[English] 日本語
Yorodumi
- EMDB-2984: 2.2 A resolution cryo-EM structure of beta-galactosidase in compl... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 2984
Title2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant inhibitor
Keywordsnear-atomic resolution cryo-electron microscopy / single-particle cryo-EM / protein complexes / PETG
SampleEscherichia coli beta-galactosidase bound to phenylethyl beta-D-thiogalactopyranoside (PETG)
SourceEscherichia coli k-12 / bacteria / image: Escherichia coli
Unidentified
Map dataB-factor corrected reconstruction of PETG-bound beta-galactosidase.
Methodsingle particle reconstruction, at 2.2 A resolution
AuthorsBartesaghi A / Merk A / Banerjee S / Matthies D / Wu X / Milne J / Subramaniam S
CitationScience, 2015, 348, 1147-1151

Science, 2015, 348, 1147-1151 StrPapers
2.2 Å resolution cryo-EM structure of β-galactosidase in complex with a cell-permeant inhibitor.
Alberto Bartesaghi / Alan Merk / Soojay Banerjee / Doreen Matthies / Xiongwu Wu / Jacqueline L S Milne / Sriram Subramaniam

DateDeposition: Apr 26, 2015 / Header (metadata) release: May 6, 2015 / Map release: May 6, 2015 / Last update: Apr 26, 2015

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5a1a
  • Surface level: 0.05
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5a1a
  • Surface level: 0.05
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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

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

Downloads & links

-
Map

Fileemd_2984.map.gz (map file in CCP4 format, 97256 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
292 pix
0.64 A/pix
= 186.004 A
292 pix
0.64 A/pix
= 186.004 A
292 pix
0.64 A/pix
= 186.004 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 0.637 A
Density
Contour Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.12121183 - 0.17074034
Average (Standard dev.)-7.7E-6 (0.01674482)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions292292292
Origin000
Limit291291291
Spacing292292292
CellA=B=C: 186.00401 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z0.6370.6370.637
M x/y/z292292292
origin x/y/z0.0000.0000.000
length x/y/z186.004186.004186.004
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS292292292
D min/max/mean-0.1210.171-0.000

-
Supplemental data

-
Sample components

-
Entire Escherichia coli beta-galactosidase bound to phenylethyl beta-D-t...

EntireName: Escherichia coli beta-galactosidase bound to phenylethyl beta-D-thiogalactopyranoside (PETG)
Details: The sample was monodisperse. / Number of components: 2 / Oligomeric State: tetramer
MassTheoretical: 465 kDa
Measured by: ProtParam tool: Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D., Bairoch A., Protein Identification and Analysis Tools on the ExPASy Server, (in) John M. Walker (ed): The Proteomics Protocols Handbook, Humana Press (2005), pp. 571-607

-
Component #1: protein, beta-galactosidase

ProteinName: beta-galactosidase / a.k.a: beta-gal, b-gal / Oligomeric Details: tetramer / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 465 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli
Source (natural)Location in cell: cytoplasm
External referencesGene Ontology: GO: 0004565 / UniProt: UniProt: P00722

-
Component #2: ligand, phenylethyl beta-D-thiogalactopyranoside

LigandName: phenylethyl beta-D-thiogalactopyranoside / a.k.a: PETG / Oligomeric Details: monomer / Details: Molecular weight of PETG is 300.37 Da. / Recombinant expression: No / Number of Copies: 4
SourceSpecies: Unidentified

+
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 2.3 mg/ml
Buffer solution: 25 mM Tris, pH 8.0, 50 mM NaCl, 2 mM MgCl2, 1.0 mM TCEP
pH: 8
Support film200 mesh Quantifoil R2/2 grids, plasma cleaned
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Temperature: 90.15 K / Humidity: 90 % / Method: Blot for 2 seconds before plunging.

-
Electron microscopy imaging

ImagingMicroscope: FEI TITAN KRIOS / Date: Dec 15, 2014 / Details: Parallel beam illumination
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 45 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 215000 X (nominal), 215000 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 215,000 times magnification.
Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 600 - 2000 nm / Energy filter: Gatan, Inc. / Energy window: 0-20 eV
Specimen HolderHolder: Liquid nitrogen cooled / Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 79.7 K ( 79.6 - 79.8 K)
CameraDetector: GATAN K2 (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 1487
Details: Every image is the average of 38 frames recorded by the direct electron detector.
Raw dataEMPIAR-10061 (Name: Averages of aligned movie frames / Category: micrographs - single frame / Data size: 12.4 TB)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D2 (2*2 fold dihedral) / Number of projections: 41123
3D reconstructionAlgorithm: phase residual minimization / Software: FREALIGN / CTF correction: each particle
Details: Final map was obtained from 41,123 particles. D2 symmetry was applied throughout refinement. Map was corrected using a B-factor of -75 A^2.
Resolution: 2.2 A / Resolution method: FSC 0.143, semi-independent
FSC plot (resolution assessment)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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