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- PDB-6j68: Structure of KIBRA and LATS1 Complex -

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Basic information

Entry
Database: PDB / ID: 6j68
TitleStructure of KIBRA and LATS1 Complex
Components
  • Peptide from Serine/threonine-protein kinase LATS1
  • Protein KIBRA
KeywordsCELL CYCLE / Tandem WW domain / Tandem PY motif / HIPPO Signaling
Function / homology
Function and homology information


inner cell mass cell fate commitment / inner cell mass cellular morphogenesis / Signaling by Hippo / regulation of ubiquitin-dependent protein catabolic process / regulation of transforming growth factor beta receptor signaling pathway / : / sister chromatid segregation / negative regulation of organ growth / regulation of actin filament polymerization / hippo signaling ...inner cell mass cell fate commitment / inner cell mass cellular morphogenesis / Signaling by Hippo / regulation of ubiquitin-dependent protein catabolic process / regulation of transforming growth factor beta receptor signaling pathway / : / sister chromatid segregation / negative regulation of organ growth / regulation of actin filament polymerization / hippo signaling / regulation of postsynaptic density assembly / regulation of intracellular estrogen receptor signaling pathway / mammary gland epithelial cell differentiation / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of protein localization to nucleus / positive regulation of NLRP3 inflammasome complex assembly / postsynaptic density, intracellular component / negative regulation of hippo signaling / keratinocyte differentiation / signaling adaptor activity / hormone-mediated signaling pathway / nuclear estrogen receptor binding / negative regulation of canonical Wnt signaling pathway / kinase binding / spindle pole / ruffle membrane / G2/M transition of mitotic cell cycle / cell migration / protein localization / midbody / transcription coactivator activity / eukaryotic translation initiation factor 2alpha kinase activity / positive regulation of MAPK cascade / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / postsynapse / protein phosphorylation / cell division / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / magnesium ion binding / protein-containing complex / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase LATS1, catalytic domain / : / WWC, C2 domain / : / : / UBA/TS-N domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. ...Serine/threonine-protein kinase LATS1, catalytic domain / : / WWC, C2 domain / : / : / UBA/TS-N domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / C2 domain / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Protein KIBRA / Serine/threonine-protein kinase LATS1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.495 Å
AuthorsLin, Z. / Yang, Z. / Ji, Z. / Zhang, M.
CitationJournal: Elife / Year: 2019
Title: Decoding WW domain tandem-mediated target recognitions in tissue growth and cell polarity.
Authors: Lin, Z. / Yang, Z. / Xie, R. / Ji, Z. / Guan, K. / Zhang, M.
History
DepositionJan 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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: Protein KIBRA
B: Protein KIBRA
C: Peptide from Serine/threonine-protein kinase LATS1
D: Peptide from Serine/threonine-protein kinase LATS1


Theoretical massNumber of molelcules
Total (without water)37,9264
Polymers37,9264
Non-polymers00
Water1,44180
1
A: Protein KIBRA
C: Peptide from Serine/threonine-protein kinase LATS1


Theoretical massNumber of molelcules
Total (without water)18,9632
Polymers18,9632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-9 kcal/mol
Surface area10640 Å2
MethodPISA
2
B: Protein KIBRA
D: Peptide from Serine/threonine-protein kinase LATS1


Theoretical massNumber of molelcules
Total (without water)18,9632
Polymers18,9632
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-9 kcal/mol
Surface area9580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.314, 62.837, 156.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein KIBRA / Kidney and brain protein / KIBRA / WW domain-containing protein 1


Mass: 16036.611 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Wwc1, Kiaa0869 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q5SXA9
#2: Protein/peptide Peptide from Serine/threonine-protein kinase LATS1 / Large tumor suppressor homolog 1 / WARTS protein kinase


Mass: 2926.220 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lats1, Warts / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: Q8BYR2, non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 3.07 Å3/Da / Density % sol: 59.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8 / Details: 0.1M Tris, 28% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97854 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 2.495→50 Å / Num. obs: 15953 / % possible obs: 99.5 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 23.6
Reflection shellResolution: 2.495→2.54 Å / Rmerge(I) obs: 0.982 / Num. unique obs: 713

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.495→49.035 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.274 750 4.97 %
Rwork0.222 --
obs0.2246 15079 94.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.495→49.035 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2190 0 0 80 2270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112258
X-RAY DIFFRACTIONf_angle_d1.2613097
X-RAY DIFFRACTIONf_dihedral_angle_d16.392814
X-RAY DIFFRACTIONf_chiral_restr0.051324
X-RAY DIFFRACTIONf_plane_restr0.005413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4948-2.68740.39471210.26382241X-RAY DIFFRACTION76
2.6874-2.95780.31031380.27232940X-RAY DIFFRACTION97
2.9578-3.38570.3221790.26792936X-RAY DIFFRACTION100
3.3857-4.26520.24411510.19793034X-RAY DIFFRACTION100
4.2652-49.0440.23651610.19323178X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 13.3476 Å / Origin y: -5.0154 Å / Origin z: -20.1226 Å
111213212223313233
T0.1144 Å2-0.0345 Å20.0028 Å2-0.1598 Å2-0.0245 Å2--0.1047 Å2
L0.0191 °2-0.0154 °20.114 °2-0.011 °20.0161 °2--0.0754 °2
S-0.0413 Å °0.025 Å °-0.0284 Å °-0.0149 Å °0.0373 Å °0.0082 Å °-0.0205 Å °0.0618 Å °0 Å °
Refinement TLS groupSelection details: all

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