[English] 日本語
Yorodumi
- EMDB-5463: Electron cryo-microscopy of WHAMM coiled-coil domain and MTs -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5463
TitleElectron cryo-microscopy of WHAMM coiled-coil domain and MTs
Map dataReconstruction of WHAMM coiled-coil domain with MTs
Sample
  • Sample: Helical structures of WHAMM coiled-coil and MTs
  • Protein or peptide: WHAMM coiled-coil with MTs
Keywordsactin nucleation / cryo-EM / membrane tubulation / microtubules / WHAMM
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 22.0 Å
AuthorsShen QT / Hsiue PP / Sinderlar CV / Welch MD / Wang HW / Campellone KG
CitationJournal: J Cell Biol / Year: 2012
Title: Structural insights into WHAMM-mediated cytoskeletal coordination during membrane remodeling.
Authors: Qing-Tao Shen / Peter P Hsiue / Charles V Sindelar / Matthew D Welch / Kenneth G Campellone / Hong-Wei Wang /
Abstract: The microtubule (MT) and actin cytoskeletons drive many essential cellular processes, yet fairly little is known about how their functions are coordinated. One factor that mediates important cross ...The microtubule (MT) and actin cytoskeletons drive many essential cellular processes, yet fairly little is known about how their functions are coordinated. One factor that mediates important cross talk between these two systems is WHAMM, a Golgi-associated protein that utilizes MT binding and actin nucleation activities to promote membrane tubulation during intracellular transport. Using cryoelectron microscopy and other biophysical and biochemical approaches, we unveil the underlying mechanisms for how these activities are coordinated. We find that WHAMM bound to the outer surface of MT protofilaments via a novel interaction between its central coiled-coil region and tubulin heterodimers. Upon the assembly of WHAMM onto MTs, its N-terminal membrane-binding domain was exposed at the MT periphery, where it can recruit vesicles and remodel them into tubular structures. In contrast, MT binding masked the C-terminal portion of WHAMM and prevented it from promoting actin nucleation. These results give rise to a model whereby distinct MT-bound and actin-nucleating populations of WHAMM collaborate during membrane tubulation.
History
DepositionAug 8, 2012-
Header (metadata) releaseSep 26, 2012-
Map releaseSep 26, 2012-
UpdateSep 26, 2012-
Current statusSep 26, 2012Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5463_1.jpg

Downloads & links

-
Map

FileDownload / File: emd_5463.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of WHAMM coiled-coil domain with MTs
Voxel sizeX=Y=Z: 7.8 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.045
Minimum - Maximum-0.05469069 - 0.18331087
Average (Standard dev.)0.007509 (±0.02738204)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 1560.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.87.87.8
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z1560.0001560.0001560.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-1500
NX/NY/NZ301301151
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0550.1830.008

-
Supplemental data

-
Sample components

-
Entire : Helical structures of WHAMM coiled-coil and MTs

EntireName: Helical structures of WHAMM coiled-coil and MTs
Components
  • Sample: Helical structures of WHAMM coiled-coil and MTs
  • Protein or peptide: WHAMM coiled-coil with MTs

-
Supramolecule #1000: Helical structures of WHAMM coiled-coil and MTs

SupramoleculeName: Helical structures of WHAMM coiled-coil and MTs / type: sample / ID: 1000 / Number unique components: 1

-
Macromolecule #1: WHAMM coiled-coil with MTs

MacromoleculeName: WHAMM coiled-coil with MTs / type: protein_or_peptide / ID: 1 / Oligomeric state: helical / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET28a

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration1.1 mg/mL
BufferpH: 6.8 / Details: 80mM PIPES, pH 6.8, 1mM MgCl2, 1mM EGTA, 0.5mM DTT
GridDetails: 200 mesh holy carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK II / Method: load 2-3 uL and blot for 2 seconds before plunging

-
Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 90 K / Max: 110 K / Average: 100 K
DateMar 1, 2011
Image recordingCategory: FILM / Film or detector model: GENERIC FILM / Digitization - Scanner: OTHER / Number real images: 110 / Average electron dose: 15 e/Å2
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 32000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider
CTF correctionDetails: each particle

+
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://pdbjlvh1.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