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- EMDB-39102: ATAT-2 bound K40Q MEC-12/MEC-7 microtubule -

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Basic information

Entry
Database: EMDB / ID: EMD-39102
TitleATAT-2 bound K40Q MEC-12/MEC-7 microtubule
Map dataMajor map
Sample
  • Complex: K40Q MEC-12/MEC-7 microtubule complexed with alpha TAT2
    • Protein or peptide: Tubulin alpha-3 chain
    • Protein or peptide: Alpha-tubulin N-acetyltransferase 2
    • Protein or peptide: Tubulin beta-1 chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: ACETYL COENZYME *A
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
KeywordsMicrotubule / luminal enzyme / PTM / STRUCTURAL PROTEIN
Function / homology
Function and homology information


positive regulation of detection of mechanical stimulus involved in sensory perception of touch / positive regulation of mechanosensory behavior / COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / Intraflagellar transport / alpha-tubulin N-acetyltransferase / tubulin N-acetyltransferase activity / detection of mechanical stimulus involved in sensory perception of touch ...positive regulation of detection of mechanical stimulus involved in sensory perception of touch / positive regulation of mechanosensory behavior / COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / Intraflagellar transport / alpha-tubulin N-acetyltransferase / tubulin N-acetyltransferase activity / detection of mechanical stimulus involved in sensory perception of touch / thigmotaxis / detection of mechanical stimulus involved in sensory perception / mechanosensory behavior / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / microtubule-based process / neuron development / regulation of microtubule cytoskeleton organization / cytoplasmic microtubule organization / response to mechanical stimulus / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / neuron projection / axon / GTPase activity / neuronal cell body / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Gcn5-related N-acetyltransferase (GNAT) domain, ATAT-type / Alpha-tubulin N-acetyltransferase / GNAT acetyltransferase, Mec-17 / Alpha-tubulin Gcn5-related N-acetyltransferase (GNAT) domain profile. / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal ...Gcn5-related N-acetyltransferase (GNAT) domain, ATAT-type / Alpha-tubulin N-acetyltransferase / GNAT acetyltransferase, Mec-17 / Alpha-tubulin Gcn5-related N-acetyltransferase (GNAT) domain profile. / 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
Similarity search - Domain/homology
Tubulin beta-1 chain / Tubulin alpha-3 chain / Alpha-tubulin N-acetyltransferase 2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLam WH / Yu D / Zhai Y / Ti S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Tubulin acetyltransferases access and modify the microtubule luminal K40 residue through anchors in taxane-binding pockets.
Authors: Jingyi Luo / Wai Hei Lam / Daqi Yu / Victor C Chao / Marc Nicholas Zopfi / Chen Jing Khoo / Chang Zhao / Shan Yan / Zheng Liu / Xiang David Li / Chaogu Zheng / Yuanliang Zhai / Shih-Chieh Ti /
Abstract: Acetylation at α-tubulin K40 is the sole post-translational modification preferred to occur inside the lumen of hollow cylindrical microtubules. However, how tubulin acetyltransferases access the ...Acetylation at α-tubulin K40 is the sole post-translational modification preferred to occur inside the lumen of hollow cylindrical microtubules. However, how tubulin acetyltransferases access the luminal K40 in micrometer-long microtubules remains unknown. Here, we use cryo-electron microscopy and single-molecule reconstitution assays to reveal the enzymatic mechanism for tubulin acetyltransferases to modify K40 in the lumen. One tubulin acetyltransferase spans across the luminal lattice, with the catalytic core docking onto two α-tubulins and the enzyme's C-terminal domain occupying the taxane-binding pockets of two β-tubulins. The luminal accessibility and enzyme processivity of tubulin acetyltransferases are inhibited by paclitaxel, a microtubule-stabilizing chemotherapeutic agent. Characterizations using recombinant tubulins mimicking preacetylated and postacetylated K40 show the crosstalk between microtubule acetylation states and the cofactor acetyl-CoA in enzyme turnover. Our findings provide crucial insights into the conserved multivalent interactions involving α- and β-tubulins to acetylate the confined microtubule lumen.
History
DepositionFeb 9, 2024-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39102.png

Downloads & links

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Map

FileDownload / File: emd_39102.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMajor map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.3719803 - 1.372556
Average (Standard dev.)-0.00017341682 (±0.036652803)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map

Fileemd_39102_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39102_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39102_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : K40Q MEC-12/MEC-7 microtubule complexed with alpha TAT2

EntireName: K40Q MEC-12/MEC-7 microtubule complexed with alpha TAT2
Components
  • Complex: K40Q MEC-12/MEC-7 microtubule complexed with alpha TAT2
    • Protein or peptide: Tubulin alpha-3 chain
    • Protein or peptide: Alpha-tubulin N-acetyltransferase 2
    • Protein or peptide: Tubulin beta-1 chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: ACETYL COENZYME *A
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

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Supramolecule #1: K40Q MEC-12/MEC-7 microtubule complexed with alpha TAT2

SupramoleculeName: K40Q MEC-12/MEC-7 microtubule complexed with alpha TAT2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: Tubulin alpha-3 chain

MacromoleculeName: Tubulin alpha-3 chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 50.165367 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MREVISIHIG QAGVQIGNAC WELYCLEHGI QPDGQMPSDQ SLGGSDDSFS TFFSETGSGR HVPRAVMVDL EPTVIDEIRT GTYRSLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLTL DRIRRLADNC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKAKLE ...String:
MREVISIHIG QAGVQIGNAC WELYCLEHGI QPDGQMPSDQ SLGGSDDSFS TFFSETGSGR HVPRAVMVDL EPTVIDEIRT GTYRSLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLTL DRIRRLADNC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKAKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCSFMVDNEA IYDICRRNLD IERPSYTNLN RLIGQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRIHF PLATFSPVIS AEKAYHEQLS VAEITNMCFE PHNQMVKCDP RHGKYMAVCL LFR GDVVPK DVNAAIATIK TKRSIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVPRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDL AALEKDYEEV GVDSMEDNGE EGDEY

UniProtKB: Tubulin alpha-3 chain

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Macromolecule #2: Alpha-tubulin N-acetyltransferase 2

MacromoleculeName: Alpha-tubulin N-acetyltransferase 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: alpha-tubulin N-acetyltransferase
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 30.434654 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEIAFDLSTI FTDNIQRLTR TDLLKYGPKR YWAVAQSIDC LGEMSSKFHG WKRVITMYDK IVDHDEEQTT YIMWEKVNGS KSILKGLLR VGYKTLYLTD NEQNQYMEKA MCILDFFVVP TEQRSGNGFK MFDEMLKAEN VTVDQCAFDK PSAALQQFLE K YYDRKDLV ...String:
MEIAFDLSTI FTDNIQRLTR TDLLKYGPKR YWAVAQSIDC LGEMSSKFHG WKRVITMYDK IVDHDEEQTT YIMWEKVNGS KSILKGLLR VGYKTLYLTD NEQNQYMEKA MCILDFFVVP TEQRSGNGFK MFDEMLKAEN VTVDQCAFDK PSAALQQFLE K YYDRKDLV WQSNKYALCS NFFIGRHPTV PFTPRQTKRA SRASSAVSSH ASSRNTSPIG RNRPRHDSVA DLMRQDMLAG VR AEVDPNS PTGLKNARDF GHRRIW

UniProtKB: Alpha-tubulin N-acetyltransferase 2

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Macromolecule #3: Tubulin beta-1 chain

MacromoleculeName: Tubulin beta-1 chain / type: protein_or_peptide / ID: 3 / Details: MEC-7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 49.306176 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MREIVHIQAG QCGNQIGSKF WEVISDEHGI DPSGQYVGDS DLQLERINVY YNEAGSNKYV PRAVLVDLEP GTMDSVRSGP FGQLFRPDN YVFGQSGAGN NWAKGHYTEG AELVDNVLDV VRKEAESTDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String:
MREIVHIQAG QCGNQIGSKF WEVISDEHGI DPSGQYVGDS DLQLERINVY YNEAGSNKYV PRAVLVDLEP GTMDSVRSGP FGQLFRPDN YVFGQSGAGN NWAKGHYTEG AELVDNVLDV VRKEAESTDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDS TFCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRS NQQYRAITVP ELTQQCFDAK NMMAACDPRH GRYLTAAAIF RGR MSMKEV DEQMLNIQNK NSSYFVDWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QEAAADEDAA EAFDGE

UniProtKB: Tubulin beta-1 chain

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Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #5: ACETYL COENZYME *A

MacromoleculeName: ACETYL COENZYME *A / type: ligand / ID: 5 / Number of copies: 1 / Formula: ACO
Molecular weightTheoretical: 809.571 Da
Chemical component information

ChemComp-ACO:
ACETYL COENZYME *A

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Macromolecule #6: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 6 / Number of copies: 2 / Formula: G2P
Molecular weightTheoretical: 521.208 Da
Chemical component information

ChemComp-G2P:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogue*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 6.8
Component:
ConcentrationName
80.0 mMPotassium PIPES
1.0 mMMagnesium chloride
1.0 mMEGTA
1.0 mMTCEP
0.05 %IGEPAL
GridModel: C-flat-1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.2 µm / Calibrated defocus min: 1.1 µm / Calibrated magnification: 47170 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 389554
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Number images used: 370802
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
Final 3D classificationNumber classes: 2 / Avg.num./class: 194737 / Software - Name: cryoSPARC (ver. 4.1.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8yal:
ATAT-2 bound K40Q MEC-12/MEC-7 microtubule

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