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- PDB-3woy: Crystal structure of CLASP2 TOG domain (TOG2) -

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Basic information

Entry
Database: PDB / ID: 3woy
TitleCrystal structure of CLASP2 TOG domain (TOG2)
ComponentsCLIP-associating protein 2
KeywordsSTRUCTURAL PROTEIN / HEAT Repeat / Microtubule binding / Tubulin / unknown / microtubule
Function / homology
Function and homology information


presynaptic cytoskeleton organization / cortical microtubule plus-end / negative regulation of wound healing, spreading of epidermal cells / vesicle targeting / microtubule anchoring / basal cortex / positive regulation of extracellular matrix disassembly / Role of ABL in ROBO-SLIT signaling / kinetochore microtubule / microtubule organizing center organization ...presynaptic cytoskeleton organization / cortical microtubule plus-end / negative regulation of wound healing, spreading of epidermal cells / vesicle targeting / microtubule anchoring / basal cortex / positive regulation of extracellular matrix disassembly / Role of ABL in ROBO-SLIT signaling / kinetochore microtubule / microtubule organizing center organization / basement membrane organization / negative regulation of focal adhesion assembly / dystroglycan binding / establishment of mitotic spindle localization / negative regulation of microtubule depolymerization / microtubule nucleation / negative regulation of stress fiber assembly / microtubule plus-end binding / exit from mitosis / regulation of microtubule-based process / regulation of axon extension / platelet-derived growth factor receptor-beta signaling pathway / Golgi organization / establishment or maintenance of cell polarity / cell leading edge / microtubule organizing center / regulation of microtubule polymerization / positive regulation of epithelial cell migration / positive regulation of exocytosis / mitotic spindle assembly / regulation of microtubule polymerization or depolymerization / axonal growth cone / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / protein tyrosine kinase binding / Resolution of Sister Chromatid Cohesion / mitotic spindle organization / regulation of actin cytoskeleton organization / spindle microtubule / trans-Golgi network / RHO GTPases Activate Formins / kinetochore / microtubule cytoskeleton organization / ruffle membrane / actin filament binding / Separation of Sister Chromatids / cell cortex / microtubule binding / microtubule / cell division / centrosome / glutamatergic synapse / Golgi apparatus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CLASP N-terminal domain / CLASP N terminal / Centrosomal protein CEP104, TOG domain / TOG domain / TOG / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
CLIP-associating protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsHayashi, I. / Maki, T.
CitationJournal: J. Mol. Biol. / Year: 2015
Title: CLASP2 Has Two Distinct TOG Domains That Contribute Differently to Microtubule Dynamics
Authors: Maki, T. / Grimaldi, A.D. / Fuchigami, S. / Kaverina, I. / Hayashi, I.
History
DepositionJan 6, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: CLIP-associating protein 2


Theoretical massNumber of molelcules
Total (without water)28,1821
Polymers28,1821
Non-polymers00
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.812, 58.812, 157.073
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein CLIP-associating protein 2 / Cytoplasmic linker-associated protein 2 / Protein Orbit homolog 2 / hOrbit2


Mass: 28182.201 Da / Num. of mol.: 1 / Fragment: UNP residues 60-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLASP2, KIAA0627 / Production host: Escherichia coli (E. coli) / References: UniProt: O75122
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20mM Tris, 3%(w/v) PEG10K , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6A10.97901, 0.97931, 0.96408
SYNCHROTRONPhoton Factory BL-5A21
Detector
TypeIDDetectorDate
ADSC QUANTUM 4r1CCDFeb 18, 2009
ADSC QUANTUM 315r2CCDOct 10, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELMADMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979011
20.979311
30.964081
411
ReflectionResolution: 2→50 Å / Num. obs: 44169 / % possible obs: 99.9 % / Observed criterion σ(F): 62 / Observed criterion σ(I): 2.9 / Biso Wilson estimate: 25.4 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2-2.011,299.6
2.01-2.091,2100
2.09-2.181,2100
2.18-2.31,2100
2.3-2.441,2100
2.44-2.631,2100
2.63-2.91,2100
2.9-3.321,2100
3.32-4.181,2100
4.18-501,299.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→42.73 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 172351.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1836 9.8 %RANDOM
Rwork0.183 ---
obs0.183 18642 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.0081 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 42.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.1→42.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 0 0 212 2166
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 299 10.2 %
Rwork0.206 2624 -
obs--94 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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