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- PDB-8whj: Crystal structure of CLASP2 TOG4 fused with LL5beta -

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Basic information

Entry
Database: PDB / ID: 8whj
TitleCrystal structure of CLASP2 TOG4 fused with LL5beta
ComponentsCLIP-associating protein 2,Pleckstrin homology-like domain family B member 2
KeywordsPROTEIN BINDING / Complex
Function / homology
Function and homology information


presynaptic cytoskeleton organization / cortical microtubule plus-end / 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 / microtubule anchoring / basal cortex / positive regulation of extracellular matrix disassembly / microtubule organizing center organization ...presynaptic cytoskeleton organization / cortical microtubule plus-end / 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 / microtubule anchoring / basal cortex / positive regulation of extracellular matrix disassembly / microtubule organizing center organization / Role of ABL in ROBO-SLIT signaling / kinetochore microtubule / establishment of mitotic spindle localization / negative regulation of focal adhesion assembly / dystroglycan binding / regulation of epithelial to mesenchymal transition / negative regulation of microtubule depolymerization / microtubule nucleation / regulation of microtubule-based process / microtubule plus-end binding / intermediate filament cytoskeleton / negative regulation of stress fiber assembly / podosome / anchoring junction / exit from mitosis / regulation of axon extension / establishment of cell polarity / establishment or maintenance of cell polarity / Golgi organization / platelet-derived growth factor receptor-beta signaling pathway / cell leading edge / regulation of microtubule polymerization / microtubule organizing center / positive regulation of exocytosis / positive regulation of epithelial cell migration / 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 / regulation of microtubule cytoskeleton organization / Resolution of Sister Chromatid Cohesion / protein tyrosine kinase binding / mitotic spindle organization / protein localization to plasma membrane / cell projection / spindle microtubule / regulation of actin cytoskeleton organization / RHO GTPases Activate Formins / trans-Golgi network / establishment of protein localization / kinetochore / microtubule cytoskeleton organization / ruffle membrane / actin filament binding / Separation of Sister Chromatids / cell migration / cell cortex / microtubule binding / microtubule / cadherin binding / cell division / centrosome / glutamatergic synapse / Golgi apparatus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PHLDB1/2/3, PH domain / : / CLASP N-terminal domain / CLASP N terminal / Centrosomal protein CEP104-like, TOG domain / TOG domain / TOG / PH domain / PH domain profile. / Pleckstrin homology domain. ...PHLDB1/2/3, PH domain / : / CLASP N-terminal domain / CLASP N terminal / Centrosomal protein CEP104-like, TOG domain / TOG domain / TOG / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Armadillo-like helical / PH-like domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / CLIP-associating protein 2 / Pleckstrin homology-like domain family B member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsJia, X. / Wei, Z.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971131 China
National Natural Science Foundation of China (NSFC)32170697 China
National Natural Science Foundation of China (NSFC)32370743 China
National Natural Science Foundation of China (NSFC)32371009 China
CitationJournal: Nat Commun / Year: 2024
Title: CLASP-mediated competitive binding in protein condensates directs microtubule growth.
Authors: Jia, X. / Lin, L. / Guo, S. / Zhou, L. / Jin, G. / Dong, J. / Xiao, J. / Xie, X. / Li, Y. / He, S. / Wei, Z. / Yu, C.
History
DepositionSep 23, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CLIP-associating protein 2,Pleckstrin homology-like domain family B member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9003
Polymers29,7581
Non-polymers1422
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.132, 51.132, 97.935
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein CLIP-associating protein 2,Pleckstrin homology-like domain family B member 2 / Cytoplasmic linker-associated protein 2 / Protein Orbit homolog 2 / hOrbit2 / Protein LL5-beta


Mass: 29758.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Author stated: A fragment of LL5beta has been linked to the C-terminal domain of CLASP2, with a thrombin cleavage site (SLVPRGSG) serving as the connecting sequence.
Source: (gene. exp.) Homo sapiens (human) / Gene: CLASP2, KIAA0627, PHLDB2, LL5B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75122, UniProt: Q86SQ0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium chloride, 0.1 M Bis-Tris pH 5.5, and 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 49279 / % possible obs: 99.8 % / Redundancy: 11.7 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.019 / Rrim(I) all: 0.067 / Χ2: 0.921 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.4-1.429.70.82224320.890.970.2670.8660.74199.8
1.42-1.4510.60.73724450.9140.9770.2310.7730.74899.7
1.45-1.48110.65624580.9330.9820.2020.6870.77399.7
1.48-1.5111.30.55924750.9490.9870.1710.5860.79199.7
1.51-1.5411.40.47924300.9630.990.1470.5010.81999.8
1.54-1.58110.41724440.9650.9910.130.4370.84899.2
1.58-1.6211.60.34224650.9790.9950.1040.3580.87299.4
1.62-1.6612.20.30724610.9850.9960.0910.3210.89299.8
1.66-1.7112.20.25624730.9870.9970.0760.2670.883100
1.71-1.7611.90.21624630.990.9970.0650.2250.893100
1.76-1.8311.80.17924540.9920.9980.0540.1880.934100
1.83-1.9110.14124600.9940.9980.0440.1481.00299
1.9-1.9912.50.11924460.9950.9990.0350.1241.032100
1.99-2.0912.40.09224620.9970.9990.0270.0961.024100
2.09-2.2212.30.07524940.99810.0220.0781.077100
2.22-2.3911.40.06424520.9980.9990.020.0671.08799.8
2.39-2.6312.50.05624730.99910.0170.0591.052100
2.63-3.0212.50.04824880.99910.0140.050.998100
3.02-3.811.70.03924800.99910.0120.040.975100
3.8-5012.20.03625240.99910.010.0370.88499.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→25.566 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1735 1993 4.05 %
Rwork0.1293 --
obs0.1311 49212 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→25.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 8 300 2245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082043
X-RAY DIFFRACTIONf_angle_d1.1722765
X-RAY DIFFRACTIONf_dihedral_angle_d12.649816
X-RAY DIFFRACTIONf_chiral_restr0.073327
X-RAY DIFFRACTIONf_plane_restr0.006350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4350.24651400.16483304X-RAY DIFFRACTION99
1.435-1.47380.17311390.13763375X-RAY DIFFRACTION100
1.4738-1.51710.17511410.11553339X-RAY DIFFRACTION100
1.5171-1.56610.16791460.11043377X-RAY DIFFRACTION100
1.5661-1.62210.16051390.10673349X-RAY DIFFRACTION99
1.6221-1.6870.1771390.10523381X-RAY DIFFRACTION100
1.687-1.76370.14491420.10783408X-RAY DIFFRACTION100
1.7637-1.85670.16571400.11593343X-RAY DIFFRACTION100
1.8567-1.9730.17981470.12093382X-RAY DIFFRACTION100
1.973-2.12530.15621390.11823383X-RAY DIFFRACTION100
2.1253-2.3390.1641440.12413396X-RAY DIFFRACTION100
2.339-2.67720.1731430.1363382X-RAY DIFFRACTION100
2.6772-3.37170.19311460.1433389X-RAY DIFFRACTION100
3.3717-25.5660.17191480.13683411X-RAY DIFFRACTION100

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