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- PDB-5b5w: Crystal structure of MOB1-LATS1 NTR domain complex -

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Basic information

Entry
Database: PDB / ID: 5b5w
TitleCrystal structure of MOB1-LATS1 NTR domain complex
Components
  • MOB kinase activator 1B
  • Serine/threonine-protein kinase LATS1
KeywordsMETAL BINDING PROTEIN/APOTOSIS / MOB1 LATS1 Hippo pathway / METAL BINDING PROTEIN-APOTOSIS complex
Function / homology
Function and homology information


inner cell mass cell fate commitment / regulation of protein autophosphorylation / inner cell mass cellular morphogenesis / Signaling by Hippo / regulation of ubiquitin-dependent protein catabolic process / regulation of transforming growth factor beta receptor signaling pathway / negative regulation of cyclin-dependent protein serine/threonine kinase activity / sister chromatid segregation / regulation of actin filament polymerization / hippo signaling ...inner cell mass cell fate commitment / regulation of protein autophosphorylation / inner cell mass cellular morphogenesis / Signaling by Hippo / regulation of ubiquitin-dependent protein catabolic process / regulation of transforming growth factor beta receptor signaling pathway / negative regulation of cyclin-dependent protein serine/threonine kinase activity / sister chromatid segregation / regulation of actin filament polymerization / hippo signaling / mammary gland epithelial cell differentiation / regulation of intracellular estrogen receptor signaling pathway / regulation of postsynaptic density assembly / regulation of organ growth / Signaling by Hippo / kinase activator activity / negative regulation of protein localization to nucleus / positive regulation of NLRP3 inflammasome complex assembly / microtubule organizing center / regulation of protein-containing complex assembly / keratinocyte differentiation / hormone-mediated signaling pathway / nuclear estrogen receptor binding / G1/S transition of mitotic cell cycle / negative regulation of canonical Wnt signaling pathway / G2/M transition of mitotic cell cycle / kinase binding / spindle pole / intracellular protein localization / midbody / protein phosphorylation / non-specific serine/threonine protein kinase / postsynapse / positive regulation of apoptotic process / cell division / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / protein kinase binding / glutamatergic synapse / magnesium ion binding / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase LATS1, catalytic domain / : / MOB kinase activator / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / : / UBA/TS-N domain / Protein kinase, C-terminal ...Serine/threonine-protein kinase LATS1, catalytic domain / : / MOB kinase activator / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / : / UBA/TS-N domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein kinase LATS1 / MOB kinase activator 1B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.957 Å
AuthorsKIM, S.-Y. / Tachioka, Y. / Mori, T. / Hakoshima, T.
CitationJournal: Sci Rep / Year: 2016
Title: Structural basis for autoinhibition and its relief of MOB1 in the Hippo pathway
Authors: Kim, S.Y. / Tachioka, Y. / Mori, T. / Hakoshima, T.
History
DepositionMay 24, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
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: MOB kinase activator 1B
U: Serine/threonine-protein kinase LATS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0373
Polymers31,9722
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-16 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.747, 71.760, 57.855
Angle α, β, γ (deg.)90.00, 101.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MOB kinase activator 1B / Mob1 homolog 1A / Mps one binder kinase activator-like 1A


Mass: 21592.697 Da / Num. of mol.: 1 / Fragment: UNP residues 33-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mob1b, Mobkl1a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BPB0
#2: Protein Serine/threonine-protein kinase LATS1 / Large tumor suppressor homolog 1 / WARTS protein kinase / h-warts


Mass: 10379.002 Da / Num. of mol.: 1 / Fragment: UNP residues 622-704
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LATS1, WARTS / Production host: Escherichia coli (E. coli)
References: UniProt: O95835, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.957→30 Å / Num. obs: 6660 / % possible obs: 94.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 21.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PI1

1pi1


Resolution: 2.957→28.296 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.98
RfactorNum. reflection% reflection
Rfree0.2704 348 5.7 %
Rwork0.2336 --
obs0.2357 6109 91.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.957→28.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 1 0 1967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032018
X-RAY DIFFRACTIONf_angle_d0.7452709
X-RAY DIFFRACTIONf_dihedral_angle_d14.642767
X-RAY DIFFRACTIONf_chiral_restr0.027286
X-RAY DIFFRACTIONf_plane_restr0.003349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.957-3.72420.36951410.32262686X-RAY DIFFRACTION85
3.7242-28.29770.25032070.21153075X-RAY DIFFRACTION97

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