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The pore structure of pneumolysin, obtained by fitting the alpha carbon trace of perfringolysin O into a cryo-EM map

by single particle reconstruction, at 29 A resolution

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#1: Biological unit as complete point assembly, Made by Jmol

#2: Depositted structure unit, Made by Jmol

#3: Superimposing with simplified surface model of EM map, EMDB-1107, Made by Jmol

#4: Superimposing with simplified surface model of EM map, EMDB-1108, Made by Jmol

#5: Superimposing with EM 3D map: EMDB-1107, Made by UCSF CHIMERA

#6: Superimposing with EM 3D map: EMDB-1108, Made by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 2bk1
TitleThe pore structure of pneumolysin, obtained by fitting the alpha carbon trace of perfringolysin O into a cryo-EM map
DescriptorPERFRINGOLYSIN O
KeywordsTOXIN, CYTOLYSIS, HEMOLYSIS, THIOL-ACTIVATED CYTOLYSIN, CRYOEM, CYTOLYTIC PROTEIN
AuthorsTilley, S.J., Orlova, E.V., Gilbert, R.J.C., Andrew, P.W., Saibil, H.R.
DateDeposition: 2005-02-10, Release: 2005-05-04
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

#1: Biological unit as complete point assembly, Made by Jmol

#2: Depositted structure unit, Made by Jmol

#3: Superimposing with simplified surface model of EM map, EMDB-1107, Made by Jmol

#4: Superimposing with simplified surface model of EM map, EMDB-1108, Made by Jmol

#5: Superimposing with EM 3D map: EMDB-1107, Made by UCSF CHIMERA

#6: Superimposing with EM 3D map: EMDB-1108, Made by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries

EMDB-1107

CiteFit

EMDB-1108

CiteFit

Cite: data citing same article

Fit: target map of fitting

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - primary
ArticleCell, Vol. 121, Issue 2, Page 247-56, Year 2005
TitleStructural basis of pore formation by the bacterial toxin pneumolysin.
AuthorsSarah J Tilley, Elena V Orlova, Robert J C Gilbert, Peter W Andrew, Helen R Saibil
School of Crystallography and Institute of Structural Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom.
KeywordsBacterial Outer Membrane Proteins (chemistry), Bacterial Proteins (chemistry), Cell Membrane (chemistry), Cholesterol (chemistry), Cryoelectron Microscopy, Liposomes (chemistry), Protein Structure, Quaternary, Protein Structure, Tertiary, Streptococcus pneumoniae (chemistry), Streptolysins (chemistry), plY protein, Streptococcus pneumoniae
LinksPII: S0092-8674(05)00232-1, DOI: 10.1016/j.cell.2005.02.033, PubMed: 15851031
Citation - 1
ArticleCell, Vol. 89, Issue 5, Page 685-92, Year 1997
TitleStructure of a cholesterol-binding, thiol-activated cytolysin and a model of its membrane form.
AuthorsJ Rossjohn, S C Feil, W J McKinstry, R K Tweten, M W Parker
The Ian Potter Foundation Protein Crystallography Laboratory, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia.
KeywordsCell Membrane (chemistry), Cholesterol (chemistry), Cytotoxins (chemistry), Membranes, Artificial, Models, Molecular, Protein Binding, Protein Folding, Sulfhydryl Compounds (metabolism)
LinksPubMed: 9182756, PII: S0092-8674(00)80251-2
Components
ID 1 : THETA-TOXIN, THIOL-ACTIVATED CYTOLYSIN
Image
DescriptionPERFRINGOLYSIN O
Typepolypeptide(L)
FragmentRESIDUES 53-500
Formula weight50096.496 Da
Number of molecules1
ID1
SourceMethod: Isolated from a genetically manipulated source
Gene: ID:1502, CLOSTRIDIUM PERFRINGENS
Host: ID:562, ESCHERICHIA COLI

LinksUniProt: P19995, Sequence view
Sample
Assembly
Aggregation statePARTICLE
DetailsTHE SAMPLE CONSISTS OF PNEUMOLYSIN IN A MEMBRANE-INSERTED PORE STATE
NamePNEUMOLYSIN
Buffer
Name8 MM NA2HP04, 1.5MM KH2PO4, 2.5 MM KCL, 0.25 MM NACL
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE
Sample preparation
Sample concentration0.05 mg/ml
Sample support
DetailsHOLEY CARBON
Vitrification
DetailsPLUNGED INTO ETHANE
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TECHNAI F20
DetailsSAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE.
Electron gun
Electron sourceFEG
Accelerating voltage200 kV
Electron dose2000 e/A**2
Illumination modeLOW DOSE
Lens
ModeBRIGHT FIELD
MagnificationNominal: 42000 X
CsNominal: 2 mm
Nominal defocusMax: 3200 nm, Min: 1100 nm
Specimen holder
Tilt angleMin: 0 degrees, Max: 0 degrees
Temperature100 Kelvin
Detector
TypeKODAK SO-163 FILM
Image scans
Number digital images135
Processing
2D projection selection
Number of particles88
Single particle entity
Symmetry typeCYCLIC
3D reconstruction
CTF correction methodPHASE FLIPPING
DetailsRESIDUES 134-142 ARE MISSING FROM THE SEQUENCE. RESIDUES CORRESPONDING TO TO TM1 AND TM2 (187-220,284-315) WERE MODELLED AS A POLY-ALANINE FLAT BETA HAIRPINS. THE OLIGOMER CAN BE GENERATED BY APPLYING 38-FOLD ROTATIONAL SYMMETRY.
Nominal pixel size3.5 A/pix
Resolution29.00 A
3D fitting
MethodTHE CRYSTAL STRUCTURE OF PERFRINOGLYSIN O (1PFO, ROSSJOHN ET AL., 1998, CELL 89, 685)WAS PLACED INTO THE CRYO-EM DENSITY MAP (EMD-1107). THE ALPHA CARBON TRACE OF PERFRINGOLYSIN 0 WAS MANUALLY POSITIONED INTO THE CRYO-EM DENSITY CORRESPONDING TO THE POSITION OF ONE SUBUNIT. THE BEST FIT WAS OBTAINED BY SEPARATING THE MONOMER INTO SIX RIGID BODIES: DOMAIN 1(91-172, 231-272 354-373), DOMAIN 2 UPPER (53- 62, 83-90, 374-381), DOMAIN 2 LOWER (63-82, 382-390), DOMAIN 3 (177-186, 221-230, 273-283, 316-353), DOMAIN 3 HAIRPINS (187- 220, 284-315), AND DOMAIN 4 (391-500). THE COMPLETE OLIGOMER (38-MER) WAS GENERATED AND CHECKED FOR CLOSE CONTACTS BOTH BY EYE AND USING THE CCP4 PROGRAM CONTACT.TO IMPROVE THE FIT SECTIONS CORRESPONDING TO 3 SUBUNITS WERE EXTRACTED FROM THE 38-MER MAP (EMD-1107) AND A 44-MER MAP AND ALIGNED. THE WEIGHTED AVERAGE WAS CALCULATED AND THE IMPROVED MAP USED FOR THE FINAL MANUAL FITTING. THE TWO SECTIONS ARE CONSISTENT TO A RESOLUTION OF 28 ANGSTROMS (0.5 CORRELATION FSC) AND THE WEIGHTED AVERAGE MAP WAS RECONSTRUCTED FROM 131 PARTICLES.
3D fitting list
3D Fitting ID1
PDB entry ID1PFO
Refine
Refine idELECTRON MICROSCOPY
Ls d res high29.00 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high29.00
Total atoms444
Protein atoms444
Download
PDB format
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pdb2bk1.ent (uncompressed file)
Header onlypdb2bk1.ent.gz
mmCIF format
mmCIF2bk1.cif.gz
XML format
All2bk1.xml.gz
No-atom2bk1-noatom.xml.gz
Ext-atom2bk1-extatom.xml.gz
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