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- PDB-1e5w: Structure of isolated FERM domain and first long helix of moesin -

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Basic information

Entry
Database: PDB / ID: 1e5w
TitleStructure of isolated FERM domain and first long helix of moesin
ComponentsMOESIN
KeywordsMEMBRANE PROTEIN / MOESIN / FERM / ERM
Function / homology
Function and homology information


regulation of lymphocyte migration / T cell aggregation / regulation of organelle assembly / T cell migration / positive regulation of early endosome to late endosome transport / membrane to membrane docking / uropod / immunological synapse formation / gland morphogenesis / positive regulation of protein localization to early endosome ...regulation of lymphocyte migration / T cell aggregation / regulation of organelle assembly / T cell migration / positive regulation of early endosome to late endosome transport / membrane to membrane docking / uropod / immunological synapse formation / gland morphogenesis / positive regulation of protein localization to early endosome / cellular response to testosterone stimulus / establishment of epithelial cell apical/basal polarity / establishment of endothelial barrier / Sensory processing of sound by outer hair cells of the cochlea / positive regulation of podosome assembly / Sensory processing of sound by inner hair cells of the cochlea / microvillus membrane / leukocyte cell-cell adhesion / regulation of cell size / leukocyte migration / pseudopodium / Recycling pathway of L1 / microvillus / T cell proliferation / cell adhesion molecule binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / filopodium / cell periphery / adherens junction / structural constituent of cytoskeleton / positive regulation of protein catabolic process / double-stranded RNA binding / Signaling by ALK fusions and activated point mutants / apical part of cell / actin binding / regulation of cell shape / basolateral plasma membrane / vesicle / cytoskeleton / blood microparticle / apical plasma membrane / focal adhesion / signaling receptor binding / positive regulation of gene expression / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / cell surface / extracellular space / extracellular exosome / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #450 / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin, alpha-helical domain / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin family C terminal / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #450 / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin, alpha-helical domain / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin family C terminal / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / MAD / Resolution: 2.7 Å
AuthorsEdwards, S.D. / Keep, N.H.
CitationJournal: Biochemistry / Year: 2001
Title: The 2.7 A Crystal Structure of the Activated Ferm Domain of Moesin: An Analysis of Structural Changes on Activation
Authors: Edwards, S.D. / Keep, N.H.
History
DepositionAug 3, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2001Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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

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Assembly

Deposited unit
A: MOESIN


Theoretical massNumber of molelcules
Total (without water)41,0541
Polymers41,0541
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)94.360, 94.360, 156.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein MOESIN


Mass: 41054.305 Da / Num. of mol.: 1 / Fragment: FERM DOMAIN AND HELIX RESIDUE 1-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: RECOMBINANT EXPRESSION IN E.COLI OF NON-FUSION PROTEIN
Plasmid: PET / Gene (production host): MOESIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): BLR / References: UniProt: P26038
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPROBABLY INVOLVED IN ANCHORING OF MAJOR CYTOSKELETAL STRUCTURES TO THE PLASMA MEMBRANE.

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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: 4.23 Å3/Da / Density % sol: 66 %
Crystal growpH: 7.5
Details: 25% ETHYLENE GLYCOL, 100MM HEPES PH7.5, 10-15 MG/ML PROTEIN, pH 7.50
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-15 mg/mlprotein1drop
2100 mMHEPES1reservoir
325 %ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87, 1.3
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 15, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.871
21.31
ReflectionResolution: 2.7→37 Å / Num. obs: 19994 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 55.3 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 4.6
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 3 / Rsym value: 0.246 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 37 Å / Num. measured all: 110406
Reflection shell
*PLUS
Highest resolution: 2.7 Å / % possible obs: 99.9 % / Num. unique obs: 2805 / Num. measured obs: 15646

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.7→37.12 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1200346.62 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1019 5.1 %RANDOM
Rwork0.254 ---
obs0.254 19994 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.5186 Å2 / ksol: 0.314713 e/Å3
Displacement parametersBiso mean: 73.5 Å2
Baniso -1Baniso -2Baniso -3
1--5.35 Å20 Å20 Å2
2---5.35 Å20 Å2
3---10.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.7→37.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2889 0 0 36 2925
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.45 160 4.9 %
Rwork0.427 3077 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88
LS refinement shell
*PLUS
Rfactor Rfree: 0.45 / Rfactor obs: 0.425

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