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- PDB-4zrk: Merlin-FERM and Lats1 complex -

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Basic information

Entry
Database: PDB / ID: 4zrk
TitleMerlin-FERM and Lats1 complex
Components
  • Merlin
  • Serine/threonine-protein kinase LATS1
KeywordsSIGNALING PROTEIN/TRANSFERASE / Merlin / FERM / Lats1 / SIGNALING PROTEIN-TRANSFERASE complex
Function / homology
Function and homology information


inner cell mass cell fate commitment / inner cell mass cellular morphogenesis / regulation of hippo signaling / RHO GTPases activate PAKs / Schwann cell proliferation / regulation of gliogenesis / regulation of ubiquitin-dependent protein catabolic process / osteoblast proliferation / regulation of transforming growth factor beta receptor signaling pathway / negative regulation of Schwann cell proliferation ...inner cell mass cell fate commitment / inner cell mass cellular morphogenesis / regulation of hippo signaling / RHO GTPases activate PAKs / Schwann cell proliferation / regulation of gliogenesis / regulation of ubiquitin-dependent protein catabolic process / osteoblast proliferation / regulation of transforming growth factor beta receptor signaling pathway / negative regulation of Schwann cell proliferation / negative regulation of osteoblast proliferation / sister chromatid segregation / negative regulation of cyclin-dependent protein serine/threonine kinase activity / Regulation of actin dynamics for phagocytic cup formation / ectoderm development / lens fiber cell differentiation / regulation of neural precursor cell proliferation / regulation of actin filament polymerization / hippo signaling / regulation of postsynaptic density assembly / regulation of stem cell proliferation / mammary gland epithelial cell differentiation / regulation of intracellular estrogen receptor signaling pathway / negative regulation of receptor signaling pathway via JAK-STAT / regulation of organ growth / cell-cell junction organization / regulation of protein localization to nucleus / Signaling by Hippo / negative regulation of protein localization to nucleus / negative regulation of cell-cell adhesion / cortical actin cytoskeleton / positive regulation of NLRP3 inflammasome complex assembly / odontogenesis of dentin-containing tooth / microtubule organizing center / cleavage furrow / mesoderm formation / regulation of neurogenesis / negative regulation of MAPK cascade / regulation of protein-containing complex assembly / keratinocyte differentiation / positive regulation of stress fiber assembly / ruffle / hormone-mediated signaling pathway / hippocampus development / nuclear estrogen receptor binding / filopodium / adherens junction / positive regulation of cell differentiation / negative regulation of canonical Wnt signaling pathway / brain development / regulation of protein stability / G1/S transition of mitotic cell cycle / spindle pole / G2/M transition of mitotic cell cycle / apical part of cell / MAPK cascade / protein localization / lamellipodium / regulation of cell population proliferation / actin binding / cell body / actin cytoskeleton organization / midbody / regulation of apoptotic process / eukaryotic translation initiation factor 2alpha kinase activity / cytoskeleton / early endosome / 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 / regulation of cell cycle / neuron projection / protein phosphorylation / positive regulation of apoptotic process / negative regulation of cell population proliferation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / protein kinase binding / nucleolus / perinuclear region of cytoplasm
Similarity search - Function
Serine/threonine-protein kinase LATS1, catalytic domain / : / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin family C terminal / Ezrin/radixin/moesin, alpha-helical domain / : ...Serine/threonine-protein kinase LATS1, catalytic domain / : / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin family C terminal / Ezrin/radixin/moesin, alpha-helical domain / : / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like / Acyl-CoA Binding Protein / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / UBA/TS-N domain / FERM domain signature 1. / FERM conserved site / Protein kinase, C-terminal / Protein kinase C terminal domain / FERM domain signature 2. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / UBA-like superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH-domain like / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase LATS1 / Merlin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.316 Å
AuthorsLin, Z. / Li, Y. / Wei, Z. / Zhang, M.
CitationJournal: Cell Res. / Year: 2015
Title: Angiomotin binding-induced activation of Merlin/NF2 in the Hippo pathway
Authors: Li, Y. / Zhou, H. / Li, F. / Chan, S.W. / Lin, Z. / Wei, Z. / Yang, Z. / Guo, F. / Lim, C.J. / Xing, W. / Shen, Y. / Hong, W. / Long, J. / Zhang, M.
History
DepositionMay 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Merlin
B: Merlin
C: Merlin
D: Merlin
E: Serine/threonine-protein kinase LATS1
F: Serine/threonine-protein kinase LATS1
G: Serine/threonine-protein kinase LATS1
H: Serine/threonine-protein kinase LATS1


Theoretical massNumber of molelcules
Total (without water)166,5958
Polymers166,5958
Non-polymers00
Water59433
1
A: Merlin
E: Serine/threonine-protein kinase LATS1


Theoretical massNumber of molelcules
Total (without water)41,6492
Polymers41,6492
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-13 kcal/mol
Surface area16450 Å2
MethodPISA
2
B: Merlin
F: Serine/threonine-protein kinase LATS1


Theoretical massNumber of molelcules
Total (without water)41,6492
Polymers41,6492
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-12 kcal/mol
Surface area16450 Å2
MethodPISA
3
C: Merlin
G: Serine/threonine-protein kinase LATS1


Theoretical massNumber of molelcules
Total (without water)41,6492
Polymers41,6492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-14 kcal/mol
Surface area16970 Å2
MethodPISA
4
D: Merlin
H: Serine/threonine-protein kinase LATS1


Theoretical massNumber of molelcules
Total (without water)41,6492
Polymers41,6492
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-12 kcal/mol
Surface area16520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.050, 110.774, 168.693
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
Merlin / Moesin-ezrin-radixin-like protein / Neurofibromin-2 / Schwannomin


Mass: 38044.910 Da / Num. of mol.: 4 / Fragment: FERM domain, UNP residues 1-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nf2, Nf-2 / Production host: Escherichia coli (E. coli) / References: UniProt: P46662
#2: Protein/peptide
Serine/threonine-protein kinase LATS1 / Large tumor suppressor homolog 1 / WARTS protein kinase / h-warts


Mass: 3603.951 Da / Num. of mol.: 4 / Fragment: UNP residues 69-100
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Sodium malonate, 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 89074 / % possible obs: 99.4 % / Redundancy: 5.9 % / Net I/σ(I): 28.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
Blu-Icedata collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ISN

1isn


Resolution: 2.316→42.78 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2786 4476 5.03 %
Rwork0.2457 --
obs0.2474 89074 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.316→42.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10259 0 0 33 10292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110532
X-RAY DIFFRACTIONf_angle_d1.23214250
X-RAY DIFFRACTIONf_dihedral_angle_d14.9513890
X-RAY DIFFRACTIONf_chiral_restr0.0541553
X-RAY DIFFRACTIONf_plane_restr0.0071804
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3163-2.34270.3671850.28541575X-RAY DIFFRACTION55
2.3427-2.37020.36911560.28632790X-RAY DIFFRACTION99
2.3702-2.39910.33351450.28472852X-RAY DIFFRACTION100
2.3991-2.42950.33681350.28092829X-RAY DIFFRACTION100
2.4295-2.46150.36151640.27242870X-RAY DIFFRACTION100
2.4615-2.49520.32181460.26632812X-RAY DIFFRACTION100
2.4952-2.53080.32481430.2752882X-RAY DIFFRACTION100
2.5308-2.56860.32431690.27312803X-RAY DIFFRACTION100
2.5686-2.60870.31231410.26362857X-RAY DIFFRACTION100
2.6087-2.65150.30031550.2562866X-RAY DIFFRACTION100
2.6515-2.69720.33731400.25842861X-RAY DIFFRACTION100
2.6972-2.74620.29521460.26872826X-RAY DIFFRACTION100
2.7462-2.7990.26931470.26562894X-RAY DIFFRACTION100
2.799-2.85620.28621400.26682881X-RAY DIFFRACTION100
2.8562-2.91830.33961460.26222860X-RAY DIFFRACTION100
2.9183-2.98610.3161990.272798X-RAY DIFFRACTION100
2.9861-3.06080.27351670.26532881X-RAY DIFFRACTION100
3.0608-3.14350.33841580.26042832X-RAY DIFFRACTION100
3.1435-3.2360.30911380.25352873X-RAY DIFFRACTION100
3.236-3.34040.30211510.25242885X-RAY DIFFRACTION100
3.3404-3.45970.28181370.24432898X-RAY DIFFRACTION100
3.4597-3.59820.29481440.24472894X-RAY DIFFRACTION100
3.5982-3.76190.25931580.24832872X-RAY DIFFRACTION100
3.7619-3.96010.2861390.23292903X-RAY DIFFRACTION99
3.9601-4.2080.25281700.21732863X-RAY DIFFRACTION100
4.208-4.53250.2391390.22512902X-RAY DIFFRACTION100
4.5325-4.9880.24711510.21792939X-RAY DIFFRACTION100
4.988-5.70840.29111580.23172910X-RAY DIFFRACTION100
5.7084-7.18640.25441740.24842958X-RAY DIFFRACTION100
7.1864-42.78720.24321350.26692732X-RAY DIFFRACTION88
Refinement TLS params.Method: refined / Origin x: 29.6378 Å / Origin y: -10.2086 Å / Origin z: -15.2736 Å
111213212223313233
T0.3868 Å20.0298 Å2-0.0374 Å2-0.4275 Å2-0.0235 Å2--0.3904 Å2
L0.075 °20.0612 °2-0.035 °2-0.2173 °2-0.0612 °2--0.0816 °2
S-0.0039 Å °-0.0566 Å °0.0478 Å °-0.0294 Å °-0.0376 Å °0.0636 Å °-0.0363 Å °0.0153 Å °0.034 Å °
Refinement TLS groupSelection details: all

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