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- PDB-4gs4: Structure of the alpha-tubulin acetyltransferase, alpha-TAT1 -

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Basic information

Entry
Database: PDB / ID: 4gs4
TitleStructure of the alpha-tubulin acetyltransferase, alpha-TAT1
ComponentsAlpha-tubulin N-acetyltransferase
KeywordsTRANSFERASE / acetyl coenzyme A binding / cytosolic
Function / homology
Function and homology information


alpha-tubulin N-acetyltransferase / tubulin N-acetyltransferase activity / alpha-tubulin acetylation / microtubule bundle / Cilium Assembly / NLRP3 inflammasome complex assembly / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / dentate gyrus development / regulation of fat cell differentiation / response to pain ...alpha-tubulin N-acetyltransferase / tubulin N-acetyltransferase activity / alpha-tubulin acetylation / microtubule bundle / Cilium Assembly / NLRP3 inflammasome complex assembly / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / dentate gyrus development / regulation of fat cell differentiation / response to pain / positive regulation of NLRP3 inflammasome complex assembly / cilium assembly / neuron development / regulation of microtubule cytoskeleton organization / response to mechanical stimulus / clathrin-coated pit / mitotic spindle / microtubule cytoskeleton organization / spermatogenesis / microtubule / axon / focal adhesion / Golgi apparatus / cytosol
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. / Gcn5-related N-acetyltransferase (GNAT) / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / Alpha-tubulin N-acetyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.112 Å
AuthorsFriedmann, D.R. / Fan, J. / Marmorstein, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of the alpha-tubulin acetyltransferase, alpha TAT1, and implications for tubulin-specific acetylation.
Authors: Friedmann, D.R. / Aguilar, A. / Fan, J. / Nachury, M.V. / Marmorstein, R.
History
DepositionAug 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-tubulin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9962
Polymers27,1871
Non-polymers8101
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.931, 130.668, 37.423
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-525-

HOH

21A-543-

HOH

DetailsThe biological assembly is composed of one molecule of alpha-tubulin acetyltransferase bound to one molecule of acetyl coenzyme A

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Components

#1: Protein Alpha-tubulin N-acetyltransferase / / Alpha-TAT / TAT / Acetyltransferase mec-17 homolog


Mass: 27186.682 Da / Num. of mol.: 1 / Fragment: catalytic domain residues 2-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATAT1, C6orf134, MEC17, Nbla00487 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): RIL
References: UniProt: Q5SQI0, alpha-tubulin N-acetyltransferase
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 298.5 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris pH 7.5, 2.7M Sodium Formate, VAPOR DIFFUSION, HANGING DROP, temperature 298.5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 1, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→39.8 Å / Num. obs: 26218

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.112→39.797 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 27.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2532 2628 10.02 %Random
Rwork0.2266 ---
obs0.2294 26218 98.25 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.308 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.4679 Å20 Å2-0 Å2
2---0.9983 Å20 Å2
3----14.4697 Å2
Refinement stepCycle: LAST / Resolution: 2.112→39.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1433 0 51 51 1535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041519
X-RAY DIFFRACTIONf_angle_d1.2822058
X-RAY DIFFRACTIONf_dihedral_angle_d17.368568
X-RAY DIFFRACTIONf_chiral_restr0.133224
X-RAY DIFFRACTIONf_plane_restr0.004261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1115-2.14990.26751230.25071056X-RAY DIFFRACTION83
2.1499-2.19130.28691270.25251148X-RAY DIFFRACTION91
2.1913-2.2360.29651300.2641204X-RAY DIFFRACTION96
2.236-2.28460.27381440.261228X-RAY DIFFRACTION99
2.2846-2.33770.24861400.2471291X-RAY DIFFRACTION99
2.3377-2.39620.34331420.25951243X-RAY DIFFRACTION100
2.3962-2.4610.36311420.2521265X-RAY DIFFRACTION100
2.461-2.53340.29861320.26251246X-RAY DIFFRACTION100
2.5334-2.61510.3111430.24271289X-RAY DIFFRACTION100
2.6151-2.70860.29081410.23681256X-RAY DIFFRACTION100
2.7086-2.8170.28851410.26861255X-RAY DIFFRACTION100
2.817-2.94520.31921340.22911253X-RAY DIFFRACTION100
2.9452-3.10040.19731500.23831288X-RAY DIFFRACTION100
3.1004-3.29450.24541360.23291230X-RAY DIFFRACTION100
3.2945-3.54880.31450.22461274X-RAY DIFFRACTION100
3.5488-3.90560.28951420.20751262X-RAY DIFFRACTION100
3.9056-4.47010.21981390.18131261X-RAY DIFFRACTION100
4.4701-5.62930.17781350.20541272X-RAY DIFFRACTION100
5.6293-39.80430.21891420.2371269X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.57274.37412.9056.7668-1.25295.9290.4887-0.7335-0.36960.692-0.2077-0.0564-0.3638-0.2109-0.19620.7872-0.08040.15770.92540.4240.71117.96210.832555.5903
23.58911.0916-0.96842.9128-0.23162.07460.0372-0.4082-0.6858-0.21520.03590.46831.0821-0.4317-0.03310.3985-0.091-0.050.26020.08050.353217.447415.088742.8459
32.1648-0.4935-0.61510.94880.40291.26880.1171-0.522-0.39570.02050.00410.02780.92390.0307-0.0170.370.1472-0.079-0.00230.07170.181432.58417.08636.4967
42.3202-0.24420.58943.55730.34542.10030.02550.1439-0.2109-0.5324-0.1148-0.41640.39320.82220.06180.24650.3827-0.05220.42660.06920.25938.913418.680832.0532
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 8:13)
2X-RAY DIFFRACTION2(chain A and resid 14:98)
3X-RAY DIFFRACTION3(chain A and resid 99:164)
4X-RAY DIFFRACTION4(chain A and resid 165:195)

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