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- PDB-6cok: Structure of the 2nd TOG domain from yeast CLASP protein STU1 -

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Basic information

Entry
Database: PDB / ID: 6cok
TitleStructure of the 2nd TOG domain from yeast CLASP protein STU1
ComponentsProtein STU1
KeywordsPROTEIN BINDING / Heat repeat / single domain
Function / homology
Function and homology information


astral microtubule depolymerization / kinetochore => GO:0000776 / mitotic spindle midzone / attachment of spindle microtubules to kinetochore / kinetochore binding / polar microtubule / microtubule organizing center / beta-tubulin binding / mitotic spindle assembly / cytoplasmic microtubule ...astral microtubule depolymerization / kinetochore => GO:0000776 / mitotic spindle midzone / attachment of spindle microtubules to kinetochore / kinetochore binding / polar microtubule / microtubule organizing center / beta-tubulin binding / mitotic spindle assembly / cytoplasmic microtubule / spindle microtubule / microtubule cytoskeleton organization / mitotic spindle / microtubule binding / cell division
Similarity search - Function
CLASP N-terminal domain / CLASP N terminal / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsMajumdar, S. / Rice, L.M.
CitationJournal: Mol. Biol. Cell / Year: 2018
Title: An isolated CLASP TOG domain suppresses microtubule catastrophe and promotes rescue.
Authors: Majumdar, S. / Kim, T. / Chen, Z. / Munyoki, S. / Tso, S.C. / Brautigam, C.A. / Rice, L.M.
History
DepositionMar 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein STU1


Theoretical massNumber of molelcules
Total (without water)36,8611
Polymers36,8611
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.412, 111.009, 44.937
Angle α, β, γ (deg.)90.00, 101.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein STU1 / Suppressor of tubulin 1


Mass: 36861.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: STU1, YBL034C, YBL0416 / Production host: Escherichia coli (E. coli) / References: UniProt: P38198
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.08 Å3/Da / Density % sol: 40.97 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 18% PEG3350, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 23899 / % possible obs: 98.6 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.04 / Net I/σ(I): 16.7
Reflection shellResolution: 1.89→1.92 Å / Rmerge(I) obs: 0.568 / Rpim(I) all: 0.33

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→40.949 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.82
RfactorNum. reflection% reflection
Rfree0.2121 1152 5 %
Rwork0.1728 --
obs0.1747 23025 95.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.89→40.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2169 0 0 161 2330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072242
X-RAY DIFFRACTIONf_angle_d0.813043
X-RAY DIFFRACTIONf_dihedral_angle_d11.3471387
X-RAY DIFFRACTIONf_chiral_restr0.047367
X-RAY DIFFRACTIONf_plane_restr0.005377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8885-1.97440.29291160.21412211X-RAY DIFFRACTION76
1.9744-2.07850.22791390.19162646X-RAY DIFFRACTION92
2.0785-2.20880.22991490.17782808X-RAY DIFFRACTION98
2.2088-2.37930.22211490.16912855X-RAY DIFFRACTION99
2.3793-2.61870.20631500.17352836X-RAY DIFFRACTION98
2.6187-2.99750.21941490.17812827X-RAY DIFFRACTION99
2.9975-3.77610.23531480.16892830X-RAY DIFFRACTION99
3.7761-40.9590.1691520.1612860X-RAY DIFFRACTION98
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)
12.87590.84151.56363.8951-1.34334.27630.29940.0558-0.159-0.2162-0.1956-0.55020.35440.32040.06570.10880.00840.04980.1977-0.04130.213115.771645.512245.6265
22.1487-0.0107-0.89851.9155-0.2680.8449-0.0520.4384-0.2994-0.32020.0140.0214-0.025-0.3667-0.06320.27890.0257-0.13520.1322-0.01960.22931.520418.653227.1715
32.26690.3185-0.90497.3246-5.4296.50020.09270.1147-0.1675-0.1655-0.0231-0.0504-0.00690.1306-0.04850.15020.005-0.02120.1205-0.07240.09992.071619.716332.1463
41.83110.4655-0.13027.2446-2.67494.73430.0726-0.0035-0.11060.26060.0909-0.2114-0.1059-0.0031-0.130.11290.03370.00160.0846-0.04130.10662.233724.431338.9047
52.27890.46180.45132.518-0.29184.4974-0.1525-0.187-0.06380.45760.0997-0.2907-0.1044-0.20910.04640.2360.0468-0.05340.1153-0.04520.16271.986632.040545.1864
62.68070.05770.03964.0947-0.66792.1652-0.01990.02240.1739-0.24490.02040.17610.0759-0.2964-0.00010.0718-0.0078-0.00010.1525-0.04560.1482-3.209442.031846.0409
72.05980.5273-0.52293.0603-0.55832.197-0.0001-0.04310.1096-0.0568-0.05940.1383-0.0475-0.05640.02120.0527-0.01780.01570.1627-0.05360.10682.091247.908749.6916
81.42520.06991.03633.9346-1.52523.3240.0843-0.30790.19120.4701-0.05260.0592-0.3623-0.0829-0.01060.1159-0.03480.03120.211-0.07240.13855.630453.784156.8674
96.9219-1.9361-1.57377.6461-0.17078.02260.3842-0.93140.42711.7285-0.1355-0.0484-0.3492-0.0579-0.15990.5918-0.25110.01820.616-0.1410.46188.93254.722862.8795
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 81 )
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 123 )
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 159 )
5X-RAY DIFFRACTION5chain 'A' and (resid 160 through 197 )
6X-RAY DIFFRACTION6chain 'A' and (resid 198 through 217 )
7X-RAY DIFFRACTION7chain 'A' and (resid 218 through 273 )
8X-RAY DIFFRACTION8chain 'A' and (resid 274 through 301 )
9X-RAY DIFFRACTION9chain 'A' and (resid 302 through 319 )

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