[English] 日本語
- EMDB-4118: CryoEM structure of the membrane pore complex of Pneumolysin at 4.5A -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 4118
TitleCryoEM structure of the membrane pore complex of Pneumolysin at 4.5A
SamplePneumolysin pore complex
SourceStreptococcus pneumoniae / bacteria / ストレプトコッカス・ニューモニアエ, 肺炎レンサ球菌
Map dataPLY pore complex
Methodsingle particle reconstruction, at 4.5 Å resolution
Authorsvan Pee K / Neuhaus A
CitationElife, 2017, 6

Elife, 2017, 6 Yorodumi Papers
CryoEM structures of membrane pore and prepore complex reveal cytolytic mechanism of Pneumolysin.
Katharina van Pee / Alexander Neuhaus / Edoardo D'Imprima / Deryck J Mills / Werner Kühlbrandt / Özkan Yildiz

Validation ReportPDB-ID: 5ly6

SummaryFull reportAbout validation report
DateDeposition: Sep 24, 2016 / Header (metadata) release: Oct 26, 2016 / Map release: Apr 5, 2017 / Last update: Aug 2, 2017

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5ly6
  • Surface level: 0.022
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5ly6
  • Imaged by Jmol
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_4118.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.4 Å/pix.
= 504. Å
360 pix
1.4 Å/pix.
= 504. Å
360 pix
1.4 Å/pix.
= 504. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.4 Å
Contour Level:0.0282 (by author), 0.02 (movie #1):
Minimum - Maximum-0.022703713 - 0.079944775
Average (Standard dev.)0.0008561607 (0.0045818426)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 504 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z504.000504.000504.000
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0230.0800.001

Supplemental data

Sample components

Entire Pneumolysin pore complex

EntireName: Pneumolysin pore complex / Number of components: 2
MassTheoretical: 2.2 MDa

Component #1: cellular-component, Pneumolysin pore complex

Cellular-componentName: Pneumolysin pore complex / Recombinant expression: No
MassTheoretical: 2.2 MDa
SourceSpecies: Streptococcus pneumoniae / bacteria / ストレプトコッカス・ニューモニアエ, 肺炎レンサ球菌
Source (engineered)Expression System: Escherichia coli bl21 / bacteria / image: Escherichia coli
Vector: pET15

Component #2: protein, Pneumolysin

ProteinName: Pneumolysin / Recombinant expression: No
MassTheoretical: 52.866066 kDa
Source (engineered)Expression System: Streptococcus pneumoniae serotype 2 (strain d39 / nctc 7466) / bacteria

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml / pH: 7
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.02 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C42 (42 fold cyclic) / Number of projections: 6461
3D reconstructionSoftware: RELION / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

Atomic model buiding

Modeling #1Refinement protocol: flexible
Input PDB model: 5AOD
Chain ID: 5AOD_A
Output model

About Yorodumi


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


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