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- PDB-4zri: Crystal structure of Merlin-FERM and Lats2 -

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Basic information

Entry
Database: PDB / ID: 4zri
TitleCrystal structure of Merlin-FERM and Lats2
Components
  • Merlin
  • Serine/threonine-protein kinase LATS2
KeywordsSIGNALING PROTEIN/TRANSFERASE / Merlin / FERM / Lats2 / 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 / regulation of organelle assembly / positive regulation of early endosome to late endosome transport / Schwann cell proliferation / regulation of gliogenesis / 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 / regulation of organelle assembly / positive regulation of early endosome to late endosome transport / Schwann cell proliferation / regulation of gliogenesis / osteoblast proliferation / regulation of transforming growth factor beta receptor signaling pathway / negative regulation of Schwann cell proliferation / negative regulation of osteoblast proliferation / positive regulation of protein localization to early endosome / negative regulation of cyclin-dependent protein serine/threonine kinase activity / ectoderm development / lens fiber cell differentiation / regulation of neural precursor cell proliferation / hippo signaling / regulation of stem cell proliferation / 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 / filopodium membrane / negative regulation of protein localization to nucleus / negative regulation of cell-cell adhesion / cortical actin cytoskeleton / positive regulation of NLRP3 inflammasome complex assembly / RHO GTPases activate PAKs / odontogenesis of dentin-containing tooth / cleavage furrow / mesoderm formation / negative regulation of cell-matrix adhesion / canonical Wnt signaling pathway / negative regulation of MAPK cascade / keratinocyte differentiation / positive regulation of stress fiber assembly / hormone-mediated signaling pathway / negative regulation of cell migration / hippocampus development / filopodium / adherens junction / positive regulation of cell differentiation / negative regulation of canonical Wnt signaling pathway / regulation of protein stability / Regulation of actin dynamics for phagocytic cup formation / centriolar satellite / G1/S transition of mitotic cell cycle / ruffle membrane / spindle pole / integrin binding / apical part of cell / MAPK cascade / protein localization / lamellipodium / regulation of cell shape / actin binding / cell body / actin cytoskeleton organization / 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 / regulation of cell cycle / neuron projection / intracellular signal transduction / protein phosphorylation / positive regulation of apoptotic process / negative regulation of cell population proliferation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / perinuclear region of cytoplasm / ATP binding / metal ion binding / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
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 ...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 / 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 / Extension to Ser/Thr-type protein kinases / 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, ATP binding site / Protein kinases ATP-binding region signature. / 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
Merlin / Serine/threonine-protein kinase LATS2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLi, F. / Zhou, H. / Long, J. / Shen, Y.
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 1.2Sep 16, 2015Group: Other
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Merlin
B: Merlin
C: Serine/threonine-protein kinase LATS2
D: Serine/threonine-protein kinase LATS2


Theoretical massNumber of molelcules
Total (without water)83,0904
Polymers83,0904
Non-polymers00
Water543
1
A: Merlin
C: Serine/threonine-protein kinase LATS2


Theoretical massNumber of molelcules
Total (without water)41,5452
Polymers41,5452
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-10 kcal/mol
Surface area16110 Å2
MethodPISA
2
B: Merlin
D: Serine/threonine-protein kinase LATS2


Theoretical massNumber of molelcules
Total (without water)41,5452
Polymers41,5452
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-12 kcal/mol
Surface area15990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.962, 100.549, 65.030
Angle α, β, γ (deg.)90.00, 105.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Merlin / Moesin-ezrin-radixin-like protein / Neurofibromin-2 / Schwannomerlin / Schwannomin


Mass: 38028.914 Da / Num. of mol.: 2 / Fragment: FERM domain, UNP residues 1-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NF2, SCH / Production host: Escherichia coli (E. coli) / References: UniProt: P35240
#2: Protein/peptide Serine/threonine-protein kinase LATS2 / Kinase phosphorylated during mitosis protein / Large tumor suppressor homolog 2 / Serine/threonine- ...Kinase phosphorylated during mitosis protein / Large tumor suppressor homolog 2 / Serine/threonine-protein kinase kpm / Warts-like kinase


Mass: 3515.967 Da / Num. of mol.: 2 / Fragment: UNP residues 68-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LATS2, KPM / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NRM7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 18% iso-Propanol, 0.1M Tris, 5% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 21376 / % possible obs: 99.3 % / Redundancy: 3.8 % / Net I/σ(I): 20.4
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2.2 / % possible all: 95

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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: 2.7→36.008 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 31.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2704 1099 5.14 %
Rwork0.2267 --
obs0.2289 21376 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→36.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4972 0 0 3 4975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015095
X-RAY DIFFRACTIONf_angle_d1.2566920
X-RAY DIFFRACTIONf_dihedral_angle_d16.4251831
X-RAY DIFFRACTIONf_chiral_restr0.079761
X-RAY DIFFRACTIONf_plane_restr0.006889
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6953-2.8180.33731360.31162366X-RAY DIFFRACTION93
2.818-2.96650.41360.30882549X-RAY DIFFRACTION99
2.9665-3.15220.33931190.29352548X-RAY DIFFRACTION100
3.1522-3.39540.31631540.26012519X-RAY DIFFRACTION100
3.3954-3.73680.30211320.24172576X-RAY DIFFRACTION100
3.7368-4.27680.24271210.21062572X-RAY DIFFRACTION100
4.2768-5.38540.25211440.19652568X-RAY DIFFRACTION100
5.3854-36.01130.21871570.19252579X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 44.1048 Å / Origin y: -6.2063 Å / Origin z: 121.3127 Å
111213212223313233
T0.4947 Å2-0.0209 Å2-0.0349 Å2-0.4228 Å20.0343 Å2--0.4438 Å2
L0.5804 °2-0.2975 °2-0.5831 °2-0.2193 °20.345 °2--1.0973 °2
S-0.0281 Å °-0.0537 Å °-0.0468 Å °-0.0039 Å °0.0281 Å °-0.012 Å °0.1153 Å °0.091 Å °-0.0019 Å °
Refinement TLS groupSelection details: all

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