EMDB-5244: Mm-cpn D386A with ATP

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 5244
Title	Mm-cpn D386A with ATP
Map	This is the density map of the Mm-cpn D386A mutant with ATP bound.
Sample	Mm-cpn D386A with ATP
Keywords	Mm-cpn, maripaludis, chaperonin
Authors	Douglas NR, Reissmann S, Zhang J, Chen B, Jakana J, Kumar R, Chiu W, Frydman J
Date	Deposition: 2010-10-29, Header release: 2011-01-24, Map release: 2011-01-24, Last update: 2011-01-24
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 0.9, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 0.9, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-3izh, Surface level: 0.9, Made by UCSF CHIMERA
Supplemental images	EMDB figure
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	PDB-3izh CiteFit EMDB-5245 Cite EMDB-5246 Cite EMDB-5247 Cite EMDB-5248 Cite EMDB-5249 Cite EMDB-5250 Cite PDB-3izi Cite PDB-3izj Cite PDB-3izk Cite PDB-3izl Cite PDB-3izm Cite PDB-3izn Cite Cite: data citing same article Fit: output model of fitting
Similar strucutres (beta)	Diagram EMDB-5258 PDB-4a0o EMDB-1961 EMDB-1960 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

File

Projections & Slices

Size of images:

Images are generated by Spider package.

Density

Data Type

Image stored as Reals

Space Group Number

Map Geometry

Unit Cell

A = 347.52 A , B = 347.52 A , C = 347.52 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees

Pixel Spacing

X = 1.81 A , Y = 1.81 A , Z = 1.81 A

CCP4 map header info

Annotation Details

This is the density map of the Mm-cpn D386A mutant with ATP bound.

Sample
Name	Mm-cpn D386A with ATP
Number of Components	2
Oligomeric State	16-mer
Theoretical Mass	0.9 MDa
Experimental Mass	0.9 MDa
Component #1: protein - Mm-cpn
Scientific name	Methanococcus maripaludis chaperonin
Common Name	Mm-cpn
Theoretical Mass	0.9 MDa
Experimental Mass	0.9 MDa
Scientific Name of Species	unidentified (NCBI Taxonomy: 32644)
Recombinant expression	Yes

Experiment
Sample Preparation
Specimen State	particle
Vitrification
Cryogen Name	ETHANE
Details	Vitrification instrument: vitrobot
Humidity	100
Instrument	FEI VITROBOT
Imaging
Microscope	JEOL 2010F
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	200 kV
Illumination Mode	FLOOD BEAM
Lens
Imaging Mode	BRIGHT FIELD
Specimen Holder
Holder	Gatan side entry ( GATAN LIQUID NITROGEN )
Camera
Detector	Gatan 4Kx4K CCD camera
Image Acquisition
Scanner	OTHER

Processing
Method	single particle reconstruction
3 D reconstruction
Software	EMAN
Resolution By Author	11
Resolution Method	FSC at 0.5 cut-off
Fitted Coordinate
PDB entry ID	PDB-3izh

Data from EMDB

Header (meta data in XML format)

Map data

FTP directory

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.4 MB .webm (WebM/VP8 format), 5.4 MB Session file for UCSF-Chimera, 26.1 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.2 MB .webm (WebM/VP8 format), 4.7 MB Session file for UCSF-Chimera, 26.2 KB

movie #3

	.mp4 (H.264/MPEG-4 AVC format), 3.7 MB .webm (WebM/VP8 format), 5.5 MB Session file for UCSF-Chimera, 6.1 MB