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- PDB-1z5w: Crystal Structure of gamma-tubulin bound to GTP -

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Basic information

Entry
Database: PDB / ID: 1z5w
TitleCrystal Structure of gamma-tubulin bound to GTP
ComponentsTubulin gamma-1 chain
KeywordsSTRUCTURAL PROTEIN / complex with GTP
Function / homology
Function and homology information


mitotic spindle microtubule / polar microtubule / gamma-tubulin complex / meiotic spindle organization / microtubule nucleation / non-motile cilium / pericentriolar material / cell leading edge / mitotic sister chromatid segregation / cytoplasmic microtubule ...mitotic spindle microtubule / polar microtubule / gamma-tubulin complex / meiotic spindle organization / microtubule nucleation / non-motile cilium / pericentriolar material / cell leading edge / mitotic sister chromatid segregation / cytoplasmic microtubule / cytoplasmic microtubule organization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / mitotic spindle organization / ciliary basal body / condensed nuclear chromosome / structural constituent of cytoskeleton / spindle / microtubule cytoskeleton organization / recycling endosome / Regulation of PLK1 Activity at G2/M Transition / apical part of cell / mitotic cell cycle / microtubule / neuron projection / centrosome / GTP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Gamma tubulin / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. ...Gamma tubulin / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / 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 / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Tubulin gamma-1 chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAldaz, H.A. / Rice, L.M. / Stearns, T. / Agard, D.A.
CitationJournal: Nature / Year: 2005
Title: Insights into microtubule nucleation from the crystal structure of human gamma-tubulin.
Authors: Aldaz, H. / Rice, L.M. / Stearns, T. / Agard, D.A.
History
DepositionMar 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin gamma-1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4593
Polymers53,9121
Non-polymers5472
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.190, 76.290, 64.810
Angle α, β, γ (deg.)90.00, 102.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tubulin gamma-1 chain / Gamma-1 tubulin / Gamma-tubulin complex component 1 / GCP-1


Mass: 53911.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUBG1, TUBG / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P23258
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM

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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: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.2
Details: Tris, KCl, PEG6000, pH 8.2, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 10, 2004
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 8638 / Num. obs: 8638 / % possible obs: 85.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 7.2
Reflection shellResolution: 3→3.14 Å / % possible all: 82

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1Z5V stripped of ligands

1z5v


Resolution: 3→29.91 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 105829.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.309 842 9.7 %RANDOM
Rwork0.247 ---
all0.254 8638 --
obs0.247 8638 85.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.0566 Å2 / ksol: 0.298871 e/Å3
Displacement parametersBiso mean: 49.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.54 Å20 Å230.86 Å2
2---23.34 Å20 Å2
3---24.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.86 Å0.74 Å
Refinement stepCycle: LAST / Resolution: 3→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3077 0 33 0 3110
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d1.34
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scbond_it1.432
X-RAY DIFFRACTIONc_scangle_it2.412.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.44 108 8.8 %
Rwork0.363 1113 -
obs--73.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4GTP_XPLOR.PARAMGTP_XPLOR.TOP

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