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

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Basic information

Entry
Database: PDB / ID: 8yal
TitleATAT-2 bound K40Q MEC-12/MEC-7 microtubule
Components
  • Alpha-tubulin N-acetyltransferase 2
  • Tubulin alpha-3 chain
  • Tubulin beta-1 chain
KeywordsSTRUCTURAL PROTEIN / Microtubule / luminal enzyme / PTM
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 / response to mechanical stimulus / regulation of microtubule cytoskeleton organization / cytoplasmic microtubule organization / 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
ACETYL COENZYME *A / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta-1 chain / Tubulin alpha-3 chain / Alpha-tubulin N-acetyltransferase 2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLam, W.H. / Yu, D. / Zhai, Y. / Ti, S.
Funding support1items
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: Lam, W.H. / Yu, D. / Zhai, Y. / Ti, S.
History
DepositionFeb 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Tubulin alpha-3 chain
C: Alpha-tubulin N-acetyltransferase 2
D: Tubulin beta-1 chain
E: Tubulin alpha-3 chain
F: Tubulin beta-1 chain
I: Alpha-tubulin N-acetyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,71111
Polymers259,8126
Non-polymers2,8985
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 3 types, 6 molecules BECIDF

#1: Protein Tubulin alpha-3 chain / Mechanosensory abnormality protein 12 / MEC-12


Mass: 50165.367 Da / Num. of mol.: 2 / Mutation: K40Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: mec-12, tba-3, C44B11.3 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P91910, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Protein Alpha-tubulin N-acetyltransferase 2 / Alpha-TAT 2 / ATAT 2 / Mec-17-like protein


Mass: 30434.654 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: atat-2, W06B11.1 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q23192, alpha-tubulin N-acetyltransferase
#3: Protein Tubulin beta-1 chain / Beta-1-tubulin


Mass: 49306.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MEC-7 / Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: mec-7, ZK154.3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P12456

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Non-polymers , 3 types, 5 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-G2P / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GMP-CPP, energy-carrying molecule analogue*YM

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: K40Q MEC-12/MEC-7 microtubule complexed with alpha TAT2
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 6.8
Buffer component
IDConc.NameBuffer-ID
180 mMPotassium PIPES1
21 mMMagnesium chloride1
31 mMEGTA1
41 mMTCEP1
50.05 %IGEPAL1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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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 / Nominal magnification: 81000 X / Calibrated magnification: 47170 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1100 nm / Calibrated defocus min: 1100 nm / Calibrated defocus max: 2200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.1.2particle selection
2EPU2.12image acquisition
4cryoSPARC4.1.2CTF correction
7UCSF Chimera1.16model fitting
9PHENIX1.19-4092model refinement
10cryoSPARC4.1.2initial Euler assignment
11cryoSPARC4.1.2final Euler assignment
12cryoSPARC4.1.2classification
13cryoSPARC4.1.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 389554
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 370802 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00315869
ELECTRON MICROSCOPYf_angle_d0.47921571
ELECTRON MICROSCOPYf_dihedral_angle_d4.8272159
ELECTRON MICROSCOPYf_chiral_restr0.0432358
ELECTRON MICROSCOPYf_plane_restr0.0042803

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