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

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
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 StrPapers
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

DateDeposition: Sep 24, 2016 / Header (metadata) release: Oct 26, 2016 / Map release: Apr 5, 2017 / Last update: Sep 24, 2016

-
Structure visualization

Movie
  • 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
3D viewer


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

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

emd_4118.png

Downloads & links

-
Map

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

Image control

Size
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour Level:0.0282 (by author), 0.02 (movie #1):
Minimum - Maximum-0.022703713 - 0.079944775
Average (Standard dev.)0.0008561607 (0.0045818426)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin000
Limit359359359
Spacing360360360
CellA=B=C: 504 Å
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
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

5aod


Chain ID: 5AOD_A
Output model

5ly6

+
About Yorodumi

-
News

-
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)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

+
Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

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