[English] 日本語
Yorodumi
- PDB-2bk1: The pore structure of pneumolysin, obtained by fitting the alpha ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

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 Å resolution / Particle / Single particle)
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 Yorodumi Papers
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- Yorodumi Papers
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.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 10, 2005 / Release: May 4, 2005
RevisionDateData content typeGroupProviderType
1.0May 4, 2005Structure modelrepositoryInitial release
1.1Jan 16, 2013Structure modelVersion format compliance
1.2Apr 19, 2017Structure modelOther

-
Structure visualization

Movie
  • Biological unit as complete point assembly
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1107
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1108
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
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)1,903,64438
Polyers1,903,64438
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation38
#2


  • idetical with deposited unit in distinct coordinate
  • point asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
#3


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

-
Components

#1: Polypeptide(L)PERFRINGOLYSIN O / THETA-TOXIN / THIOL-ACTIVATED CYTOLYSIN / Coordinate model: Cα atoms only


Mass: 50095.902 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

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

-
Sample preparation

ComponentName: PNEUMOLYSIN / Type: COMPLEX
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
Details: 8 MM NA2HP04, 1.5MM KH2PO4, 2.5 MM KCL, 0.25 MM NACL
pH: 6.95
SpecimenConc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: PLUNGED INTO ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20
Details: SAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 42000 / Nominal defocus max: 3200 nm / Nominal defocus min: 1100 nm / Cs: 2 mm
Specimen holderTemperature: 100 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 135
Radiation wavelengthRelative weight: 1

-
Processing

CTF correctionDetails: PHASE FLIPPING
SymmetryPoint symmetry: C38
3D reconstructionResolution: 29 Å / Number of particles: 88 / Nominal pixel size: 3.5
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.
Symmetry type: POINT
Atomic model buildingDetails: METHOD--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.
Ref protocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 1PFO
Least-squares processHighest resolution: 29 Å
Refine hist #LASTHighest resolution: 29 Å
Number of atoms included #LASTProtein: 444 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 444

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more