EMDB-2001: ATP-triggered molecular mechanics of the chaperonin GroEL

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 2001
Authors	Clare DK, Vasishtan D, Stagg S, Quispe J, Farr GW, Topf M, Horwich AL, Saibil HR
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 0.2, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 0.2, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-4aau, Surface level: 0.2, Made by UCSF CHIMERA
Supplemental images	EMD2001.jpeg
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	PDB-4aau CiteFit EMDB-1997 Cite EMDB-1998 Cite EMDB-1999 Cite EMDB-2000 Cite EMDB-2002 Cite EMDB-2003 Cite PDB-4aaq Cite PDB-4aar Cite PDB-4aas Cite PDB-4ab2 Cite PDB-4ab3 Cite Cite: data citing same article Fit: output model of fitting
Similar strucutres (beta)	Diagram PDB-4aau PDB-4ab3 EMDB-1999 PDB-4aas EMDB-2002 EMDB-1047 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Cell, Vol. 149, Issue 1, Page 113-23, Year 2012
Title	ATP-triggered conformational changes delineate substrate-binding and -folding mechanics of the GroEL chaperonin.
Authors	Daniel K Clare, Daven Vasishtan, Scott Stagg, Joel Quispe, George W Farr, Maya Topf, Arthur L Horwich, Helen R Saibil Crystallography and Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK.
Keywords	Adenosine Triphosphate (metabolism, 56-65-5), Bacteria (chemistry), Chaperonin 10 (metabolism), Chaperonin 60 (chemistry), Cryoelectron Microscopy, Escherichia coli (chemistry), Escherichia coli Proteins (chemistry), GroE protein, E coli, Heat-Shock Proteins (chemistry), Hydrophobic and Hydrophilic Interactions, Protein Conformation, Protein Folding
Links	PII: S0092-8674(12)00287-5, DOI: 10.1016/j.cell.2012.02.047, PubMed: 22445172, PMC: PMC3326522

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 = 387.84 A , B = 387.84 A , C = 387.84 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees

Pixel Spacing

X = 2.02 A , Y = 2.02 A , Z = 2.02 A

CCP4 map header info

Annotation Details

The GroEL-ATP14 Rd1-Rd3 map is one of seven maps calculated from a heterogenous sample

Sample
Name	GroEL-ATP14 Rd1-Rd3
Number of Components	2
Oligomeric State	Tetradecamer of GroEL with 14 ATP molecules bound
Theoretical Mass	0.8 MDa
Experimental Mass	0.8 MDa
Component #1: protein - GroEL
Scientific name	hsp60
Common Name	GroEL
Theoretical Mass	0.056 MDa
Experimental Mass	0.056 MDa
Details	ATPase Mutant, D398A
Oligomeric Details	tetradecamer
Number of Copies	14
Scientific Name of Species	Escherichia coli (NCBI Taxonomy: 562)
Recombinant expression	Yes
Natural Source	Cell Location: cytoplasm
Engineered Source	Exp System: Escherichia coli (NCBI Taxonomy: 562)
Links	Gene Ontology: GO:0042026, InterPro: IPR:002423
Component #2: ligand - ATP
Scientific name	ATP
Theoretical Mass	0.00055 MDa
Experimental Mass	0.00055 MDa
Details	ATP is bound to all 14 subunits
Scientific Name of Species	synthetic construct (NCBI Taxonomy: 32630)
Recombinant expression	No

Experiment
Sample Preparation
Specimen Conc	4 mg/ml
Specimen Support Details	cflat grids r2/2
Specimen State	particle
Buffer	Details: 50 mM Tris-HCl pH 7.4, 50 mM KCl, 10 mM MgCl2 and 200uM ATP pH: 7.4
Vitrification
Method	grids were blotted for 2-3 seconds
Cryogen Name	ETHANE
Time Resolved State	vitrified within 30 seconds
Details	Vitrification instrument: Vitrobot
Humidity	100
Instrument	FEI VITROBOT
Temperature	95 Kelvin
Imaging
Microscope	FEI TECNAI F20
Details	The data was collected with leginon at SCRIPPS
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	120 kV
Electron Dose	15 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Calibrated: 148500 X
Nominal Cs	2 mm
Imaging Mode	BRIGHT FIELD
Defocus	700 nm - 3500 nm
Specimen Holder
Holder	Eucentric ( GATAN LIQUID NITROGEN )
Temperature	95 Kelvin ( 95 Kelvin - 95 Kelvin )
Camera
Detector	Gatan Ultrascan 4000 4K CCD camera
Image Acquisition

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	projection matching
Euler Angles Details	theta 80-100, phi 0-51.42
Software	SPIDER, IMAGIC
CTF Correction	each particle was phase flipped
Details	SIRT was used to reconstruct the final map
Resolution By Author	8.5
Resolution Method	FSC at 0.5 cut-off
Single Particle
Number of Projections	6500
Details	The particles were automatically picked using FindEM
Atomic Model Fitting
Model #0
Target Criteria	cross-correlation coefficient
Details	Protocol: Flexible fitting
Software	Chimera, Flex-EM, NAMD2.6
Refinement Protocol	flexible
Refinement Space	REAL
Fitted Coordinate
PDB entry ID	PDB-4aau

Data from EMDB

Header (meta data in XML format)

Map data

Images

FTP directory

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.5 MB .webm (WebM/VP8 format), 5.4 MB Session file for UCSF-Chimera, 26.5 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.2 MB .webm (WebM/VP8 format), 4.8 MB Session file for UCSF-Chimera, 26.6 KB

movie #3

	.mp4 (H.264/MPEG-4 AVC format), 3.8 MB .webm (WebM/VP8 format), 5.7 MB Session file for UCSF-Chimera, 5.5 MB