/pix
= 319.2 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.33 A
Density
Contour Level:0.95 (by author), 1.05 (movie #1):
Minimum - Maximum-1.7838 - 2.47715
Average (Standard dev.)0.0335325 (0.191107)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin-120-120-120
Limit119119119
Spacing240240240
CellA=B=C: 319.2 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.331.331.33
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z319.200319.200319.200
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-120-120-120
NC/NR/NS240240240
D min/max/mean-1.7842.4770.034

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Supplemental data

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Sample components

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Entire Lidless Mm-cpn

EntireName: Lidless Mm-cpn / Number of components: 1 / Oligomeric State: 16-mer
MassTheoretical: 960 kDa / Experimental: 960 kDa

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Component #1: protein, Lidless Methanococcus maripaludis chaperonin

ProteinName: Lidless Methanococcus maripaludis chaperonin / a.k.a: Lidless Mm-cpn / Oligomeric Details: 16-mer / Recombinant expression: Yes / Number of Copies: 16
MassTheoretical: 960 kDa / Experimental: 960 kDa
SourceSpecies: Methanococcus maripaludis / archaea / メタノコッカス・マリパルディス
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Sample preparation

Specimen stateparticle
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Humidity: 100 % / Method: 1 blot 3 seconds / Details: Vitrification instrument: Vitrobot

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Electron microscopy imaging

ImagingMicroscope: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 80000 X (nominal), 112000 X (calibrated)
Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Cs: 4.1 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3000 nm / Energy filter: in column omega filter / Energy window: 0-10 eV
Specimen HolderHolder: side-entry / Model: JEOL 3200FSC CRYOHOLDER / Temperature: 100 K
CameraDetector: GENERIC GATAN (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D8 (2*8 fold dihedral)
3D reconstructionAlgorithm: Projection-match / Software: EMAN / CTF correction: Each micrograph / Resolution: 8 A / Resolution method: FSC 0.5

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Atomic model buiding

Output model

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