EMDB-5391: 8-fold symmetric rATcpn-alpha in apo state

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 5391
Title	8-fold symmetric rATcpn-alpha in apo state
Map	Reconstruction of the 8-fold symmetric class of apo rATcpn-alpha
Sample	rATcpn-alpha in apo state
Keywords	Group II chaperonin, thermosome
Authors	Zhang K, Wang L, Liu YX, Wang X, Gao B, Hu ZJ, Ji G, Chan KY, Schulten K, Dong ZY, Sun F
Date	Deposition: 2012-02-07, Header release: 2012-02-16, Last update: 2012-02-16
Map data status	On hold (released when the article is published)
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Related Structure Data
Related Entries	EMDB-5390 Cite EMDB-5392 Cite EMDB-5393 Cite EMDB-5394 Cite EMDB-5395 Cite EMDB-5396 Cite EMDB-5397 Cite EMDB-5398 Cite EMDB-5399 Cite EMDB-5400 Cite EMDB-5401 Cite EMDB-5402 Cite EMDB-5403 Cite PDB-3j1b Fit? Cite: data citing same article Fit?: input model of fitting or unreleased data (?)

Article
Citation - Primary
Article	To Be Published
Title	Structural insights into the intra-ring cooperation of the heteromeric group II chaperonin
Authors	Zhang K, Wang L, Liu YX, Wang X, Gao B, Hu ZJ, Ji G, Chan KY, Schulten K, Dong ZY, Sun F

File

On hold (released when the article is published)

Density

Data Type

Image stored as Reals

Space Group Number

Map Geometry

Unit Cell

A= B= C: 268.704 A
Alpha=beta=gamma: 90 degrees

Pixel Spacing

X= Y= Z: 0.933 A

Annotation Details

Reconstruction of the 8-fold symmetric class of apo rATcpn-alpha

Sample
Name	rATcpn-alpha in apo state
Number of Components	1
Oligomeric State	hexadecamer
Theoretical Mass	0.96MDa
Details	This sample contains about 90% 8-fold symmetric particles and about 10% 9-fold symmetric particles
Experimental Mass	0.96MDa
Component #1: protein - rATcpn-alpha
Scientific name	Group II chaperonin alpha
Common Name	rATcpn-alpha
Theoretical Mass	0.96 MDa
Experimental Mass	0.96 MDa
Oligomeric Details	hexadecamer
Number of Copies	1
Scientific Name of Species	Acidianus tengchongensis
Common Name of Species	Archaea
NCBI taxonomy	146920
Strain	S5T
Recombinant expression	Yes
Engineered Source	Vector: PET-23b NCBI taxonomy: 562 Expression system: Escherichia coli

Experiment
Sample Preparation
Specimen Conc	3 mg/ml
Specimen Support Details	400-mesh GiGTM grid with holes of 2 um diameter and 2 um spacing
Specimen State	particle
Buffer	Details: 25 mM Tris-HCl, pH 7.5, 12 mM MgCl2, 50 mM KCl pH: 7.5
Vitrification
Method	Blot for 4 seconds before plunging
Cryogen Name	ETHANE
Humidity	100
Instrument	FEI VITROBOT MARK IV
Temperature	100 Kelvin
Imaging
Microscope	FEI TITAN KRIOS
Date	23-JUL-2010
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	300 kV
Electron Dose	20 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 96000, Calibrated: 96000
Astigmatism	Objective lens astigmatism was corrected at 96,000 times magnification
Nominal Cs	2.7 mm
Imaging Mode	BRIGHT FIELD
Defocus	1500 nm - 3500 nm
Specimen Holder
Model	GATAN LIQUID NITROGEN
Camera
Detector	Gatan Ultrascan 4000 Model 895
Image Acquisition
Number of Digital Images	3424
Quant Bit Number	32

Processing
Method	single particle reconstruction
3D reconstruction
Software	Spider,EMAN1.9
CTF Correction	The whole micrograph
Resolution By Author	4.9 A
Resolution Method	FSC at 0.5 cut-off
Single Particle
Number of Projections	55460
Atomic Model Fitting
Model #0
Details	Protocol: Rigid body and Molecular Dynamics Flexible Fitting. symmetry-restrained MDFF
Software	Chimera
Refinement Protocol	flexible
Refinement Space	REAL
PDB Entry ID	3KO1 PDB-3ko1
PDB Chain ID	A
Fitted Coordinate
PDB entry ID	PDB-3j1b

Download
Data from EMDB
Header (meta data in XML format)	emd-5391.xml (7.6 KB)
FTP directory	ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5391