EMDB-1984: Symmetrized cryo-EM reconstruction of E. coli DegQ 24-...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1984
Authors	Malet H, Canellas F, Sawa J, Yan J, Thalassinos K, Ehrmann M, Clausen T, 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: 3, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 3, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-4a9g, Surface level: 3, Made by UCSF CHIMERA
Supplemental images	EMD-1984.gif
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	PDB-4a9g CiteFit EMDB-1981 Cite EMDB-1982 Cite EMDB-1983 Cite PDB-4a8a Cite PDB-4a8b Cite PDB-4a8c Cite PDB-4a8d Cite Cite: data citing same article Fit: output model of fitting
Similar strucutres (beta)	Diagram PDB-4a9g EMDB-1862 EMDB-5289 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Nat. Struct. Mol. Biol., Vol. 19, Issue 2, Page 152-7, Year 2012
Title	Newly folded substrates inside the molecular cage of the HtrA chaperone DegQ.
Authors	Hélène Malet, Flavia Canellas, Justyna Sawa, Jun Yan, Konstantinos Thalassinos, Michael Ehrmann, Tim Clausen, Helen R Saibil Institute of Structural and Molecular Biology, Crystallography, Birkbeck College, London, UK.
Keywords	Cryoelectron Microscopy, DegQ protein, E coli (3.4.21.-), Escherichia coli (enzymology), Escherichia coli Proteins (chemistry), Models, Molecular, Molecular Chaperones (chemistry), Muramidase (chemistry, 3.2.1.17), Protein Multimerization, Protein Structure, Quaternary, Serine Endopeptidases (chemistry, 3.4.21.-)
Links	DOI: 10.1038/nsmb.2210, PubMed: 22245966, PMC: PMC3272482

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 = 420 A , B = 420 A , C = 420 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees

Pixel Spacing

X = 1.4 A , Y = 1.4 A , Z = 1.4 A

CCP4 map header info

Annotation Details

Symmetrized cryo-EM reconstruction of Escherichia coli DegQ 24-mer in complex with beta-casein substrates

Sample
Name	Escherichia coli DegQ 24-mer in complex with beta-casein
Number of Components	2
Oligomeric State	Beta-casein monomers bound to one DegQ 24-mer
Theoretical Mass	1.1 MDa
Details	The exact molecular weight of the complex is unknown as it is not known how many beta-casein substrates are bound
Mass-estimation Method	Size exclusion chromatography
Experimental Mass	1.1 MDa
Component #1: protein - DegQ
Scientific name	DegQ
Theoretical Mass	0.045 MDa
Experimental Mass	0.045 MDa
Oligomeric Details	24-mer
Number of Copies	24
Scientific Name of Species	Escherichia coli (NCBI Taxonomy: 562)
Strain	K12
Recombinant expression	Yes
Natural Source	Cell Location: Periplasm
Engineered Source	Exp System: Escherichia coli (NCBI Taxonomy: 562) Vector: pET26b
Component #2: protein - Beta-casein
Scientific name	Beta-casein
Theoretical Mass	0.024 MDa
Experimental Mass	0.024 MDa
Oligomeric Details	Monomer
Scientific Name of Species	Bos taurus (NCBI Taxonomy: 9913)
Common Name of Species	Bovine
Recombinant expression	No
Links	InterPro: IPR:016345

Experiment
Sample Preparation
Specimen Conc	0.2 mg/ml
Specimen Support Details	C-flat grids (CF-2/2-4C-100 Protochips)
Specimen State	particle
Buffer	Details: 20 mM HEPES/NaOH, 150 mM NaCl pH: 7.5
Vitrification
Method	Blot for 2 seconds before plunging
Cryogen Name	ETHANE
Details	Vitrification instrument: Manual plunger
Instrument	HOMEMADE PLUNGER
Imaging
Microscope	FEI TECNAI F20
Details	Low dose mode
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	200 kV
Electron Dose	15 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 50000 X, Calibrated: 50000 X
Astigmatism	objective lens astigmatism was corrected at 150,000 times magnification
Nominal Cs	2 mm
Imaging Mode	BRIGHT FIELD
Defocus	1000 nm - 3000 nm
Specimen Holder
Holder	Single tilt cryo ( GATAN LIQUID NITROGEN )
Tilt Angle	0 degrees - 0 degrees
Temperature	91 Kelvin ( 90 Kelvin - 92 Kelvin )
Camera
Detector	Kodak SO163 film
Image Acquisition
Scanner	ZEISS SCAI
Number of Digital Images	100
Sampling Size	7 microns
Quant Bit Number	8

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	Common line, projection matching
Software	IMAGIC-5, SPIDER
CTF Correction	Phase flipping, full CTF correction
Resolution By Author	7.5
Resolution Method	FSC at 0.5 cut-off
Single Particle
Number of Projections	9848
Atomic Model Fitting
Model #0
Refinement Space	REAL
Software	Chimera, Flex-EM
Target Criteria	Cross-correlation, energy
Details	Protocol: Rigid body and flexible fitting. Protease and PDZ1 trimers extracted from pdb entry 3STJ.
Refinement Protocol	flexible
Model #1
Refinement Space	REAL
Details	Protocol: Rigid body and flexible fitting. Protease and PDZ1 trimers extracted from pdb entry 3STJ.
Software	Chimera, Flex-EM
Refinement Protocol	flexible
Target Criteria	Cross-correlation, energy
Model #2
Refinement Protocol	flexible
Target Criteria	Cross-correlation, energy
Details	Protocol: Rigid body and flexible fitting. Protease and PDZ1 trimers extracted from pdb entry 3STJ.
Refinement Space	REAL
Software	Chimera, Flex-EM
Model #3
Refinement Protocol	rigid body
Target Criteria	Cross-correlation, energy
Details	Protocol: Rigid body. PDZ2 domain modelled with MODELLER from E. coli DegP pdb entry 3CS0.
Refinement Space	REAL
Software	MODELLER, Chimera, Flex-EM
Fitted Coordinate
PDB entry ID	PDB-4a9g

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), 3.4 MB .webm (WebM/VP8 format), 5.4 MB Session file for UCSF-Chimera, 26.4 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.2 MB .webm (WebM/VP8 format), 4.9 MB Session file for UCSF-Chimera, 26.5 KB

movie #3

	.mp4 (H.264/MPEG-4 AVC format), 3.7 MB .webm (WebM/VP8 format), 5.7 MB Session file for UCSF-Chimera, 1.8 MB