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- PDB-7lwh: Human neurofibromin 2/merlin residues 1-339 in complex with LATS1 -

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Basic information

Entry
Database: PDB / ID: 7lwh
TitleHuman neurofibromin 2/merlin residues 1-339 in complex with LATS1
Components
  • Merlin
  • Serine/threonine-protein kinase LATS1
KeywordsCELL ADHESION / actin / cancer / cell junction / cell migration / cell signaling / inositol phospholipid / neurofibromatosis type 2 / plasma membrane
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 / regulation of gliogenesis / regulation of ubiquitin-dependent protein catabolic process / positive regulation of early endosome to late endosome transport / Schwann cell proliferation / negative regulation of tyrosine phosphorylation of STAT protein / osteoblast proliferation ...inner cell mass cell fate commitment / inner cell mass cellular morphogenesis / regulation of hippo signaling / regulation of organelle assembly / regulation of gliogenesis / regulation of ubiquitin-dependent protein catabolic process / positive regulation of early endosome to late endosome transport / Schwann cell proliferation / negative regulation of tyrosine phosphorylation of STAT protein / osteoblast proliferation / regulation of transforming growth factor beta receptor signaling pathway / negative regulation of Schwann cell proliferation / cytoplasmic sequestering of protein / negative regulation of osteoblast proliferation / sister chromatid segregation / positive regulation of protein localization to early endosome / ectoderm development / lens fiber cell differentiation / regulation of neural precursor cell proliferation / regulation of actin filament polymerization / hippo signaling / regulation of stem cell proliferation / regulation of organ growth / regulation of intracellular estrogen receptor signaling pathway / negative regulation of receptor signaling pathway via JAK-STAT / mammary gland epithelial cell differentiation / negative regulation of cyclin-dependent protein serine/threonine kinase activity / cell-cell junction organization / regulation of protein localization to nucleus / filopodium membrane / Signaling by Hippo / negative regulation of protein localization to nucleus / spindle pole body / negative regulation of cell-matrix adhesion / negative regulation of cell-cell adhesion / cortical actin cytoskeleton / odontogenesis of dentin-containing tooth / RHO GTPases activate PAKs / cleavage furrow / mesoderm formation / regulation of protein-containing complex assembly / negative regulation of MAPK cascade / keratinocyte differentiation / positive regulation of stress fiber assembly / hormone-mediated signaling pathway / negative regulation of cell migration / filopodium / hippocampus development / nuclear estrogen receptor binding / positive regulation of cell differentiation / adherens junction / regulation of protein stability / negative regulation of canonical Wnt signaling pathway / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / spindle pole / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / MAPK cascade / integrin binding / apical part of cell / lamellipodium / positive regulation of peptidyl-serine phosphorylation / regulation of cell shape / actin binding / midbody / cell body / actin cytoskeleton organization / regulation of apoptotic process / early endosome / cytoskeleton / non-specific serine/threonine protein kinase / regulation of cell cycle / neuron projection / positive regulation of apoptotic process / protein phosphorylation / negative regulation of cell population proliferation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleolus / protein kinase binding / perinuclear region of cytoplasm / magnesium ion binding / ATP binding / membrane / nucleus / plasma membrane / cytosol / 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 / Ezrin/radixin/moesin-like ...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 / Ezrin/radixin/moesin-like / : / 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 / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH-like domain superfamily / Ubiquitin-like 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
IMIDAZOLE / Serine/threonine-protein kinase LATS1 / Merlin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.606 Å
AuthorsPrimi, M.C. / Rangarajan, E.S. / Izard, T.
Funding support1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)
CitationJournal: Matrix Biol Plus / Year: 2021
Title: Conformational flexibility determines the Nf2/merlin tumor suppressor functions.
Authors: Primi, M.C. / Rangarajan, E.S. / Patil, D.N. / Izard, T.
History
DepositionMar 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Merlin
B: Serine/threonine-protein kinase LATS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1606
Polymers42,8612
Non-polymers2994
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-1 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.241, 84.241, 95.859
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 40207.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NF2, SCH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P35240
#2: Protein/peptide Serine/threonine-protein kinase LATS1 / Large tumor suppressor homolog 1 / WARTS protein kinase / h-warts


Mass: 2653.021 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: O95835, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 600 mM imidazole (pH 6.5), 15% (w/v) polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→63.3 Å / Num. obs: 55750 / % possible obs: 99 % / Redundancy: 13.5 % / Biso Wilson estimate: 24.7 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.5
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2710 / CC1/2: 0.877 / % possible all: 97

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Aimlessdata scaling
autoPROCdata processing
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4zrk

4zrk


Resolution: 1.606→63.28 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.859 / SU R Cruickshank DPI: 0.092 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.101 / SU Rfree Blow DPI: 0.097 / SU Rfree Cruickshank DPI: 0.091
RfactorNum. reflection% reflectionSelection details
Rfree0.2325 2748 -RANDOM
Rwork0.205 ---
obs0.2064 55750 99.6 %-
Displacement parametersBiso mean: 33.45 Å2
Baniso -1Baniso -2Baniso -3
1-3.1184 Å20 Å20 Å2
2---9.0257 Å20 Å2
3---5.9073 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.606→63.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2821 0 21 423 3265
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083001HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.874049HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1117SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes530HARMONIC5
X-RAY DIFFRACTIONt_it3001HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion370SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2937SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion14.78
LS refinement shellResolution: 1.61→1.62 Å
RfactorNum. reflection% reflection
Rfree0.3008 62 -
Rwork0.2311 --
obs0.2351 1115 97.03 %

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