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- PDB-4k92: A Cryptic TOG Domain with a Distinct Architecture Underlies CLASP... -

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Basic information

Entry
Database: PDB / ID: 4k92
TitleA Cryptic TOG Domain with a Distinct Architecture Underlies CLASP-Dependent Bipolar Spindle Formation
ComponentsCLIP-associating protein 1
KeywordsSTRUCTURAL PROTEIN / HEAT-Repeat TOG domain / Regulator of Microtubule Dynamics / Tubulin / Cytoplasm Microtubule Cytoskeleton
Function / homology
Function and homology information


centrosomal corona / negative regulation of microtubule polymerization or depolymerization / establishment of spindle orientation / negative regulation of wound healing, spreading of epidermal cells / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / vesicle targeting / regulation of gastrulation / cortical microtubule cytoskeleton / microtubule anchoring / basal cortex ...centrosomal corona / negative regulation of microtubule polymerization or depolymerization / establishment of spindle orientation / negative regulation of wound healing, spreading of epidermal cells / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / vesicle targeting / regulation of gastrulation / cortical microtubule cytoskeleton / microtubule anchoring / basal cortex / positive regulation of extracellular matrix disassembly / microtubule organizing center organization / establishment of epithelial cell polarity / astral microtubule organization / kinetochore binding / Role of ABL in ROBO-SLIT signaling / kinetochore microtubule / establishment of mitotic spindle localization / microtubule plus-end / dystroglycan binding / regulation of epithelial to mesenchymal transition / negative regulation of microtubule depolymerization / microtubule nucleation / microtubule plus-end binding / microtubule bundle formation / negative regulation of stress fiber assembly / exit from mitosis / regulation of focal adhesion assembly / establishment or maintenance of cell polarity / Golgi organization / microtubule organizing center / positive regulation of exocytosis / positive regulation of epithelial cell migration / mitotic spindle assembly / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of microtubule polymerization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / 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 / regulation of microtubule cytoskeleton organization / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / mitotic spindle organization / spindle microtubule / RHO GTPases Activate Formins / kinetochore / microtubule cytoskeleton organization / mitotic spindle / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / cell cortex / microtubule binding / cell division / centrosome / Golgi apparatus / membrane / cytosol
Similarity search - Function
CLASP N-terminal domain / CLASP N terminal / : / XMAP215/Dis1/CLASP, TOG domain / Centrosomal protein CEP104-like, TOG domain / TOG domain / TOG / HEAT repeat profile. / HEAT, type 2 / Leucine-rich Repeat Variant ...CLASP N-terminal domain / CLASP N terminal / : / XMAP215/Dis1/CLASP, TOG domain / Centrosomal protein CEP104-like, TOG domain / TOG domain / TOG / HEAT repeat profile. / HEAT, type 2 / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.005 Å
AuthorsLeano, J.B. / Rogers, S.L. / Slep, K.C.
CitationJournal: Structure / Year: 2013
Title: A cryptic TOG domain with a distinct architecture underlies CLASP-dependent bipolar spindle formation.
Authors: Leano, J.B. / Rogers, S.L. / Slep, K.C.
History
DepositionApr 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CLIP-associating protein 1
B: CLIP-associating protein 1


Theoretical massNumber of molelcules
Total (without water)61,7712
Polymers61,7712
Non-polymers00
Water6,792377
1
A: CLIP-associating protein 1


Theoretical massNumber of molelcules
Total (without water)30,8861
Polymers30,8861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CLIP-associating protein 1


Theoretical massNumber of molelcules
Total (without water)30,8861
Polymers30,8861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.284, 66.492, 138.934
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTwo molecules are in the asymmetric unit. The domain functions as a monomer within the context of the full length protein.

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Components

#1: Protein CLIP-associating protein 1 / Cytoplasmic linker-associated protein 1 / Multiple asters homolog 1 / Protein Orbit homolog 1 / hOrbit1


Mass: 30885.682 Da / Num. of mol.: 2 / Fragment: TOG2, UNP residues 284-552
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLASP1, KIAA0622, MAST1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q7Z460
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: equal volume of 10 mg/ml hCLASP1 TOG2 and well solution containing 22% PEG3350, 200mM Sodium citrate, pH 8.25 were mixed together and equilibrated over 1 ml of well solution., VAPOR ...Details: equal volume of 10 mg/ml hCLASP1 TOG2 and well solution containing 22% PEG3350, 200mM Sodium citrate, pH 8.25 were mixed together and equilibrated over 1 ml of well solution., VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.980377 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 1, 2009
RadiationMonochromator: APS ID22 Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980377 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 36434 / % possible obs: 92.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rsym value: 0.09
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 1278 / Rsym value: 0.278 / % possible all: 64.9

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.005→19.997 Å / SU ML: 0.16 / σ(F): 0.62 / Phase error: 21.66 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2099 1960 5.38 %Rfree is calculated using a 5% subset of the data that are removed randomly from the original data and excluded from refinement.
Rwork0.1832 ---
all0.1846 36434 --
obs0.1846 36434 92.3 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine analyzeLuzzati coordinate error obs: 0.16 Å / Luzzati d res low obs: 20 Å / Luzzati sigma a obs: 0.917 Å
Refinement stepCycle: LAST / Resolution: 2.005→19.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3912 0 0 377 4289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143992
X-RAY DIFFRACTIONf_angle_d1.1515388
X-RAY DIFFRACTIONf_dihedral_angle_d15.9871474
X-RAY DIFFRACTIONf_chiral_restr0.089610
X-RAY DIFFRACTIONf_plane_restr0.005688
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.0047-2.05480.287790.22331525152558
2.0548-2.11030.25491180.21671980198075
2.1103-2.17230.24691120.19592250225085
2.1723-2.24230.24951500.19762348234890
2.2423-2.32230.22241490.19072463246394
2.3223-2.41520.26651430.18942531253196
2.4152-2.52490.241450.19342587258798
2.5249-2.65770.2631540.20242588258898
2.6577-2.82380.21081430.19482641264199
2.8238-3.04110.24051520.21352628262899
3.0411-3.34590.2431470.190826712671100
3.3459-3.82710.18531550.169426872687100
3.8271-4.81060.15671530.1527452745100
4.8106-19.99840.16351600.172728302830100
Refinement TLS params.Method: refined / Origin x: 1.5255 Å / Origin y: 33.1506 Å / Origin z: 76.5931 Å
111213212223313233
T0.1616 Å20.013 Å20.0174 Å2-0.1729 Å2-0.0114 Å2--0.176 Å2
L0.4544 °2-0.1942 °20.2615 °2-0.5594 °2-0.4799 °2--0.9024 °2
S0.0499 Å °0.0131 Å °-0.0217 Å °-0.0589 Å °-0.0709 Å °-0.0128 Å °0.0242 Å °0.0225 Å °0.0151 Å °
Refinement TLS groupSelection details: all

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