PDB-3los: Atomic Model of Mm-cpn in the Closed State

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 3los
Title	Atomic Model of Mm-cpn in the Closed State
Descriptor	Chaperonin
Keywords	CHAPERONE, Group II chaperonin, Protein Folding, Mm-cpn, Single Particle Reconstruction, Methanococcus maripaludis, Chaperone, ATP-binding, Nucleotide-binding
Authors	Zhang, 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.
Date	Deposition: 2010-02-04, Release: 2010-03-16
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
Movies	Movie Page #1: Depositted structure unit, Made by Jmol #2: Superimposing with EM 3D map: EMDB-5137, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-5137 CiteFit EMDB-5138 Cite EMDB-5139 Cite EMDB-5140 Cite PDB-3iyf Cite Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram EMDB-5137 EMDB-5145 EMDB-5246 EMDB-5249 PDB-3izj List of similar structure data about Omokage system

Article
Citation - primary
Article	Nature, Vol. 463, Issue 7279, Page 379-83, Year 2010
Title	Mechanism of folding chamber closure in a group II chaperonin.
Authors	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 Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.
Keywords	Adenosine Triphosphate (chemistry, 56-65-5), Allosteric Regulation, Binding Sites, Cryoelectron Microscopy, Group II Chaperonins (chemistry, 3.6.1.-), Hydrolysis (drug effects), Methanococcus (chemistry), Models, Molecular, Protein Binding, Protein Conformation (drug effects), Protein Folding, Protein Subunits (chemistry), Structure-Activity Relationship
Links	DOI: 10.1038/nature08701, PubMed: 20090755, PMC: PMC2834796

Components
ID 1 : Chaperonin GroEL (Thermosome, HSP60 family)
Image
Description	Chaperonin
Type	polymer
Formula weight	58290.793 Da
Number of molecules	16
Source	Method: Isolated from a genetically manipulated source Gene: hsp60, MMP1515, ID:39152, Methanococcus maripaludis Host: ID:562, Escherichia coli
Links	UniProt: Q877G8, Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Composition	16-mer
Experimental Mass	0.96
Theoretical Mass	0.96
Name	Mm-cpn with 1mM ATP/AlFx
Num components	1
Entity assembly
Name	Methanococcus maripaludis chaperonin
Type	PROTEIN
Buffer
Name	ATPase buffer
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE (CRYO EM)
Sample preparation
pH	7.5
Vitrification
Cryogen name	ETHANE
Humidity	100
Instrument	Vitrobot
Method	1 blot 3 seconds

Electron Microscopy
Imaging
Microscope	model: JEM3200FSC
Electron gun
Electron source	FIELD EMISSION GUN
Accelerating voltage	300 kV
Electron dose	20 e/A**2
Illumination mode	FLOOD BEAM
Lens
Mode	BRIGHT FIELD
Magnification	calibrated: 112000 X, nominal: 80000 X
Cs	nominal: 4.1 mm
Astigmatism	objective lens astigmatism was corrected at 100,000 times magnification
Detector distance	0.0
Nominal defocus	max: 3000 nm, min: 1000 nm
Energy filter	in column omega filter
Energy window	0-10 eV
Specimen holder
Specimen holder	model: JEM3200FSC CRYOHOLDER, type: side-entry
Tilt angle	min: 0.0 degrees, max: 0.0 degrees
Temperature	100 Kelvin
Detector
Type	Gatan 4kX4k CCD Camera

Processing
Single particle entity
Symmetry type	DIHEDRAL
3D reconstruction
CTF correction method	Each micrograph
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.
Method	Projection-match
Resolution	4.3 A
Resolution method	FSC at 0.5 cut-off
Software	EMAN
3D fitting
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.
Refine hist
Total atoms	63712
Protein atoms	63712