PDB-3izm: Mm-cpn wildtype with ATP - EM Navigator

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Mm-cpn wildtype with ATP

by single particle reconstruction, at 7.2 A resolution

Movie

Orientation:

#1: Depositted structure unit, Made by Jmol

#2: Superimposing with EM 3D map: EMDB-5249, Made by UCSF CHIMERA

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 3izm
Title	Mm-cpn wildtype with ATP
Descriptor	Chaperonin
Keywords	CHAPERONE, Mm-cpn, maripaludis, chaperonin
Authors	Douglas, N.R., Reissmann, S., Zhang, J., Chen, B., Jakana, J., Kumar, R., Chiu, W., Frydman, J.
Date	Deposition: 2010-10-30, Release: 2011-02-02
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-5249, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-5249 CiteFit EMDB-5244 Cite EMDB-5245 Cite EMDB-5246 Cite EMDB-5247 Cite EMDB-5248 Cite EMDB-5250 Cite PDB-3izh Cite PDB-3izi Cite PDB-3izj Cite PDB-3izk Cite PDB-3izl Cite PDB-3izn Cite Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-3izi PDB-3izj EMDB-1398 EMDB-5137 EMDB-5249 List of similar structure data about Omokage system

Article
Citation - primary
Article	Cell, Vol. 144, Issue 2, Page 240-52, Year 2011
Title	Dual action of ATP hydrolysis couples lid closure to substrate release into the group II chaperonin chamber.
Authors	Nicholai R Douglas, Stefanie Reissmann, Junjie Zhang, Bo Chen, Joanita Jakana, Ramya Kumar, Wah Chiu, Judith Frydman Department of Biology, Stanford University, Stanford, CA 94305-5020, USA.
Keywords	Adenosine Triphosphatases (metabolism, 3.6.1.-), Adenosine Triphosphate (metabolism, 56-65-5), Allosteric Regulation, Archaeal Proteins (chemistry), Binding Sites, Group II Chaperonins (chemistry, 3.6.1.-), Methanococcus (metabolism), Models, Molecular, Protein Folding
Links	PII: S0092-8674(10)01435-2, DOI: 10.1016/j.cell.2010.12.017, PubMed: 21241893, PMC: PMC3055171

Components
ID 1 : Chaperonin GroEL (Thermosome, HSP60 family)
Image
Description	Chaperonin
Type	polymer
Formula weight	55295.145 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	0.9
Theoretical Mass	0.9
Name	Mm-cpn wildtype with ATP
Num components	2
Entity assembly
Name	Methanococcus maripaludis chaperonin
Type	PROTEIN
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE (CRYO EM)
Vitrification
Cryogen name	ETHANE
Humidity	100
Instrument	vitribot

Electron Microscopy
Imaging
Microscope	model: JEM3200FSC
Electron gun
Electron source	FIELD EMISSION GUN
Accelerating voltage	200 kV
Illumination mode	FLOOD BEAM
Lens
Mode	BRIGHT FIELD
Detector distance	0.0
Specimen holder
Specimen holder	model: GATAN LIQUID NITROGEN, type: Gatan side entry
Tilt angle	min: 0.0 degrees, max: 0.0 degrees
Detector
Type	Gatan 4Kx4K CCD camera

Processing
2D projection selection
Software name	Rosetta
Single particle entity
Symmetry type	DIHEDRAL
3D reconstruction
Resolution	7.2 A
Resolution method	FSC at 0.5 cut-off
Software	EMAN
3D fitting
Refinement Space	REAL
Software name	Rosetta
Refine hist
Total atoms	61632
Protein atoms	61632

PDB format

All

pdb3izm.ent (uncompressed file)

Header only

mmCIF format

mmCIF

XML format

All

No-atom

3izm-noatom.xml.gz

Ext-atom

3izm-extatom.xml.gz

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.5 MB .webm (WebM/VP8 format), 4.7 MB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.7 MB .webm (WebM/VP8 format), 5.4 MB