[English] 日本語
Yorodumi
- EMDB-7793: Thermostablilized dephosphorylated chicken CFTR -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 7793
TitleThermostablilized dephosphorylated chicken CFTR
Map dataSharpened SuperRes PPase-treated chTS map w/o filter by local resolution
SampleCFTRCystic fibrosis transmembrane conductance regulator
  • Cystic fibrosis transmembrane conductance regulator
  • ligand
SourceGallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / 4.3 Å resolution
AuthorsFay JF / Riordan JR
CitationJournal: Biochemistry / Year: 2018
Title: Cryo-EM Visualization of an Active High Open Probability CFTR Anion Channel.
Authors: Jonathan F Fay / Luba A Aleksandrov / Timothy J Jensen / Liying L Cui / Joseph N Kousouros / Lihua He / Andrei A Aleksandrov / Drew S Gingerich / John R Riordan / James Z Chen
Validation ReportPDB-ID: 6d3r

SummaryFull reportAbout validation report
DateDeposition: Apr 16, 2018 / Header (metadata) release: May 30, 2018 / Map release: Oct 17, 2018 / Last update: Nov 7, 2018

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.28
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.28
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6d3r
  • Surface level: 0.28
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_7793.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
0.69 Å/pix.
= 275.462 Å
400 pix
0.69 Å/pix.
= 275.462 Å
400 pix
0.69 Å/pix.
= 275.462 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.68866 Å
Density
Contour Level:0.28 (by author), 0.28 (movie #1):
Minimum - Maximum-0.58422506 - 1.126942
Average (Standard dev.)0.0034539183 (0.035053395)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin0.00.00.0
Limit399.0399.0399.0
Spacing400400400
CellA=B=C: 275.46234 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6886550.6886550.688655
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z275.462275.462275.462
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.5841.1270.003

-
Supplemental data

-
Mask #1

Fileemd_7793_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

-
Sample components

-
Entire CFTR

EntireName: CFTR / Number of components: 3

-
Component #1: cellular-component, CFTR

Cellular-componentName: CFTRCystic fibrosis transmembrane conductance regulator
Recombinant expression: No
SourceSpecies: Gallus gallus (chicken)

-
Component #2: protein, Cystic fibrosis transmembrane conductance regulator

ProteinName: Cystic fibrosis transmembrane conductance regulator / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 162.637438 kDa
SourceSpecies: Gallus gallus (chicken)
Source (engineered)Expression System: Cricetinae (hamsters)

-
Component #3: ligand, ADENOSINE-5'-TRIPHOSPHATE

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 48 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image acquisition

Raw dataEMPIAR-10219 (Title: Cryo-electron microscopy data of thermostabilized avian CFTR
Data size: 10.0
Data #1: Binned Particle stacks and meta data for cryo-EM structures of phosphorylated and dephosphorylated avian CFTR [micrographs - single frame])

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 30219
3D reconstructionSoftware: cryoSPARC / Resolution: 4.3 Å / Resolution method: FSC 1/2 BIT CUT-OFF
FSC plot
(resolution estimation)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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

+
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

+
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

Read more

-
Yorodumi

Thousand views of thousand structures

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

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more