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- PDB-1sgh: Moesin FERM domain bound to EBP50 C-terminal peptide -

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Basic information

Entry
Database: PDB / ID: 1sgh
TitleMoesin FERM domain bound to EBP50 C-terminal peptide
Components
  • Ezrin-radixin-moesin binding phosphoprotein 50
  • Moesin
KeywordsSTRUCTURAL PROTEIN / FERM-peptide complex
Function / homology
Function and homology information


import across plasma membrane / channel activator activity / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / regulation of lymphocyte migration / glutathione transport / T cell aggregation / dopamine receptor binding / renal phosphate ion absorption ...import across plasma membrane / channel activator activity / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / regulation of lymphocyte migration / glutathione transport / T cell aggregation / dopamine receptor binding / renal phosphate ion absorption / gamma-aminobutyric acid transmembrane transporter activity / gamma-aminobutyric acid import / cerebrospinal fluid circulation / regulation of organelle assembly / microvillus assembly / T cell migration / positive regulation of monoatomic ion transmembrane transport / positive regulation of early endosome to late endosome transport / negative regulation of sodium ion transport / membrane to membrane docking / bile acid secretion / maintenance of epithelial cell apical/basal polarity / uropod / plasma membrane organization / stereocilium tip / cilium organization / intracellular phosphate ion homeostasis / immunological synapse formation / gland morphogenesis / myosin II binding / positive regulation of protein localization to early endosome / phospholipase C-activating dopamine receptor signaling pathway / growth factor receptor binding / establishment of Golgi localization / fibroblast migration / type 3 metabotropic glutamate receptor binding / plasma membrane protein complex / cellular response to testosterone stimulus / establishment of epithelial cell apical/basal polarity / negative regulation of fibroblast migration / establishment of endothelial barrier / chloride channel regulator activity / negative regulation of platelet-derived growth factor receptor signaling pathway / auditory receptor cell stereocilium organization / Sensory processing of sound by outer hair cells of the cochlea / positive regulation of podosome assembly / nuclear migration / Sensory processing of sound by inner hair cells of the cochlea / regulation of protein kinase activity / microvillus membrane / regulation of cell size / leukocyte cell-cell adhesion / renal absorption / leukocyte migration / pseudopodium / Recycling pathway of L1 / microvillus / transport across blood-brain barrier / negative regulation of mitotic cell cycle / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / phosphatase binding / endomembrane system / T cell proliferation / beta-2 adrenergic receptor binding / positive regulation of intrinsic apoptotic signaling pathway / protein-membrane adaptor activity / sperm midpiece / cell adhesion molecule binding / ruffle / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / filopodium / protein localization to plasma membrane / cell periphery / PDZ domain binding / morphogenesis of an epithelium / brush border membrane / adherens junction / sensory perception of sound / negative regulation of canonical Wnt signaling pathway / negative regulation of ERK1 and ERK2 cascade / structural constituent of cytoskeleton / beta-catenin binding / Wnt signaling pathway / adenylate cyclase-activating dopamine receptor signaling pathway / positive regulation of protein catabolic process / : / double-stranded RNA binding / Signaling by ALK fusions and activated point mutants / actin cytoskeleton / apical part of cell / actin binding / regulation of cell shape / actin cytoskeleton organization / protein-containing complex assembly / basolateral plasma membrane / vesicle / transmembrane transporter binding / cytoskeleton / blood microparticle / apical plasma membrane
Similarity search - Function
EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / 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 ...EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / 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) / 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 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / 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
Na(+)/H(+) exchange regulatory cofactor NHE-RF1 / Moesin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsFinnerty, C.M. / Chambers, D. / Ingraffea, J. / Faber, H.R. / Karplus, P.A. / Bretscher, A.
CitationJournal: J.Cell.Sci. / Year: 2004
Title: The EBP50-moesin interaction involves a binding site regulated by direct masking on the FERM domain
Authors: Finnerty, C.M. / Chambers, D. / Ingraffea, J. / Faber, H.R. / Karplus, P.A. / Bretscher, A.
History
DepositionFeb 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Moesin
B: Ezrin-radixin-moesin binding phosphoprotein 50


Theoretical massNumber of molelcules
Total (without water)39,5592
Polymers39,5592
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)127.600, 70.500, 62.800
Angle α, β, γ (deg.)90.00, 106.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Moesin / Membrane-organizing extension spike protein


Mass: 34969.348 Da / Num. of mol.: 1 / Fragment: FERM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSN / Plasmid: pQE16 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P26038
#2: Protein/peptide Ezrin-radixin-moesin binding phosphoprotein 50 / EBP50 / Na+ / /H+ / exchange regulatory cofactor NHE-RF / NHERF-1 / Regulatory cofactor of Na+ / ...EBP50 / Na+ / /H+ / exchange regulatory cofactor NHE-RF / NHERF-1 / Regulatory cofactor of Na+ / /H+ / exchanger / Sodium-hydrogen exchanger regulatory factor 1 / Solute carrier family 9 isoform 3 regulatory factor 1 / Coordinate model: Cα atoms only


Mass: 4589.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: this sequence ocurrs naturally in humans / References: UniProt: O14745

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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: 3.43 Å3/Da / Density % sol: 64.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris, PEG 4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.943 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 4, 2000
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.943 Å / Relative weight: 1
ReflectionResolution: 3.5→11.07 Å / Num. all: 6801 / Num. obs: 6801 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 104 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.094 / Net I/σ(I): 6.6
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2 / Num. unique all: 969 / Rsym value: 0.343 / % possible all: 99.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EF1

1ef1


Resolution: 3.5→11.07 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: As noted by Finnerty et al. in the primary citation of this structure, a model for the bound peptide was not included in the refinement due to the very low resolution of the analysis. ...Details: As noted by Finnerty et al. in the primary citation of this structure, a model for the bound peptide was not included in the refinement due to the very low resolution of the analysis. However, as part of the structure interpretation, a 38-residue peptide had been approximately modeled into the difference electron density that corresponds to the bound peptide. To maximize the value of this coordinate set, the CA coordinates of the approximately modeled peptide are included in this PDB deposition with an occupancy of zero.
RfactorNum. reflection% reflectionSelection details
Rfree0.401 585 10 %Random
Rwork0.338 ---
all-6801 --
obs-6801 99 %-
Displacement parameters
Baniso -1Baniso -3Baniso -2
1--69 Å2-22 Å2-
2---38 Å2
3--31 Å2-
Refinement stepCycle: LAST / Resolution: 3.5→11.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 0 0 2482
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.012
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_deg1.75
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shellResolution: 3.5→3.61 Å /
RfactorNum. reflection
Rfree0.631 46
Rwork0.449 603

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