PDB-4a8a: Asymmetric cryo-EM reconstruction of E. coli DegQ 12-me...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 4a8a
Title	Asymmetric cryo-EM reconstruction of E. coli DegQ 12-mer in complex with lysozyme
Descriptor	PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ (E.C.3.4.21.107) LYSOZYME C (E.C.3.2.1.17)
Keywords	HYDROLASE/HYDROLASE, HYDROLASE-HYDROLASE COMPLEX, CHAPERONE
Authors	Malet, H., Canellas, F., Sawa, J., Yan, J., Thalassinos, K., Ehrmann, M., Clausen, T., Saibil, H.R.
Date	Deposition: 2011-11-20, Release: 2011-12-28
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Compound details	ENGINEERED RESIDUE IN CHAIN A, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN C, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN D, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN E, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN F, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN G, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN H, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN I, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN J, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN K, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN L, SER 214 TO ALA
Structure Visualization
Movies	Movie Page #1: Depositted structure unit, Made by Jmol #2: Superimposing with EM 3D map: EMDB-1981, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1981 CiteFit EMDB-1982 Cite EMDB-1983 Cite EMDB-1984 Cite PDB-4a8b Cite PDB-4a8c Cite PDB-4a8d Cite PDB-4a9g Cite PDB-132l PDB-193l PDB-194l PDB-1a2y PDB-1aki PDB-1at5 PDB-1at6 PDB-1azf PDB-1b0d PDB-1b2k PDB-1bgi PDB-1bhz PDB-1bvk PDB-1bvx PDB-1bwh PDB-1bwi PDB-1bwj PDB-1c08 PDB-1c10 PDB-1dpw PDB-1dpx PDB-1dqj PDB-1e8l PDB-1f0w PDB-1f10 PDB-1f3j PDB-1fdl PDB-1flq PDB-1flu PDB-1flw PDB-1fly PDB-1fn5 PDB-1g7h PDB-1g7i PDB-1g7j PDB-1g7l PDB-1g7m PDB-1gpq PDB-1gwd PDB-1gxv PDB-1gxx PDB-1h6m PDB-1h87 PDB-1hc0 PDB-1hel PDB-1hem PDB-1hen PDB-1heo PDB-1hep PDB-1heq PDB-1her PDB-1hew PDB-1hf4 PDB-1hsw PDB-1hsx PDB-1ic4 PDB-1ic5 PDB-1ic7 PDB-1iee PDB-1io5 PDB-1ioq PDB-1ior PDB-1ios PDB-1iot PDB-1ir7 PDB-1ir8 PDB-1ir9 PDB-1j1o PDB-1j1p PDB-1j1x PDB-1ja2 PDB-1ja4 PDB-1ja6 PDB-1ja7 PDB-1jis PDB-1jit PDB-1jiy PDB-1jj0 PDB-1jj1 PDB-1jj3 PDB-1jpo PDB-1jto PDB-1jtt PDB-1kip PDB-1kiq PDB-1kir PDB-1kxw PDB-1kxx PDB-1kxy PDB-1lcn PDB-1lj3 PDB-1lj4 PDB-1lje PDB-1ljf PDB-1ljg PDB-1ljh PDB-1lji PDB-1ljj PDB-1ljk PDB-1lkr PDB-1lks PDB-1lma PDB-1lpi PDB-1lsa PDB-1lsb PDB-1lsc PDB-1lsd PDB-1lse PDB-1lsf PDB-1lsg PDB-1lsm PDB-1lsn PDB-1lsy PDB-1lsz PDB-1lyo PDB-1lys PDB-1lyz PDB-1lz8 PDB-1lz9 PDB-1lza PDB-1lzb PDB-1lzc PDB-1lzd PDB-1lze PDB-1lzg PDB-1lzh PDB-1lzn PDB-1lzt PDB-1mel PDB-1mlc PDB-1n4f PDB-1nby PDB-1nbz PDB-1ndg PDB-1ndm PDB-1p2c PDB-1ps5 PDB-1qio PDB-1qtk PDB-1rcm PDB-1rfp PDB-1ri8 PDB-1rjc PDB-1sf4 PDB-1sf6 PDB-1sf7 PDB-1sfb PDB-1sfg PDB-1sq2 PDB-1t3p PDB-1t6v PDB-1ua6 PDB-1uc0 PDB-1uco PDB-1uia PDB-1uib PDB-1uic PDB-1uid PDB-1uie PDB-1uif PDB-1uig PDB-1uih PDB-1uuz PDB-1v7s PDB-1v7t PDB-1vat PDB-1vau PDB-1vdp PDB-1vdq PDB-1vds PDB-1vdt PDB-1ved PDB-1vfb PDB-1w6z PDB-1wtm PDB-1wtn PDB-1xei PDB-1xej PDB-1xek PDB-1xfp PDB-1xgp PDB-1xgq PDB-1yik PDB-1yil PDB-1ykx PDB-1yky PDB-1ykz PDB-1yl0 PDB-1yl1 PDB-1yqv PDB-1z55 PDB-1zmy PDB-2a6u PDB-2a7d PDB-2a7f PDB-2aub PDB-2b5z PDB-2blx PDB-2bly PDB-2bpu PDB-2c8o PDB-2c8p PDB-2cds PDB-2cgi PDB-2d4i PDB-2d4j PDB-2d4k PDB-2d6b PDB-2d91 PDB-2fbb PDB-2hfm PDB-2iff PDB-2lym PDB-2lyo PDB-2lyz PDB-2lzh PDB-2lzt PDB-2vb1 PDB-2w1l PDB-2w1m PDB-2w1x PDB-2w1y PDB-2war PDB-2x0a PDB-2xbr PDB-2xbs PDB-2xjw PDB-2xth PDB-2ybh PDB-2ybi PDB-2ybj PDB-2ybl PDB-2ybm PDB-2ybn PDB-2ydg PDB-3hfm PDB-3lym PDB-3lyo PDB-3lyt PDB-3lyz PDB-3lzt PDB-3zvq PDB-4a7d PDB-4lym PDB-4lyo PDB-4lyt PDB-4lyz PDB-4lzt PDB-5lym PDB-5lyt PDB-5lyz PDB-6lyt PDB-6lyz PDB-7lyz PDB-8lyz PDB-9lyz Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-4a8c EMDB-1983 EMDB-2096 EMDB-2097 EMDB-1981 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

Components
ID 1 : PROTEASE DO, DEGQ
Image
Description	PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
Type	polymer
Mutation	YES
Formula weight	45543.152 Da
Number of molecules	12
Ec	3.4.21.107
Source	Method: Isolated from a genetically manipulated source Gene: K-12, PERIPLASM, ID:83333, ESCHERICHIA COLI Host: ID:469008, ESCHERICHIA COLI , BL21(DE3), PET26B, PLASMID
Links	UniProt: P39099, Sequence view
ID 2 : 1,4-BETA-N-ACETYLMURAMIDASE C, ALLERGEN GAL D IV, GAL D 4
Image
Description	LYSOZYME C
Type	polymer
Formula weight	14331.238 Da
Number of molecules	1
Ec	3.2.1.17
Source	Method: Isolated from a natural source Common name: CHICKEN NCBI taxonomy: ID:9031 Organism scientific: GALLUS GALLUS Tissue: EGG WHITE
Links	UniProt: P00698, Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Details	QUALITY OF THE MICROGRAPH CHECKED WITH THE CTF
Name	ESCHERICHIA COLI DEGQ GALLUS GALLUS LYSOZYME
Buffer
Name	20 MM HEPES/NAOH, 150 MM NACL
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE
Sample preparation
pH	7.5
Sample concentration	0.2 mg/ml
Sample support
Details	CARBON
Vitrification
Details	VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- MANUAL PLUNGER, METHOD- BLOT FOR 2 SECONDS BEFORE PLUNGING,

Electron Microscopy
Imaging
Microscope	model: 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
Mode	BRIGHT FIELD
Magnification	calibrated: 50000 X, nominal: 50000 X
Cs	nominal: 2 mm
Nominal defocus	max: 3000 nm, min: 1000 nm
Specimen holder
Tilt angle	min: -0.1 degrees, max: 0 degrees
Temperature	91 Kelvin
Detector
Type	KODAK SO163 FILM
Image scans
Number digital images	100

Processing
2D projection selection
Number of particles	13432
Software name	IMAGIC-5, SPIDER
Single particle entity
Symmetry type	MIXED SYMMETRY
3D reconstruction
Actual pixel size	2.8 A/pix
CTF correction method	PHASE FLIPPING
Details	SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1981. (DEPOSITION ID: 10364).
Method	COMMON LINE, PROJECTION MATCHING
Nominal pixel size	2.8 A/pix
Resolution	14.2 A
3D fitting
Method	RIGID BODY AND FLEXIBLE FITTING
Refinement Protocol	X-RAY
Refinement Space	REAL
Target criteria	CROSS-CORRELATION, ENERGY
3D fitting list
PDB entry ID	3STJ PDB-3stj
Refine
Ls d res high	14.20 A
ID	1
Refine hist
D res high	14.20
Total atoms	4749
Protein atoms	4749