EMDB-1982: Symmetrized cryo-EM reconstruction of E. coli DegQ 12-...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1982
Title	Symmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in complex with lysozymes
Map	Symmetrized cryo-EM map of Escherichia coli DegQ 12-mer in complex with lysozymes
Sample	Escherichia coli DegQ 12-mer in complex with lysozyme substrates
Keywords	Chaperone, Protease
Authors	Malet H, Canellas F, Sawa J, Yan J, Thalassinos K, Ehrmann M, Clausen T, Saibil HR
Date	Deposition: 2011-11-06, Header release: 2011-12-07, Map release: 2011-12-21, Last update: 2012-02-03
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 0.1, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 0.1, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-4a8b, Surface level: 0.1, Made by UCSF CHIMERA
Supplemental images	emd-1982.tif
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	PDB-4a8b CiteFit EMDB-1981 Cite EMDB-1983 Cite EMDB-1984 Cite PDB-4a8a Cite PDB-4a8c Cite PDB-4a8d Cite PDB-4a9g Cite Cite: data citing same article Fit: output model of fitting
Similar strucutres (beta)	Diagram EMDB-1981 PDB-4a8a EMDB-1505 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= B= C: 358.4 A
Alpha=beta=gamma: 90 degrees

Pixel Spacing

X= Y= Z: 2.8 A

CCP4 map header info

Annotation Details

Symmetrized cryo-EM map of Escherichia coli DegQ 12-mer in complex with lysozymes

Sample
Name	Escherichia coli DegQ 12-mer in complex with lysozyme substrates
Number of Components	2
Oligomeric State	Six lysozyme monomers bound to one DegQ 12-mer
Theoretical Mass	0.625MDa
Details	-
Mass-estimation Method	Native mass spectrometry, size exclusion chromatography
Experimental Mass	0.625MDa
Component #1: protein - DegQ
Scientific name	DegQ
Theoretical Mass	0.045 MDa
Experimental Mass	0.045 MDa
Oligomeric Details	Dodecamer
Number of Copies	12
Scientific Name of Species	Escherichia coli
NCBI taxonomy	562
Strain	K-12
Recombinant expression	Yes
Natural Source	Cell Location: Periplasm
Engineered Source	NCBI taxonomy: 562 Expression system: Escherichia coli Vector: pET26b
Component #2: protein - Lysozyme
Scientific name	Lysozyme
Theoretical Mass	0.0143 MDa
Experimental Mass	0.0143 MDa
Oligomeric Details	Monomer
Number of Copies	6
Scientific Name of Species	Gallus gallus
Common Name of Species	Chicken
NCBI taxonomy	9031
Recombinant expression	No
Natural Source	Organ Or Tissue: Egg white
Links	Inter Pro: IPR:002152, Gene Ontology: GO:0003796

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, Calibrated: 50000
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
Model	GATAN LIQUID NITROGEN
Tilt Angle	0 degrees - 0 degrees
Temperature	91 K ( 90 - 92 K)
Camera
Detector	Kodak SO163 film
Image Acquisition
Scanner	ZEISS SCAI
Sampling Size	7
Quant Bit Number	8

Processing
Method	single particle reconstruction
3D reconstruction
Algorithm	Common line, projection matching
Software	IMAGIC-5, SPIDER
CTF Correction	Phase flipping
Resolution By Author	13 A
Resolution Method	FSC at 0.5 cut-off
Single Particle
Number of Projections	13432
Atomic Model Fitting
Model #0
Details	Protocol: Rigid body and flexible fitting. Protease and PDZ1 trimers extracted from pdb entry 3STJ.
Refinement Protocol	flexible
Refinement Space	REAL
Target Criteria	Cross-correlation, energy
Software	Chimera, Flex-EM
PDB Entry ID	3STJ PDB-3stj
PDB Chain ID	3STJ_A, 3STJ_B, 3STJ_C
Model #1
Refinement Space	REAL
Target Criteria	Cross-correlation, energy
Refinement Protocol	rigid body
Details	Protocol: Rigid body fitting. PDZ2 domain modelled with MODELLER.
Software	MODELLER, Chimera, Flex-EM
PDB Entry ID	3CS0 PDB-3cs0
Model #2
Details	Protocol: Rigid body
Software	Flex-EM
Refinement Protocol	rigid body
Target Criteria	Cross-correlation, energy
Refinement Space	REAL
PDB Entry ID	1DPX PDB-1dpx
PDB Chain ID	1DPX_A
Fitted Coordinate
PDB entry ID	PDB-4a8b