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- EMDB-41169: GMPCPP-microtubule decorated with Abl2-557-1090 -

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Basic information

Entry
Database: EMDB / ID: EMD-41169
TitleGMPCPP-microtubule decorated with Abl2-557-1090
Map dataGaussian smoothed map of GMPCPP-microtubule decorated with Abl2-557-1090
Sample
  • Complex: GMPCPP-microtubules decorated with Abl2-557-1090.
    • Complex: GMPCPP-microtubule
      • Protein or peptide: alpha-tubulin
      • Protein or peptide: beta-tubulin
    • Complex: Abl2-557-1090
      • Protein or peptide: Abl2 C-terminals (557-1090)
KeywordsMicrotubule / Abl2 / PROTEIN FIBRIL
Function / homology
Function and homology information


positive regulation of oxidoreductase activity / Role of ABL in ROBO-SLIT signaling / regulation of cell motility / exploration behavior / negative regulation of Rho protein signal transduction / regulation of endocytosis / actin monomer binding / positive regulation of T cell migration / RAC3 GTPase cycle / regulation of cell adhesion ...positive regulation of oxidoreductase activity / Role of ABL in ROBO-SLIT signaling / regulation of cell motility / exploration behavior / negative regulation of Rho protein signal transduction / regulation of endocytosis / actin monomer binding / positive regulation of T cell migration / RAC3 GTPase cycle / regulation of cell adhesion / cellular response to retinoic acid / Negative regulation of FLT3 / positive regulation of establishment of T cell polarity / phosphotyrosine residue binding / RAC1 GTPase cycle / regulation of autophagy / regulation of actin cytoskeleton organization / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / protein modification process / epidermal growth factor receptor signaling pathway / structural constituent of cytoskeleton / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / microtubule cytoskeleton organization / actin filament binding / actin cytoskeleton / manganese ion binding / mitotic cell cycle / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / protein tyrosine kinase activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cell adhesion / protein kinase activity / hydrolase activity / GTPase activity / GTP binding / magnesium ion binding / signal transduction / ATP binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / : / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin ...F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / : / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Tubulin alpha-1A chain / Tubulin beta chain / Tyrosine-protein kinase ABL2
Similarity search - Component
Biological speciesSus scrofa (pig) / Homo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsLyu W / Duan D / Chai P
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS112121 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH115939 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS105640 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R56MH122449 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM142959 United States
National Institutes of Health/Office of the DirectorS10OD023603 United States
CitationJournal: Curr Biol / Year: 2023
Title: Abl2 repairs microtubules and phase separates with tubulin to promote microtubule nucleation.
Authors: Daisy Duan / Wanqing Lyu / Pengxin Chai / Shaojie Ma / Kuanlin Wu / Chunxiang Wu / Yong Xiong / Nenad Sestan / Kai Zhang / Anthony J Koleske /
Abstract: Abl family kinases are evolutionarily conserved regulators of cell migration and morphogenesis. Genetic experiments in Drosophila suggest that Abl family kinases interact functionally with ...Abl family kinases are evolutionarily conserved regulators of cell migration and morphogenesis. Genetic experiments in Drosophila suggest that Abl family kinases interact functionally with microtubules to regulate axon guidance and neuronal morphogenesis. Vertebrate Abl2 binds to microtubules and promotes their plus-end elongation, both in vitro and in cells, but the molecular mechanisms by which Abl2 regulates microtubule (MT) dynamics are unclear. We report here that Abl2 regulates MT assembly via condensation and direct interactions with both the MT lattice and tubulin dimers. We find that Abl2 promotes MT nucleation, which is further facilitated by the ability of the Abl2 C-terminal half to undergo liquid-liquid phase separation (LLPS) and form co-condensates with tubulin. Abl2 binds to regions adjacent to MT damage, facilitates MT repair via fresh tubulin recruitment, and increases MT rescue frequency and lifetime. Cryo-EM analyses strongly support a model in which Abl2 engages tubulin C-terminal tails along an extended MT lattice conformation at damage sites to facilitate repair via fresh tubulin recruitment. Abl2Δ688-790, which closely mimics a naturally occurring splice isoform, retains binding to the MT lattice but does not bind tubulin, promote MT nucleation, or increase rescue frequency. In COS-7 cells, MT reassembly after nocodazole treatment is greatly slowed in Abl2 knockout COS-7 cells compared with wild-type cells, and these defects are rescued by re-expression of Abl2, but not Abl2Δ688-790. We propose that Abl2 locally concentrates tubulin to promote MT nucleation and recruits it to defects in the MT lattice to enable repair and rescue.
History
DepositionJul 3, 2023-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateNov 22, 2023-
Current statusNov 22, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41169.png

Downloads & links

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Map

FileDownload / File: emd_41169.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGaussian smoothed map of GMPCPP-microtubule decorated with Abl2-557-1090
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 360 pix.
= 585.216 Å		1.63 Å/pix.
x 360 pix.
= 585.216 Å		1.63 Å/pix.
x 360 pix.
= 585.216 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.6256 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.16605136 - 0.44604802
Average (Standard dev.)0.0025302658 (±0.059693385)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 585.216 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41169_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Original map of GMPCPP-microtubule decorated with Abl2-557-1090

Fileemd_41169_additional_1.map
AnnotationOriginal map of GMPCPP-microtubule decorated with Abl2-557-1090
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of GMPCPP-microtubule decorated with Abl2-557-1090

Fileemd_41169_half_map_1.map
AnnotationHalf map B of GMPCPP-microtubule decorated with Abl2-557-1090
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of GMPCPP-microtubule decorated with Abl2-557-1090

Fileemd_41169_half_map_2.map
AnnotationHalf map A of GMPCPP-microtubule decorated with Abl2-557-1090
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GMPCPP-microtubules decorated with Abl2-557-1090.

EntireName: GMPCPP-microtubules decorated with Abl2-557-1090.
Components
  • Complex: GMPCPP-microtubules decorated with Abl2-557-1090.
    • Complex: GMPCPP-microtubule
      • Protein or peptide: alpha-tubulin
      • Protein or peptide: beta-tubulin
    • Complex: Abl2-557-1090
      • Protein or peptide: Abl2 C-terminals (557-1090)

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Supramolecule #1: GMPCPP-microtubules decorated with Abl2-557-1090.

SupramoleculeName: GMPCPP-microtubules decorated with Abl2-557-1090. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 0.5 kDa/nm

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Supramolecule #2: GMPCPP-microtubule

SupramoleculeName: GMPCPP-microtubule / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Sus scrofa (pig) / Organ: brain

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Supramolecule #3: Abl2-557-1090

SupramoleculeName: Abl2-557-1090 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: alpha-tubulin

MacromoleculeName: alpha-tubulin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVD LEPTVIDEVR TGTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL D RIRKLADQ CTGLQGFSVF HSFGGGTGSG FTSLLMERLS VDYGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVD LEPTVIDEVR TGTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL D RIRKLADQ CTGLQGFSVF HSFGGGTGSG FTSLLMERLS VDYGKKSKLE FSIYPAPQVS TA VVEPYNS ILTTHTTLEH SDCAFMVDNE AIYDICRRNL DIERPTYTNL NRLIGQIVSS ITA SLRFDG ALNVDLTEFQ TNLVPYPRAH FPLATYAPVI SAEKAYHEQL SVAEITNACF EPAN QMVKC DPRHGKYMAC CLLYRGDVVP KDVNAAIATI KTKRTIQFVD WCPTGFKVGI NYEPP TVVP GGDLAKVQRA VCMLSNTTAI AEAWARLDHK FDLMYAKRAF VHWYVGEGME EGEFSE ARE DMAALEKDYE EVGVDSVEGE GEEEGEEY

UniProtKB: Tubulin alpha-1A chain

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Macromolecule #2: beta-tubulin

MacromoleculeName: beta-tubulin / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLE PGTMDSVRSG PFGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV V RKESESCD CLQGFQLTHS LGGGTGSGMG TLLISKIREE YPDRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLE PGTMDSVRSG PFGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV V RKESESCD CLQGFQLTHS LGGGTGSGMG TLLISKIREE YPDRIMNTFS VVPSPKVSDT VV EPYNATL SVHQLVENTD ETYCIDNEAL YDICFRTLKL TTPTYGDLNH LVSATMSGVT TCL RFPGQL NADLRKLAVN MVPFPRLHFF MPGFAPLTSR GSQQYRALTV PELTQQMFDA KNMM AACDP RHGRYLTVAA VFRGRMSMKE VDEQMLNVQN KNSSYFVEWI PNNVKTAVCD IPPRG LKMS ATFIGNSTAI QELFKRISEQ FTAMFRRKAF LHWYTGEGMD EMEFTEAESN MNDLVS EYQ QYQDATADEQ GEFEEEGEED EA

UniProtKB: Tubulin beta chain

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Macromolecule #3: Abl2 C-terminals (557-1090)

MacromoleculeName: Abl2 C-terminals (557-1090) / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGQQVGRVGE APGLQQPQPR GIRGSSAARP SGRRRDPAGR TTETGFNIFT QHDHFASCVE DGFEGDKTG GSSPEALHRP YGCDVEPQAL NEAIRWSSKE NLLGATESDP NLFVALYDFV A SGDNTLSI TKGEKLRVLG YNQNGEWSEV RSKNGQGWVP SNYITPVNSL ...String:
MGQQVGRVGE APGLQQPQPR GIRGSSAARP SGRRRDPAGR TTETGFNIFT QHDHFASCVE DGFEGDKTG GSSPEALHRP YGCDVEPQAL NEAIRWSSKE NLLGATESDP NLFVALYDFV A SGDNTLSI TKGEKLRVLG YNQNGEWSEV RSKNGQGWVP SNYITPVNSL EKHSWYHGPV SR SAAEYLL SSLINGSFLV RESESSPGQL SISLRYEGRV YHYRINTTAD GKVYVTAESR FST LAELVH HHSTVADGLV TTLHYPAPKC NKPTVYGVSP IHDKWEMERT DITMKHKLGG GQYG EVYVG VWKKYSLTVA VKTLKEDTME VEEFLKEAAV MKEIKHPNLV QLLGVCTLEP PFYIV TEYM PYGNLLDYLR ECNREEVTAV VLLYMATQIS SAMEYLEKKN FIHRDLAARN CLVGEN HVV KVADFGLSRL MTGDTYTAHA GAKFPIKWTA PESLAYNTFS IKSDVWAFGV LLWEIAT YG MSPYPGIDLS QVYDLLEKGY RMEQPEGCPP KVYELMRACW KWSPADRPSF AETHQAFE T MFHDSSISEE VAEELGRAAS SSSVVPYLPR LPILPSKTRT LKKQVENKEN IEGAQDATE NSASSLAPGF IRGAQASSGS PALPRKQRDK SPSSLLEDAK ETCFTRDRKG GFFSSFMKKR NAPTPPKRS SSFREMENQP HKKYELTGNF SSVASLQHAD GFSFTPAQQE ANLVPPKCYG G SFAQRNLC NDDGGGGGGS GTAGGGWSGI TGFFTPRLIK KTLGLRAGKP TASDDTSKPF PR SNSTSSM SSGLPEQDRM AMTLPRNCQR SKLQLERTVS TSSQPEENVD RANDMLPKKS EES AAPSRE RPKAKLLPRG ATALPLRTPS GDLAITEKDP PGVGVAGVAA APKGKEKNGG ARLG MAGVP EDGEQPGWPS PAKAAPVLPT THNHKVPVLI SPTLKHTPAD VQLIGTDSQG NKFKL LSEH QVTSSGDKDR PRRVKPKCAP PPPPVMRLLQ HPSICSDPTE EPTALTAGQS TSETQE GGK KAALGAVPIS GKAGRPVMPP PQVPLPTSSI SPAKMANGTA GTKVALRKTK QAAEKIS AD KISKEALLEC ADLLSSALTE PVPNSQLVDT GHQLLDYCSG YVDCIPQTRN KFAFREAV S KLELSLQELQ VSSAAAGVPG TNPVLNNLLS CVQEISDVVQ R

UniProtKB: Tyrosine-protein kinase ABL2

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration1 mg/mL
BufferpH: 6.8
Details: 80 mM PIPES, pH 6.8, 1 mM MgCl2, 1 mM EGTA, 1 mM GMPCPP
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.2 µm / Calibrated magnification: 36000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 82.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 0 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 84826
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 2)
FSC plot (resolution estimation)

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