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- PDB-8whk: Crystal structure of CLASP2 in complex with LL5beta -

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Basic information

Entry
Database: PDB / ID: 8whk
TitleCrystal structure of CLASP2 in complex with LL5beta
Components
  • CLIP-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 / positive regulation of extracellular matrix disassembly / basal cortex / 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 / positive regulation of extracellular matrix disassembly / basal cortex / 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
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: 2.401 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,3213
Polymers33,2852
Non-polymers351
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-6 kcal/mol
Surface area15490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.434, 69.294, 134.451
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 26443.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLASP2, KIAA0627 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75122
#2: Protein Pleckstrin homology-like domain family B member 2 / Protein LL5-beta


Mass: 6841.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHLDB2, LL5B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q86SQ0
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.11 Å3/Da / Density % sol: 60.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammolium sulfate, 0.1 M Bis-Tris pH 6.5, and 25% w/v PEG 3,350

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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: 2.4→50 Å / Num. obs: 17283 / % possible obs: 99.8 % / Redundancy: 11.2 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.02 / Rrim(I) all: 0.068 / Χ2: 1.026 / Net I/σ(I): 7.4 / Num. measured all: 193778
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.4-2.44101.0998290.8210.950.3551.1570.93498.7
2.44-2.4910.50.8398510.910.9760.2660.8820.91499.5
2.49-2.53110.7338260.9270.9810.2270.7690.93799.8
2.53-2.5911.30.6848630.9430.9850.210.7160.931100
2.59-2.6411.80.5618540.9730.9930.1690.5870.9299.9
2.64-2.711.50.488330.9670.9920.1450.5020.95100
2.7-2.7711.30.3938650.9780.9940.120.4110.97499.9
2.77-2.8510.30.3148470.9780.9950.1010.330.977100
2.85-2.9311.50.2548370.9910.9980.0780.2661.016100
2.93-3.0212.10.1998580.9910.9980.0590.2081.025100
3.02-3.13120.1538460.9950.9990.0460.161.05599.9
3.13-3.2611.80.1298620.9950.9990.0390.1351.10299.9
3.26-3.4111.80.0978580.9970.9990.030.1021.18599.8
3.41-3.5811.50.0798600.9970.9990.0250.0831.235100
3.58-3.8110.50.0578770.9980.9990.0190.061.1499.9
3.81-4.1120.0498780.9980.9990.0150.0511.12100
4.1-4.5211.80.0458770.99910.0140.0471.055100
4.52-5.1711.30.0418740.99910.0130.0430.981100
5.17-6.5110.50.0449110.99910.0140.0461.04899.9
6.51-50100.0319770.99910.010.0330.97499.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.401→25.312 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2427 836 5.01 %
Rwork0.2061 --
obs0.208 16702 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.401→25.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2207 0 1 33 2241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022241
X-RAY DIFFRACTIONf_angle_d0.6173024
X-RAY DIFFRACTIONf_dihedral_angle_d11.316873
X-RAY DIFFRACTIONf_chiral_restr0.021360
X-RAY DIFFRACTIONf_plane_restr0.003384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.401-2.55080.34421310.28452489X-RAY DIFFRACTION96
2.5508-2.74750.27531390.27072633X-RAY DIFFRACTION100
2.7475-3.02360.37231380.26582634X-RAY DIFFRACTION100
3.0236-3.46020.30241400.26652649X-RAY DIFFRACTION100
3.4602-4.35590.23551410.19222680X-RAY DIFFRACTION100
4.3559-25.3120.18531470.16232781X-RAY DIFFRACTION99
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)
12.124-0.3003-1.33512.34462.19974.2197-0.26120.19770.13680.3418-0.79290.3251-0.6307-0.24380.88050.98210.0888-0.34010.69490.00351.0168-18.185181.44133.2315
29.24960.08392.29452.17263.98528.9835-0.78331.9899-0.0798-1.01710.6709-0.1545-0.37450.78170.07190.6826-0.00570.00440.54350.04660.5066-9.820275.56920.8567
38.3671-0.3291.68356.9138-1.07336.78750.1641-0.1489-0.2039-0.0539-0.2672-0.38580.15530.3760.08120.4027-0.0611-0.09820.390.0460.3743-6.018275.961313.8885
44.9522-0.82992.16937.5694-3.9596.1216-0.37970.54170.890.1496-0.1733-0.599-0.31910.93130.46430.5381-0.0691-0.10040.66130.14620.56411.49569.892230.5371
50.89440.16290.23873.06813.89296.05090.0490.1952-0.0128-1.0615-0.23260.366-0.8644-0.30760.18211.09470.0584-0.04940.4690.04290.625412.828363.913252.5784
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1253 through 1271 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1272 through 1293 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1294 through 1371 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1372 through 1477 )
5X-RAY DIFFRACTION5chain 'B' and (resid 721 through 770 )

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