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- EMDB-5244: Mm-cpn D386A with ATP -

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Basic information

Database: EMDB / ID: 5244
TitleMm-cpn D386A with ATP
KeywordsMm-cpn / maripaludis / chaperonin
SampleMm-cpn D386A with ATP
SourceMethanococcus maripaludis / archaea / メタノコッカス・マリパルディス
Map dataThis is the density map of the Mm-cpn D386A mutant with ATP bound.
Methodsingle particle reconstruction, at 11 Å resolution
AuthorsDouglas NR / Reissmann S / Zhang J / Chen B / Jakana J / Kumar R / Chiu W / Frydman J
CitationCell, 2011, 144, 240-252

Cell, 2011, 144, 240-252 Yorodumi Papers
Dual action of ATP hydrolysis couples lid closure to substrate release into the group II chaperonin chamber.
Nicholai R Douglas / Stefanie Reissmann / Junjie Zhang / Bo Chen / Joanita Jakana / Ramya Kumar / Wah Chiu / Judith Frydman

Validation ReportPDB-ID: 3izh

SummaryFull reportAbout validation report
DateDeposition: Oct 29, 2010 / Header (metadata) release: Jan 24, 2011 / Map release: Jan 24, 2011 / Last update: Dec 24, 2014

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.9
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.9
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-3izh
  • Surface level: 0.9
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_5244.map.gz (map file in CCP4 format, 27649 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.81 Å/pix.
= 347.52 Å
192 pix
1.81 Å/pix.
= 347.52 Å
192 pix
1.81 Å/pix.
= 347.52 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.81 Å
Contour Level:0.9 (by author), 0.9 (movie #1):
Minimum - Maximum-0.4199383 - 2.34022236
Average (Standard dev.)0.07127716 (0.25745445)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 347.52 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.811.811.81
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z347.520347.520347.520
start NX/NY/NZ-62-62-62
MAP C/R/S123
start NC/NR/NS-96-96-96
D min/max/mean-0.4202.3400.071

Supplemental data

Sample components

Entire Mm-cpn D386A with ATP

EntireName: Mm-cpn D386A with ATP / Number of components: 1 / Oligomeric State: 16-mer
MassTheoretical: 900 kDa / Experimental: 900 kDa

Component #1: protein, chaperonin

ProteinName: chaperonin / a.k.a: Mm-cpn / Recombinant expression: Yes
MassTheoretical: 900 kDa / Experimental: 900 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 /

Experimental details

Sample preparation

Specimen stateparticle
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Humidity: 100 % / Details: Vitrification instrument: vitrobot

Electron microscopy imaging

ImagingMicroscope: JEOL 2010F
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderHolder: Gatan side entry / Model: GATAN LIQUID NITROGEN
CameraDetector: GENERIC GATAN (4k x 4k)

Image acquisition

Image acquisitionScanner: OTHER

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D8 (2*8 fold dihedral)
3D reconstructionSoftware: EMAN / Resolution: 11 Å / Resolution method: FSC 0.5

Atomic model buiding

Output model

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