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- PDB-4zrj: Structure of Merlin-FERM and CTD -

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Basic information

Entry
Database: PDB / ID: 4zrj
TitleStructure of Merlin-FERM and CTD
Components(Merlin) x 2
KeywordsSIGNALING PROTEIN / Merlin / FERM / CTD
Function / homology
Function and homology information


regulation of hippo signaling / regulation of organelle assembly / Schwann cell proliferation / positive regulation of early endosome to late endosome transport / regulation of gliogenesis / osteoblast proliferation / negative regulation of Schwann cell proliferation / negative regulation of osteoblast proliferation / positive regulation of protein localization to early endosome / ectoderm development ...regulation of hippo signaling / regulation of organelle assembly / Schwann cell proliferation / positive regulation of early endosome to late endosome transport / regulation of gliogenesis / osteoblast proliferation / negative regulation of Schwann cell proliferation / negative regulation of osteoblast proliferation / positive regulation of protein localization to early endosome / ectoderm development / lens fiber cell differentiation / regulation of neural precursor cell proliferation / regulation of stem cell proliferation / negative regulation of receptor signaling pathway via JAK-STAT / cell-cell junction organization / regulation of protein localization to nucleus / filopodium membrane / negative regulation of cell-cell adhesion / cortical actin cytoskeleton / odontogenesis of dentin-containing tooth / RHO GTPases activate PAKs / cleavage furrow / mesoderm formation / negative regulation of cell-matrix adhesion / negative regulation of MAPK cascade / positive regulation of stress fiber assembly / negative regulation of cell migration / hippocampus development / adherens junction / filopodium / positive regulation of cell differentiation / regulation of protein stability / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / integrin binding / apical part of cell / MAPK cascade / regulation of cell shape / lamellipodium / cell body / actin binding / actin cytoskeleton organization / regulation of apoptotic process / early endosome / cytoskeleton / regulation of cell cycle / neuron projection / negative regulation of cell population proliferation / nucleolus / perinuclear region of cytoplasm / nucleus / membrane / plasma membrane / cytoplasm / 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 / Acyl-CoA Binding Protein ...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 / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / PH-domain like / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / PH-like domain superfamily / Roll / Ubiquitin-like domain superfamily / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLin, Z. / Li, F. / 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 1.2Feb 19, 2020Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 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: Merlin
B: Merlin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,21710
Polymers48,4802
Non-polymers7378
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-29 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.895, 68.202, 82.320
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 / Schwannomerlin / Schwannomin


Mass: 37730.621 Da / Num. of mol.: 1 / 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 Merlin / Moesin-ezrin-radixin-like protein / Neurofibromin-2 / Schwannomerlin / Schwannomin


Mass: 10749.181 Da / Num. of mol.: 1 / Fragment: C terminal domain, UNP residues 506-595 / Mutation: S518D, A585W
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
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 1.97 Å3/Da / Density % sol: 37.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M Bis-Tris, 21% PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 17339 / % possible obs: 99.5 % / Redundancy: 7.2 % / Net I/σ(I): 26.3
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 7.3 / % possible all: 98.6

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Processing

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

1isn


Resolution: 2.3→31.505 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 1749 10.09 %
Rwork0.1863 --
obs0.1925 17339 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→31.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3045 0 48 107 3200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083149
X-RAY DIFFRACTIONf_angle_d1.0974242
X-RAY DIFFRACTIONf_dihedral_angle_d16.8071160
X-RAY DIFFRACTIONf_chiral_restr0.074467
X-RAY DIFFRACTIONf_plane_restr0.004534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2922-2.35960.28071370.17751213X-RAY DIFFRACTION93
2.3596-2.43570.26881420.17851257X-RAY DIFFRACTION96
2.4357-2.52280.31021410.18821258X-RAY DIFFRACTION97
2.5228-2.62370.27281440.18571260X-RAY DIFFRACTION97
2.6237-2.74310.25631440.17861291X-RAY DIFFRACTION98
2.7431-2.88760.23991430.18231292X-RAY DIFFRACTION98
2.8876-3.06840.28481460.19231294X-RAY DIFFRACTION99
3.0684-3.30510.28361450.17831304X-RAY DIFFRACTION99
3.3051-3.63720.23541460.17251321X-RAY DIFFRACTION99
3.6372-4.16250.19061490.16461338X-RAY DIFFRACTION100
4.1625-5.24040.2151570.18011363X-RAY DIFFRACTION100
5.2404-31.50780.26781550.24511399X-RAY DIFFRACTION98

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