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- PDB-3cb2: Crystal structure of human gamma-tubulin bound to GDP -

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Basic information

Entry
Database: PDB / ID: 3cb2
TitleCrystal structure of human gamma-tubulin bound to GDP
Componentstubulin gamma-1 chain
KeywordsSTRUCTURAL PROTEIN / HYDROLASE / tubulin / lattice / microtubule / nucleation / GTPase / lateral interaction
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 / cytoplasmic microtubule / mitotic sister chromatid segregation ...mitotic spindle microtubule / polar microtubule / gamma-tubulin complex / meiotic spindle organization / microtubule nucleation / non-motile cilium / pericentriolar material / cell leading edge / cytoplasmic microtubule / mitotic sister chromatid segregation / 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 / recycling endosome / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / 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 / cytoplasm / cytosol
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'-DIPHOSPHATE / Tubulin gamma-1 chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 Å
AuthorsRice, L.M. / Montabana, E.A. / Agard, D.A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: The lattice as allosteric effector: structural studies of alphabeta- and gamma-tubulin clarify the role of GTP in microtubule assembly
Authors: Rice, L.M. / Montabana, E.A. / Agard, D.A.
History
DepositionFeb 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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
B: tubulin gamma-1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9664
Polymers108,0802
Non-polymers8862
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-28.7 kcal/mol
Surface area32580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.744, 108.755, 83.347
Angle α, β, γ (deg.)90.00, 96.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein tubulin gamma-1 chain / E.C.3.6.5.6 / Gamma-1-tubulin / Gamma-tubulin complex component 1 / GCP-1


Mass: 54039.828 Da / Num. of mol.: 2
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, EC: 3.6.5.6
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.16 Å3/Da / Density % sol: 42.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.2
Details: top solution: 83 mM HEPES pH 7.2, 1.2M KCl, 20% PEG6000, 1mM GDP; reservoir: 83mM HEPES pH 7.2, 0.6M KCl, 20% PEG6000, 1 mM GDP. Protein was mixed 1:1 or 1:2 with top solution, and ...Details: top solution: 83 mM HEPES pH 7.2, 1.2M KCl, 20% PEG6000, 1mM GDP; reservoir: 83mM HEPES pH 7.2, 0.6M KCl, 20% PEG6000, 1 mM GDP. Protein was mixed 1:1 or 1:2 with top solution, and equilibrated over the reservoir solution., VAPOR DIFFUSION, temperature 298K

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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 315 / Detector: CCD / Date: Dec 6, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.303→82.76 Å / Num. all: 40179 / Num. obs: 38587 / % possible obs: 98.9 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.303→2.38 Å / % possible all: 97

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1Z5V stripped of sidechains and ligands

1z5v


Resolution: 2.303→82.76 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.905 / SU B: 6.367 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.365 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23786 2005 5 %RANDOM
Rwork0.18654 ---
all0.18908 38587 --
obs0.18908 38151 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.015 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.07 Å2
2--0.71 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.303→82.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6578 0 56 378 7012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226773
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.9629230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3885846
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05523.953301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.388151050
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3711542
X-RAY DIFFRACTIONr_chiral_restr0.0750.21060
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025140
X-RAY DIFFRACTIONr_nbd_refined0.190.23075
X-RAY DIFFRACTIONr_nbtor_refined0.2990.24641
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2455
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.213
X-RAY DIFFRACTIONr_mcbond_it0.5651.54378
X-RAY DIFFRACTIONr_mcangle_it0.96526841
X-RAY DIFFRACTIONr_scbond_it1.15432733
X-RAY DIFFRACTIONr_scangle_it1.8474.52389
LS refinement shellResolution: 2.303→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 161 -
Rwork0.203 2741 -
obs-2632 96.28 %

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