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- PDB-2bk1: The pore structure of pneumolysin, obtained by fitting the alpha ... -

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Entry
Database: PDB / ID: 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
Specimen sourceClostridium perfringens / bacteria / C. Welchii, ウェルシュ菌, クロストリジウム・パーフリンゲンス
MethodElectron microscopy (29 A resolution / Single particle / Vitreous ice)
AuthorsTilley, S.J. / Orlova, E.V. / Gilbert, R.J.C. / Andrew, P.W. / Saibil, H.R.
CitationCell, 2005, 121, 247-256

primary. Cell, 2005, 121, 247-256 StrPapers
Structural basis of pore formation by the bacterial toxin pneumolysin.
Sarah J Tilley / Elena V Orlova / Robert J C Gilbert / Peter W Andrew / Helen R Saibil

#1. Cell(Cambridge,Mass.), 1997, 89, 685- StrPapers
Structure of a Cholesterol-Binding, Thiol-Activated Cytolysin and a Model of its Membrane Form
Rossjohn, J. / Feil, S.C. / Mckinstry, W.J. / Tweten, R.K. / Parker, M.W.

DateDeposition: Feb 10, 2005 / Release: May 4, 2005 / Last modification: Jan 16, 2013

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-1107
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  • Simplified surface model + fitted atomic model
  • EMDB-1108
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Assembly

Deposited unit
A: PERFRINGOLYSIN O


Theoretical massNumber of molelcules
Total (without water)50,0961
Polyers50,0961
Non-polymers00
Water0
#1
A: PERFRINGOLYSIN O
x 38


Theoretical massNumber of molelcules
Total (without water)1,903,66738
Polyers1,903,66738
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation38
#2


  • idetical with deposited unit in distinct coordinate
  • point asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
PAU


  • idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

#1: Polypeptide(L)PERFRINGOLYSIN O / THETA-TOXIN / THIOL-ACTIVATED CYTOLYSIN


Mass: 50096.496 Da / Num. of mol.: 1 / Fragment: RESIDUES 53-500
Source: (gene. exp.) Clostridium perfringens / bacteria / C. Welchii, ウェルシュ菌, クロストリジウム・パーフリンゲンス
References: UniProt: P19995

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE

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Sample preparation

Assembly of specimenName: PNEUMOLYSIN / Aggregation state: PARTICLE
Details: THE SAMPLE CONSISTS OF PNEUMOLYSIN IN A MEMBRANE-INSERTED PORE STATE
Buffer solutionName: 8 MM NA2HP04, 1.5MM KH2PO4, 2.5 MM KCL, 0.25 MM NACL
Sample preparationSample conc.: 0.05 mg/ml
Specimen supportDetails: HOLEY CARBON
VitrificationDetails: PLUNGED INTO ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TECHNAI F20
Details: SAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE.
Electron gunElectron source: FEG / Accelerating voltage: 200 kV / Electron dose: 2000 e/A2 / Illumination mode: LOW DOSE
Electron lensMode: BRIGHT FIELD / Nominal magnification: 42000 X / Nominal defocus max: 3200 nm / Nominal defocus min: 1100 nm / Cs: 2 mm
Specimen holderTemperature: 100 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
CameraType: KODAK SO-163 FILM
EM image scansNumber digital images: 135
Radiation wavelengthRelative weight: 1

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Processing

Image selectionNumber of particles: 88
EM single particle entitySymmetry type: CYCLIC
3D reconstructionResolution: 29 A / Nominal pixel size: 3.5 A/pix / CTF correction method: PHASE FLIPPING
Details: RESIDUES 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.
Atomic model buildingMethod: THE 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.
Atomic model buildingPDB-ID: 1PFO
Least-squares processHighest resolution: 29 A
Refine hist #LASTHighest resolution: 29 A
Number of atoms included #LASTProtein: 444 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 444

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