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- PDB-1isn: Crystal structure of merlin FERM domain -

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Basic information

Entry
Database: PDB / ID: 1isn
TitleCrystal structure of merlin FERM domain
Componentsmerlin
KeywordsCELL ADHESION / FERM domain
Function / homology
Function and homology information


regulation of hippo signaling / RHO GTPases activate PAKs / Schwann cell proliferation / regulation of gliogenesis / osteoblast proliferation / negative regulation of Schwann cell proliferation / negative regulation of osteoblast proliferation / Regulation of actin dynamics for phagocytic cup formation / ectoderm development / lens fiber cell differentiation ...regulation of hippo signaling / RHO GTPases activate PAKs / Schwann cell proliferation / regulation of gliogenesis / osteoblast proliferation / negative regulation of Schwann cell proliferation / negative regulation of osteoblast proliferation / Regulation of actin dynamics for phagocytic cup formation / 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 / negative regulation of cell-cell adhesion / cortical actin cytoskeleton / odontogenesis of dentin-containing tooth / cleavage furrow / mesoderm formation / regulation of neurogenesis / negative regulation of MAPK cascade / positive regulation of stress fiber assembly / ruffle / hippocampus development / adherens junction / filopodium / positive regulation of cell differentiation / brain development / regulation of protein stability / apical part of cell / MAPK cascade / lamellipodium / regulation of cell population proliferation / 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 / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsShimizu, T. / Seto, A. / Maita, N. / Hamada, K. / Tsukita, S. / Tsukita, S. / Hakoshima, T.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structural basis for neurofibromatosis type 2. Crystal structure of the merlin FERM domain.
Authors: Shimizu, T. / Seto, A. / Maita, N. / Hamada, K. / Tsukita, S. / Tsukita, S. / Hakoshima, T.
History
DepositionDec 13, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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

Downloads & links

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Assembly

Deposited unit
A: merlin


Theoretical massNumber of molelcules
Total (without water)38,3671
Polymers38,3671
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.408, 67.408, 179.137
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein merlin


Mass: 38367.320 Da / Num. of mol.: 1 / Fragment: FERM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: neurofibromatosis type 2 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P46662

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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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG6000, LiCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
113.6 mg/mlprotein1drop
210 mMMES1droppH6.8
37.5 %PEG60001drop
4150 mM1dropNaCl
5250 mM1dropLiCl
60.5 mMdithiothreitol1drop
750 mMHEPES1reservoirpH7.0
815 %PEG60001reservoir
9500 mM1reservoirLiCl

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9198 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 10, 2000
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 8825 / Num. obs: 8807 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 50.8 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.4
Reflection shellResolution: 2.9→3.03 Å / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.4 / % possible all: 75.8
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 32050 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 75.8 % / Rmerge(I) obs: 0.316

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DPSdata reduction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GC6

1gc6


Resolution: 2.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 907 11.6 %RANDOM
Rwork0.229 ---
all0.237 8728 --
obs0.235 7821 --
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2617 0 0 0 2617
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d1.24
LS refinement shellResolution: 2.9→3.03 Å
RfactorNum. reflection
Rfree0.4065 83
Rwork0.3728 -
obs-796
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor all: 0.237 / Rfactor obs: 0.229 / Rfactor Rfree: 0.284 / Rfactor Rwork: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.24
LS refinement shell
*PLUS
Highest resolution: 2.9 Å / Rfactor Rfree: 0.4065 / Rfactor Rwork: 0.3728 / Rfactor obs: 0.373

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