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- PDB-1h4r: Crystal Structure of the FERM domain of Merlin, the Neurofibromat... -

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Basic information

Entry
Database: PDB / ID: 1h4r
TitleCrystal Structure of the FERM domain of Merlin, the Neurofibromatosis 2 Tumor Suppressor Protein.
ComponentsMERLIN
KeywordsSTRUCTURAL PROTEIN / FERM / NEUROFIBROMATOSIS / NF2 / CYTOSKELETON / ANTI-ONCOGENE
Function / homology
Function and homology information


regulation of hippo signaling / regulation of organelle assembly / regulation of gliogenesis / positive regulation of early endosome to late endosome transport / Schwann cell proliferation / negative regulation of tyrosine phosphorylation of STAT protein / osteoblast proliferation / negative regulation of Schwann cell proliferation / negative regulation of osteoblast proliferation / positive regulation of protein localization to early endosome ...regulation of hippo signaling / regulation of organelle assembly / regulation of gliogenesis / positive regulation of early endosome to late endosome transport / Schwann cell proliferation / negative regulation of tyrosine phosphorylation of STAT protein / 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-matrix adhesion / 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 MAPK cascade / positive regulation of stress fiber assembly / negative regulation of cell migration / filopodium / hippocampus development / positive regulation of cell differentiation / adherens junction / regulation of protein stability / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / MAPK cascade / integrin binding / apical part of cell / lamellipodium / regulation of cell shape / actin binding / cell body / 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 / membrane / nucleus / plasma membrane / cytosol / cytoplasm
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) / PH-domain like / FERM central domain / 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 / Ubiquitin-like domain superfamily / Roll / 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: 1.8 Å
AuthorsCooper, D.R. / Kang, B.S. / Sheffield, P. / Devedjiev, Y. / Derewenda, Z.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: The Structure of the Ferm Domain of Merlin, the Neurofibromatosis Type 2 Gene Product.
Authors: Kang, B.S. / Cooper, D.R. / Devedjiev, Y. / Derewenda, U. / Derewenda, Z.S.
History
DepositionMay 14, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MERLIN
B: MERLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5528
Polymers73,9762
Non-polymers5766
Water15,511861
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)87.018, 89.328, 96.764
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


Mass: 36987.848 Da / Num. of mol.: 2 / Fragment: FERM DOMAIN RESIDUES 1-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: RECOMBINANTLY EXPRESSED IN BL21-RIL CELLS AS A HEXA-HISTIDINE AND GST TAGGED PROTEIN. THE TAG WAS REMOVED BY RTEV CLEAVAGE.
Plasmid: PHGM313 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35240
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 861 / Source method: isolated from a natural source / Formula: H2O
Compound detailsACTS AS A MEMBRANE STABILIZING PROTEIN.
Sequence detailsN-TERMINAL GLYCINE IS FROM RTEV CLEAVAGE.

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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: 2.5 Å3/Da / Density % sol: 51.4 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: THE PROTEIN WAS CRYSTALLIZED USING HANGING-DROP VAPOR DIFFUSION WIHTH 56% AMMONIUM SULFATE, 2% DIOXANE, 100 MM CACODYLATE, PH 6.5. A 1:1 RATIO OF PROTEIN TO WELL SOLUTION WAS USED.
Crystal grow
*PLUS
Temperature: 294 K / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
256 %saturatedammonium sulfate1reservoir
32 %dioxane1reservoir
40.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.92
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 68182 / % possible obs: 95.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 2.33 / % possible all: 97.2
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Num. obs: 68222 / % possible obs: 95.4 % / Redundancy: 3.6 %
Reflection shell
*PLUS
% possible obs: 97.2 % / Num. unique obs: 6875 / Rmerge(I) obs: 0.622

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Processing

Software
NameVersionClassification
REFMAC5.0.36refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GC6.PDB

1gc6


Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.675 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 985 1.5 %RANDOM
Rwork0.193 ---
obs-66303 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4912 0 30 861 5803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225040
X-RAY DIFFRACTIONr_bond_other_d0.0010.024555
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.391.966803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg0.759310620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1230.2726
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025465
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021050
X-RAY DIFFRACTIONr_nbd_refined0.2250.31069
X-RAY DIFFRACTIONr_nbd_other0.2090.34442
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2390.5687
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.328
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.373
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3460.555
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8051.52940
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5124759
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2232100
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7064.52044
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.268 77
Rwork0.26 4917
Software
*PLUS
Name: REFMAC / Version: 5.0.36 18/01/2001 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 5 Å / Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.39
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.847 Å / Rfactor Rfree: 0.268 / % reflection Rfree: 77 % / Rfactor Rwork: 0.26 / Num. reflection Rwork: 4917

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