[English] 日本語
Yorodumi
- EMDB-20532: Toll receptor EM map from Topaz picks -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20532
TitleToll receptor EM map from Topaz picks
Map dataSharpened map after CryoSparc 2.9 non-uniform refinement using DoG picks
Sample
  • Complex: Toll receptor
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsRapp M / Bepler T / Morin A / Brasch J / Shapiro L / Noble AJ / Berger B
Funding support United States, 9 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM081871 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01-MH114817 United States
National Science Foundation (NSF, United States)DGE-1644869 United States
Other privateSimons Foundation / SF349247 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM128303 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Other governmentNew York State Office of Science, Technology and Academic Research (NYSTAR) United States
National Institutes of Health/Office of the DirectorOD019994 United States
Other privateAgouron Institute / F00316 United States
CitationJournal: Nat Methods / Year: 2019
Title: Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs.
Authors: Tristan Bepler / Andrew Morin / Micah Rapp / Julia Brasch / Lawrence Shapiro / Alex J Noble / Bonnie Berger /
Abstract: Cryo-electron microscopy is a popular method for the determination of protein structures; however, identifying a sufficient number of particles for analysis can take months of manual effort. Current ...Cryo-electron microscopy is a popular method for the determination of protein structures; however, identifying a sufficient number of particles for analysis can take months of manual effort. Current computational approaches find many false positives and require ad hoc postprocessing, especially for unusually shaped particles. To address these shortcomings, we develop Topaz, an efficient and accurate particle-picking pipeline using neural networks trained with a general-purpose positive-unlabeled learning method. This framework enables particle detection models to be trained with few sparsely labeled particles and no labeled negatives. Topaz retrieves many more real particles than conventional picking methods while maintaining low false-positive rates, is capable of picking challenging unusually shaped proteins (for example, small, non-globular and asymmetric particles), produces more representative particle sets and does not require post hoc curation. We demonstrate the performance of Topaz on two difficult datasets and three conventional datasets. Topaz is modular, standalone, free and open source ( http://topaz.csail.mit.edu ).
History
DepositionJul 31, 2019-
Header (metadata) releaseSep 11, 2019-
Map releaseSep 11, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.53
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.53
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20532.png

Downloads & links

-
Map

FileDownload / File: emd_20532.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map after CryoSparc 2.9 non-uniform refinement using DoG picks
Voxel sizeX=Y=Z: 0.832 Å
Density
Contour LevelBy AUTHOR: 0.53 / Movie #1: 0.53
Minimum - Maximum-2.008821 - 3.3242455
Average (Standard dev.)0.0012220803 (±0.046381347)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8320.8320.832
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z266.240266.240266.240
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-2.0093.3240.001

-
Supplemental data

-
Mask #1

Fileemd_20532_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharpened map after CryoSparc 2.9 non-uniform refinement using...

Fileemd_20532_additional.map
AnnotationUnsharpened map after CryoSparc 2.9 non-uniform refinement using DoG picks
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharpened map after CryoSparc 2.9 non-uniform refinement using...

Fileemd_20532_additional_1.map
AnnotationUnsharpened map after CryoSparc 2.9 non-uniform refinement using DoG picks
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map after CryoSparc 2.9 non-uniform refinement using DoG picks

Fileemd_20532_half_map_1.map
AnnotationHalf map after CryoSparc 2.9 non-uniform refinement using DoG picks
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map after CryoSparc 2.9 non-uniform refinement using DoG picks

Fileemd_20532_half_map_2.map
AnnotationHalf map after CryoSparc 2.9 non-uniform refinement using DoG picks
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Toll receptor

EntireName: Toll receptor
Components
  • Complex: Toll receptor

-
Supramolecule #1: Toll receptor

SupramoleculeName: Toll receptor / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly) / Recombinant cell: S2
Molecular weightTheoretical: 105 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Average electron dose: 73.48 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 1010937 / Details: Topaz picking
CTF correctionSoftware:
Namedetails
CTFFIND (ver. 4)estimated
cryoSPARC (ver. 2.9)corrected

Details: Estimated with CTFFind4, applied with cryosparc 2.9
Startup modelType of model: OTHER / Details: Cryosparc 2.9 ab-initio reconstruction
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.9) / Details: Cryosparc 2.9 ab-initio reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.9) / Details: non-uniform refinement
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.9) / Number images used: 1006089
DetailsMotioncor2 frame aligned

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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