[English] 日本語
Yorodumi
- EMDB-15957: Direct observation of the conformational state of formin mDia1 di... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15957
TitleDirect observation of the conformational state of formin mDia1 dimer along the actin filament
Map dataActin filament core encircled by a formin mDia1 dimer.
Sample
  • Complex: Actin barbed-end bound by formin mDia1 dimer in his "open state"
    • Organelle or cellular component: Formin mDia1 dimer
    • Organelle or cellular component: Alpha Actin subunits assembled in helicoidal F-actin filament
KeywordsActin binding protein / Complex / actin filament / formin / MOTOR PROTEIN
Biological speciesMus musculus (house mouse) / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / negative staining / Resolution: 30.0 Å
AuthorsMaufront J / Guichard B / Cao L / Di Cicco A / Jegou A / Romet-Lemonne G / Bertin A
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-16-CE11-0013-01 France
CitationJournal: Am J Public Health / Year: 1976
Title: Task delegation to physician extenders--some comparisons.
Abstract: This study uses a task delegation questionnaire to compare 1973 physician extender practices in seven primary care-oriented sites with a physician attitude survey made in 1969. One additional site ...This study uses a task delegation questionnaire to compare 1973 physician extender practices in seven primary care-oriented sites with a physician attitude survey made in 1969. One additional site using no physician extenders was included as a control. The study involves both major types of physician extenders (physician assistants and nurse practitioners) in ambulatory practices with at least one year of experience in using such personnel. With minor exceptions, actual task delegation patterns conform with the 1969 attitudes of physicians as to which tasks "could and should" be delegated to physician extenders.
History
DepositionOct 14, 2022-
Header (metadata) releaseDec 7, 2022-
Map releaseDec 7, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15957.png

Downloads & links

-
Map

FileDownload / File: emd_15957.map.gz / Format: CCP4 / Size: 18.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationActin filament core encircled by a formin mDia1 dimer.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.13 Å/pix.
x 170 pix.
= 362.1 Å		2.13 Å/pix.
x 170 pix.
= 362.1 Å		2.13 Å/pix.
x 170 pix.
= 362.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.13 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0129
Minimum - Maximum-0.025502361 - 0.06334296
Average (Standard dev.)0.0005592919 (±0.0033808304)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions170170170
Spacing170170170
CellA=B=C: 362.1 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_15957_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Actin filament core encircled by a formin mDia1 dimer.

Fileemd_15957_half_map_1.map
AnnotationActin filament core encircled by a formin mDia1 dimer.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Actin filament core encircled by a formin mDia1 dimer.

Fileemd_15957_half_map_2.map
AnnotationActin filament core encircled by a formin mDia1 dimer.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Actin barbed-end bound by formin mDia1 dimer in his "open state"

EntireName: Actin barbed-end bound by formin mDia1 dimer in his "open state"
Components
  • Complex: Actin barbed-end bound by formin mDia1 dimer in his "open state"
    • Organelle or cellular component: Formin mDia1 dimer
    • Organelle or cellular component: Alpha Actin subunits assembled in helicoidal F-actin filament

-
Supramolecule #1: Actin barbed-end bound by formin mDia1 dimer in his "open state"

SupramoleculeName: Actin barbed-end bound by formin mDia1 dimer in his "open state"
type: complex / ID: 1 / Parent: 0

-
Supramolecule #2: Formin mDia1 dimer

SupramoleculeName: Formin mDia1 dimer / type: organelle_or_cellular_component / ID: 2 / Parent: 1
Source (natural)Organism: Mus musculus (house mouse)

-
Supramolecule #3: Alpha Actin subunits assembled in helicoidal F-actin filament

SupramoleculeName: Alpha Actin subunits assembled in helicoidal F-actin filament
type: organelle_or_cellular_component / ID: 3 / Parent: 1
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation #1

Preparation ID1
Concentration0.04 mg/mL
BufferpH: 7.8
StainingType: NEGATIVE / Material: Uranyl Formate

-
Sample preparation #2

Preparation ID2
Concentration0.01 mg/mL
BufferpH: 7.8
StainingType: NEGATIVE / Material: Uranyl Formate

-
Electron microscopy

MicroscopeFEI TECNAI 20
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm

+
Image processing

Particle selectionNumber selected: 20919
Startup modelType of model: INSILICO MODEL
In silico model: Structural models of a formin dimer encircling actin filament was generated within UCSF Chimera based on FH2-actin atomic structure PDB 1Y64 and actin filament atomic structure PDB ...In silico model: Structural models of a formin dimer encircling actin filament was generated within UCSF Chimera based on FH2-actin atomic structure PDB 1Y64 and actin filament atomic structure PDB 5OOE then low-pass filtered at 50 angstrom.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 717
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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