[English] 日本語
Yorodumi
- EMDB-6701: 3D cryo-EM reconstruction of Microtubule-WHAMM complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6701
Title3D cryo-EM reconstruction of Microtubule-WHAMM complex
Map data
Sample
  • Complex: Ternary complex of alpha,beta-tubulin dimer with microtubule binding motif of WHAMM
    • Protein or peptide: WASP homolog-associated protein with actin, membranes and microtubules
Keywordsmicrotubule / helical reconstruction / STRUCTURAL PROTEIN
Function / homology
Function and homology information


small GTPase binding => GO:0031267 / regulation of cell cycle => GO:0051726 / plasma membrane tubulation / Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / positive regulation of actin nucleation / : / focal adhesion assembly / lamellipodium assembly / endoplasmic reticulum to Golgi vesicle-mediated transport ...small GTPase binding => GO:0031267 / regulation of cell cycle => GO:0051726 / plasma membrane tubulation / Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / positive regulation of actin nucleation / : / focal adhesion assembly / lamellipodium assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / actin filament organization / cytoplasmic vesicle membrane / actin binding / microtubule binding / microtubule / Golgi membrane / cytosol / cytoplasm
Similarity search - Function
WASP homologue-associated protein with actin, membranes and microtubules / JMY/WHAMM, middle domain / JMY/WHAMM, N-terminal / Junction-mediating and -regulatory protein / N-terminal of Junction-mediating and WASP homolog-associated / WH2 domain / WH2 domain profile.
Similarity search - Domain/homology
WASP homolog-associated protein with actin, membranes and microtubules
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsLiu T / Wang HW
CitationJournal: J Mol Biol / Year: 2017
Title: Structural Insights of WHAMM's Interaction with Microtubules by Cryo-EM.
Authors: Tianyang Liu / Anbang Dai / Yong Cao / Rui Zhang / Meng-Qiu Dong / Hong-Wei Wang /
Abstract: WASP homolog associated with actin, membranes, and microtubules (WHAMM) is a vertebrate protein functioning in membrane tubulation for intracellular membrane trafficking and specific organelle ...WASP homolog associated with actin, membranes, and microtubules (WHAMM) is a vertebrate protein functioning in membrane tubulation for intracellular membrane trafficking and specific organelle formation. Composed of multiple domains, WHAMM can bind to membrane and microtubule (MT) and promote actin polymerization nucleation. Previous work revealed that WHAMM's activity to promote actin nucleation is repressed upon binding to MTs. Here, we discovered that WHAMM interacts with αβ-tubulin through a small peptide motif within its MT-binding domain. We reconstructed a high-resolution structure of WHAMM's MT-binding motif (MBM) assembling around MTs using cryo-electron microscopy and verified it with chemical cross-linking and mass spectrometry analysis. We also detected a conformational switch of this motif between the non-MT-bound state and the MT-bound state. These discoveries provide new insights into the mechanism by which WHAMM coordinates actin and MT networks, the two major cytoskeletal systems involved in membrane trafficking and membrane remodeling.
History
DepositionJan 25, 2017-
Header (metadata) releaseJun 21, 2017-
Map releaseJul 5, 2017-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.31
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.31
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6701.png

Downloads & links

-
Map

FileDownload / File: emd_6701.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.306 Å
Density
Contour LevelBy AUTHOR: 4.31 / Movie #1: 4.31
Minimum - Maximum-5.524707 - 13.060722
Average (Standard dev.)-0.02982369 (±0.88838786)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 668.672 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3061.3061.306
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z668.672668.672668.672
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-256-256-256
NC/NR/NS512512512
D min/max/mean-5.52513.061-0.030

-
Supplemental data

-
Sample components

-
Entire : Ternary complex of alpha,beta-tubulin dimer with microtubule bind...

EntireName: Ternary complex of alpha,beta-tubulin dimer with microtubule binding motif of WHAMM
Components
  • Complex: Ternary complex of alpha,beta-tubulin dimer with microtubule binding motif of WHAMM
    • Protein or peptide: WASP homolog-associated protein with actin, membranes and microtubules

-
Supramolecule #1: Ternary complex of alpha,beta-tubulin dimer with microtubule bind...

SupramoleculeName: Ternary complex of alpha,beta-tubulin dimer with microtubule binding motif of WHAMM
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: WASP homolog-associated protein with actin, membranes and microtubules

MacromoleculeName: WASP homolog-associated protein with actin, membranes and microtubules
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.414182 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
IQMKRDKIKE EEQKKKEWIN QERQKTLQRL RSFK

UniProtKB: WASP homolog-associated protein with actin, membranes and microtubules

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 6.8
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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 8.6 Å
Applied symmetry - Helical parameters - Δ&Phi: -25.762 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8000

+
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