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- PDB-5b6b: Complex of LATS1 and phosphomimetic MOB1b -

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Basic information

Entry
Database: PDB / ID: 5b6b
TitleComplex of LATS1 and phosphomimetic MOB1b
Components
  • MOB kinase activator 1B
  • Serine/threonine-protein kinase LATS1
KeywordsMETAL BINDING PROTEIN/SIGNALING PROTEIN / MOB1 LATS1 Hippo pathway / METAL BINDING PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


inner cell mass cell fate commitment / inner cell mass cellular morphogenesis / regulation of protein autophosphorylation / Signaling by Hippo / regulation of ubiquitin-dependent protein catabolic process / sister chromatid segregation / cytoplasmic sequestering of protein / regulation of transforming growth factor beta receptor signaling pathway / hippo signaling / regulation of actin filament polymerization ...inner cell mass cell fate commitment / inner cell mass cellular morphogenesis / regulation of protein autophosphorylation / Signaling by Hippo / regulation of ubiquitin-dependent protein catabolic process / sister chromatid segregation / cytoplasmic sequestering of protein / regulation of transforming growth factor beta receptor signaling pathway / hippo signaling / regulation of actin filament polymerization / mammary gland epithelial cell differentiation / regulation of intracellular estrogen receptor signaling pathway / negative regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of organ growth / kinase activator activity / negative regulation of protein localization to nucleus / microtubule organizing center / protein kinase activator activity / regulation of protein-containing complex assembly / keratinocyte differentiation / hormone-mediated signaling pathway / nuclear estrogen receptor binding / negative regulation of canonical Wnt signaling pathway / protein localization / kinase binding / spindle pole / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / positive regulation of peptidyl-serine phosphorylation / midbody / peptidyl-serine phosphorylation / non-specific serine/threonine protein kinase / positive regulation of protein phosphorylation / positive regulation of apoptotic process / cell division / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / magnesium ion binding / ATP binding / nucleus / metal ion binding / 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 / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. ...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 / 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
MOB kinase activator 1B / Serine/threonine-protein kinase LATS1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.536 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 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: 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
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
J: Serine/threonine-protein kinase LATS1
B: MOB kinase activator 1B
C: Serine/threonine-protein kinase LATS1
D: MOB kinase activator 1B
E: Serine/threonine-protein kinase LATS1
F: MOB kinase activator 1B
G: Serine/threonine-protein kinase LATS1
H: MOB kinase activator 1B
I: Serine/threonine-protein kinase LATS1
K: MOB kinase activator 1B
L: Serine/threonine-protein kinase LATS1
M: MOB kinase activator 1B
N: Serine/threonine-protein kinase LATS1
O: MOB kinase activator 1B
P: Serine/threonine-protein kinase LATS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,24331
Polymers285,47216
Non-polymers77115
Water00
1
A: MOB kinase activator 1B
J: Serine/threonine-protein kinase LATS1
B: MOB kinase activator 1B
C: Serine/threonine-protein kinase LATS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5708
Polymers71,3684
Non-polymers2024
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8240 Å2
ΔGint-61 kcal/mol
Surface area26220 Å2
MethodPISA
2
D: MOB kinase activator 1B
E: Serine/threonine-protein kinase LATS1
K: MOB kinase activator 1B
L: Serine/threonine-protein kinase LATS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5708
Polymers71,3684
Non-polymers2024
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-57 kcal/mol
Surface area25710 Å2
MethodPISA
3
F: MOB kinase activator 1B
G: Serine/threonine-protein kinase LATS1
H: MOB kinase activator 1B
I: Serine/threonine-protein kinase LATS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5708
Polymers71,3684
Non-polymers2024
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-67 kcal/mol
Surface area25740 Å2
MethodPISA
4
M: MOB kinase activator 1B
N: Serine/threonine-protein kinase LATS1
O: MOB kinase activator 1B
P: Serine/threonine-protein kinase LATS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5347
Polymers71,3684
Non-polymers1663
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-44 kcal/mol
Surface area25260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.646, 301.437, 127.379
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 25304.953 Da / Num. of mol.: 8 / Mutation: T35D, T22D
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


Mass: 10379.002 Da / Num. of mol.: 8 / Fragment: UNP residues 621-703
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lats1, Warts / Production host: Escherichia coli (E. coli)
References: UniProt: Q8BYR2, non-specific serine/threonine protein kinase
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / 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: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, sodium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 41452 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 19.9
Reflection shellResolution: 3.56→30 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B5W

5b5w


Resolution: 3.536→48.644 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2656 1998 5.01 %
Rwork0.2223 --
obs0.2245 39860 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.536→48.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16611 0 15 0 16626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00517042
X-RAY DIFFRACTIONf_angle_d1.04222889
X-RAY DIFFRACTIONf_dihedral_angle_d18.1586435
X-RAY DIFFRACTIONf_chiral_restr0.1572430
X-RAY DIFFRACTIONf_plane_restr0.0032942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5363-3.62470.35691370.28562499X-RAY DIFFRACTION94
3.6247-3.72270.32461380.27452698X-RAY DIFFRACTION100
3.7227-3.83220.29941530.24882696X-RAY DIFFRACTION100
3.8322-3.95580.32161330.24432667X-RAY DIFFRACTION100
3.9558-4.09710.2731450.24272692X-RAY DIFFRACTION100
4.0971-4.26110.28761360.22342681X-RAY DIFFRACTION100
4.2611-4.45490.21741470.20152701X-RAY DIFFRACTION100
4.4549-4.68960.22851420.20032704X-RAY DIFFRACTION100
4.6896-4.98310.25411360.19392713X-RAY DIFFRACTION100
4.9831-5.36740.26731510.20872721X-RAY DIFFRACTION100
5.3674-5.90670.27821430.2222713X-RAY DIFFRACTION100
5.9067-6.75950.26021390.25262739X-RAY DIFFRACTION100
6.7595-8.50880.26421470.22272773X-RAY DIFFRACTION100
8.5088-48.64850.23771510.20132865X-RAY DIFFRACTION99

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