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Symmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in complex with a binding peptide

by single particle reconstruction, at 7.5 A resolution

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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-1983, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 4a8c
TitleSymmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in complex with a binding peptide
DescriptorPERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ (E.C.3.4.21.107)
KeywordsHYDROLASE, CHAPERONE
AuthorsMalet, H., Canellas, F., Sawa, J., Yan, J., Thalassinos, K., Ehrmann, M., Clausen, T., Saibil, H.R.
DateDeposition: 2011-11-20, Release: 2012-01-11
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Compound detailsENGINEERED 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
MoviesMovie Page

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-1983, Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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EMDB-1983

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Article
Citation - primary
ArticleNat. Struct. Mol. Biol., Vol. 19, Issue 2, Page 152-7, Year 2012
TitleNewly folded substrates inside the molecular cage of the HtrA chaperone DegQ.
AuthorsHélène 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.
KeywordsCryoelectron 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.-)
LinksDOI: 10.1038/nsmb.2210, PubMed: 22245966, PMC: PMC3272482
Components
ID 1 : PROTEASE DO, DEGQ
Image
DescriptionPERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
Typepolypeptide(L)
MutationYES
Formula weight45543.152 Da
Number of molecules12
ID1
Ec3.4.21.107
SourceMethod: Isolated from a genetically manipulated source
Gene: K-12, ID:83333, ESCHERICHIA COLI
Host: ID:469008, ESCHERICHIA COLI

, BL21(DE3), PET26B, PLASMID
LinksUniProt: P39099, Sequence view
Sample
Assembly
Aggregation statePARTICLE
NameESCHERICHIA COLI DEGQ 12- MER IN COMPLEX WITH A BINDING PEPTIDE
Buffer
Name20 MM HEPES/NAOH, 150 MM NACL
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE
Sample preparation
pH7.5
Sample concentration0.2 mg/ml
Sample support
DetailsCARBON
Vitrification
DetailsVITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- MANUAL PLUNGER, METHOD- BLOT FOR 2 SECONDS BEFORE PLUNGING,
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TECNAI F20
DetailsLOW DOSE MODE
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage200 kV
Electron dose15 e/A**2
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 50000 X, Nominal: 50000 X
CsNominal: 2 mm
Nominal defocusMax: 3000 nm, Min: 1000 nm
Specimen holder
Tilt angleMin: -0.1 degrees, Max: 0 degrees
Temperature91 Kelvin
Detector
TypeKODAK SO163 FILM
Image scans
Number digital images110
Processing
2D projection selection
Number of particles29432
Software nameIMAGIC-5, SPIDER
Single particle entity
Symmetry typeMIXED SYMMETRY
3D reconstruction
Actual pixel size1.4 A/pix
CTF correction methodPHASE FLIPPING, FULL CTF CORRECTION
DetailsDEGQ 12-MER WERE OBTAINED IN PRESENCE OF A PEPTIDE. THE PEPTIDE SEQUENCE IS SPMFKGVLDMMYGGMRGYQV THE NUMBER OF PEPTIDES BOUND TO DEGQ 12-MER IS UNKNOWN. THE PEPTIDES ARE NOT MODELLED DUE TO THE RESOLUTION OF THE MAP. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1983. (DEPOSITION ID: 10374).
MethodCOMMON LINE, PROJECTION MATCHING
Nominal pixel size1.4 A/pix
Resolution7.5 A
3D fitting
MethodRIGID BODY AND FLEXIBLE FITTING
Refinement ProtocolX-RAY
Refinement SpaceREAL
Target criteriaCROSS-CORRELATION, ENERGY
3D fitting list
3D Fitting ID1
PDB entry ID3STJ
Refine
Refine idELECTRON MICROSCOPY
Ls d res high7.50 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high7.50
Total atoms4740
Protein atoms4740
Download
PDB format
Allpdb4a8c.ent.gz
pdb4a8c.ent (uncompressed file)
Header onlypdb4a8c.ent.gz
mmCIF format
mmCIF4a8c.cif.gz
XML format
All4a8c.xml.gz
No-atom4a8c-noatom.xml.gz
Ext-atom4a8c-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.9 MB
.webm (WebM/VP8 format), 4.1 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.7 MB