[English] 日本語
Yorodumi
- PDB-3los: Atomic Model of Mm-cpn in the Closed State -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 3los
TitleAtomic Model of Mm-cpn in the Closed State
DescriptorChaperonin
KeywordsCHAPERONE / Group II chaperonin / Protein Folding / Mm-cpn / Single Particle Reconstruction / Methanococcus maripaludis / Chaperone / ATP-binding / Nucleotide-binding
Specimen sourceMethanococcus maripaludis / archaea / メタノコッカス・マリパルディス
MethodElectron microscopy (4.3 Å resolution / Particle / Single particle)
AuthorsZhang, J. / Baker, M.L. / Schroeder, G. / Douglas, N.R. / Reissmann, S. / Jakana, J. / Dougherty, M. / Fu, C.J. / Levitt, M. / Ludtke, S.J. / 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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 4, 2010 / Release: Mar 16, 2010
RevisionDateData content typeGroupProviderType
1.0Mar 16, 2010Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
A: Chaperonin
B: Chaperonin
C: Chaperonin
D: Chaperonin
E: Chaperonin
F: Chaperonin
G: Chaperonin
H: Chaperonin
I: Chaperonin
J: Chaperonin
K: Chaperonin
L: Chaperonin
M: Chaperonin
N: Chaperonin
O: Chaperonin
P: Chaperonin


Theoretical massNumber of molelcules
Total (without water)932,64416
Polyers932,64416
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Polypeptide(L)
Chaperonin / Chaperonin GroEL (Thermosome / HSP60 family)


Mass: 58290.262 Da / Num. of mol.: 16
Source: (gene. exp.) Methanococcus maripaludis / archaea / メタノコッカス・マリパルディス
References: UniProt: Q877G8

Molecular function

Biological process

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

-
Sample preparation

Component
IDNameTypeDetailsParent ID
1Mm-cpn with 1mM ATP/AlFxCOMPLEX16-mer0
2Methanococcus maripaludis chaperonin1
Molecular weightValue: 0.96 deg. / Units: MEGADALTONS / Experimental value: NO
Buffer solutionName: ATPase buffer / Details: ATPase buffer / pH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Method: 1 blot 3 seconds

-
Electron microscopy imaging

MicroscopyMicroscope model: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 80000 / Calibrated magnification: 112000 / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 4.1 mm
Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Camera length: 0 mm
Specimen holderSpecimen holder model: JEOL 3200FSC CRYOHOLDER / Specimen holder type: side-entry / Temperature: 100 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
EM imaging opticsEnergyfilter name: in column omega filter / Energyfilter upper: 10 eV / Energyfilter lower: 0 eV
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M
Radiation wavelengthRelative weight: 1

-
Processing

EM softwareName: EMAN / Category: RECONSTRUCTION
CTF correctionDetails: Each micrograph
SymmetryPoint symmetry: D8
3D reconstructionMethod: Projection-match / Resolution: 4.3 Å / Resolution method: FSC 0.5 CUT-OFF
Details: THE SINGLE SUBUNIT MODEL OF MM-CPN WAS MANUALLY BUILT IN THE CRYO-EM DENSITY USING COOT. THE ENTIRE 16-SUBUNIT COMPLEX WAS GENERATED BASED ON THE D8 SYMMETRY.
Symmetry type: POINT
Atomic model buildingDetails: DETAILS--THE SINGLE SUBUNIT MODEL OF MM-CPN WAS MANUALLY BUILT IN THE CRYO-EM DENSITY USING COOT. THE ENTIRE 16-SUBUNIT COMPLEX WAS GENERATED BASED ON THE D8 SYMMETRY.
Number of atoms included #LASTProtein: 63712 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 63712

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more