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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 / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / regulation of lymphocyte migration / T cell aggregation / glutathione transport / dopamine receptor binding / renal phosphate ion absorption / gamma-aminobutyric acid transmembrane transporter activity ...import across plasma membrane / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / regulation of lymphocyte migration / T cell aggregation / glutathione transport / dopamine receptor binding / renal phosphate ion absorption / gamma-aminobutyric acid transmembrane transporter activity / gamma-aminobutyric acid import / regulation of organelle assembly / cerebrospinal fluid circulation / negative regulation of sodium ion transport / microvillus assembly / positive regulation of early endosome to late endosome transport / membrane to membrane docking / gland morphogenesis / bile acid secretion / positive regulation of monoatomic ion transmembrane transport / maintenance of epithelial cell apical/basal polarity / regulation of protein kinase activity / channel activator activity / uropod / stereocilium tip / cilium organization / plasma membrane organization / immunological synapse formation / intracellular phosphate ion homeostasis / myosin II binding / positive regulation of protein localization to early endosome / growth factor receptor binding / phospholipase C-activating dopamine receptor signaling pathway / 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 / chloride channel regulator activity / establishment of endothelial barrier / auditory receptor cell stereocilium organization / positive regulation of podosome assembly / nuclear migration / negative regulation of platelet-derived growth factor receptor signaling pathway / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / beta-2 adrenergic receptor binding / microvillus membrane / leukocyte cell-cell adhesion / regulation of cell size / leukocyte migration / renal absorption / pseudopodium / Recycling pathway of L1 / microvillus / negative regulation of mitotic cell cycle / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / transport across blood-brain barrier / T cell migration / endomembrane system / phosphatase binding / positive regulation of intrinsic apoptotic signaling pathway / cell adhesion molecule binding / T cell proliferation / protein-membrane adaptor activity / sperm midpiece / ruffle / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / filopodium / protein localization to plasma membrane / cell periphery / morphogenesis of an epithelium / PDZ domain binding / adherens junction / brush border membrane / sensory perception of sound / negative regulation of canonical Wnt signaling pathway / structural constituent of cytoskeleton / negative regulation of ERK1 and ERK2 cascade / Wnt signaling pathway / beta-catenin binding / positive regulation of protein catabolic process / adenylate cyclase-activating dopamine receptor signaling pathway / double-stranded RNA binding / Signaling by ALK fusions and activated point mutants / actin cytoskeleton / apical part of cell / regulation of cell shape / actin binding / actin cytoskeleton organization / protein-containing complex assembly / basolateral plasma membrane / vesicle / blood microparticle / transmembrane transporter binding / cytoskeleton / apical plasma membrane / negative regulation of cell population proliferation
Similarity search - Function
EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / : / 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 ...EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / : / 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 / 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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