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- PDB-5x1g: WHAMM's Microtubule binding motif -

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Basic information

Entry
Database: PDB / ID: 5x1g
TitleWHAMM's Microtubule binding motif
ComponentsWASP homolog-associated protein with actin, membranes and microtubules
KeywordsSTRUCTURAL PROTEIN / microtubule / helical reconstruction
Function / homology
Function and homology information


plasma membrane tubulation / Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / positive regulation of actin nucleation / focal adhesion assembly / RHOD GTPase cycle / lamellipodium assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / actin filament organization ...plasma membrane tubulation / Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / positive regulation of actin nucleation / focal adhesion assembly / RHOD GTPase cycle / lamellipodium assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / actin filament organization / cytoplasmic vesicle membrane / small GTPase binding / actin binding / microtubule binding / microtubule / Golgi membrane / cytosol / cytoplasm
Similarity search - Function
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsLiu, T. / Wang, H.W.
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, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Other / Category: atom_sites / cell / em_image_scans
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
C: WASP homolog-associated protein with actin, membranes and microtubules


Theoretical massNumber of molelcules
Total (without water)4,4141
Polymers4,4141
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2500 Å2

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Components

#1: Protein/peptide WASP homolog-associated protein with actin, membranes and microtubules / WAS protein homology region 2 domain-containing protein 1 / WH2 domain-containing protein 1


Mass: 4414.182 Da / Num. of mol.: 1 / Fragment: UNP residues 513-546
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WHAMM, KIAA1971, WHDC1 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q8TF30

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Ternary complex of alpha,beta-tubulin dimer with microtubule binding motif of WHAMM
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -25.762 ° / Axial rise/subunit: 8.6 Å / Axial symmetry: C1
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8000 / Symmetry type: HELICAL

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