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- PDB-8ciu: The FERM domain of human moesin mutant H288A -

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Basic information

Entry
Database: PDB / ID: 8ciu
TitleThe FERM domain of human moesin mutant H288A
ComponentsMoesin
KeywordsPROTEIN BINDING / PIP / FERM domain
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 / positive regulation of podosome assembly / Sensory processing of sound by outer hair cells of the cochlea / 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 / blood microparticle / cytoskeleton / apical plasma membrane / signaling receptor binding / focal adhesion / positive regulation of gene expression / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / cell surface / extracellular space / extracellular exosome / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 / Ezrin/radixin/moesin-like / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain ...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 / Ezrin/radixin/moesin-like / 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 / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.393 Å
AuthorsBradshaw, W.J. / Katis, V.L. / Koekemoer, L. / Bountra, C. / von Delft, F. / Brennan, P.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)5U54AG065187-03 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Discovery of FERM domain protein-protein interaction inhibitors for MSN and CD44 as a potential therapeutic approach for Alzheimer's disease.
Authors: Du, Y. / Bradshaw, W.J. / Leisner, T.M. / Annor-Gyamfi, J.K. / Qian, K. / Bashore, F.M. / Sikdar, A. / Nwogbo, F.O. / Ivanov, A.A. / Frye, S.V. / Gileadi, O. / Brennan, P.E. / Levey, A.I. / ...Authors: Du, Y. / Bradshaw, W.J. / Leisner, T.M. / Annor-Gyamfi, J.K. / Qian, K. / Bashore, F.M. / Sikdar, A. / Nwogbo, F.O. / Ivanov, A.A. / Frye, S.V. / Gileadi, O. / Brennan, P.E. / Levey, A.I. / Axtman, A.D. / Pearce, K.H. / Fu, H. / Katis, V.L.
History
DepositionFeb 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2Nov 1, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.3Nov 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.4Nov 29, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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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)41,0741
Polymers41,0741
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18820 Å2
Unit cell
Length a, b, c (Å)117.075, 117.075, 62.719
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 41074.316 Da / Num. of mol.: 1 / Mutation: H288A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSN / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P26038
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM ammonium acetate, 100 mM tris, 32% propan-2-ol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.39→55.3 Å / Num. obs: 12176 / % possible obs: 68.6 % / Redundancy: 50.9 % / CC1/2: 1 / Net I/σ(I): 21.6
Reflection shellResolution: 2.39→2.76 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 82705 / CC1/2: 0.787 / % possible all: 29.3

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
DIALSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.393→55.28 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.819 / SU R Cruickshank DPI: 1.063 / Cross valid method: FREE R-VALUE / SU R Blow DPI: 1.447 / SU Rfree Blow DPI: 0.4 / SU Rfree Cruickshank DPI: 0.399
RfactorNum. reflection% reflectionSelection details
Rfree0.3078 1043 -RANDOM
Rwork0.2382 ---
obs0.2441 12176 68.6 %-
Displacement parametersBiso mean: 72.34 Å2
Baniso -1Baniso -2Baniso -3
1--21.4515 Å20 Å20 Å2
2---21.4515 Å20 Å2
3---42.9029 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.393→55.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2687 0 0 86 2773
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112759HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.153729HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d988SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes472HARMONIC5
X-RAY DIFFRACTIONt_it2759HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion354SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2125SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion20.21
LS refinement shellResolution: 2.393→2.52 Å
RfactorNum. reflection% reflection
Rfree0.4644 18 -
Rwork0.2879 --
obs--9.61 %
Refinement TLS params.Origin x: -17.387 Å / Origin y: -39.9717 Å / Origin z: -2.5028 Å
111213212223313233
T-0.5872 Å20.1003 Å2-0.0369 Å2--0.6639 Å2-0.0194 Å2--0.3975 Å2
L3.0464 °20.8542 °20.4087 °2-1.8305 °20.612 °2--1.2564 °2
S-0.1494 Å °0.0378 Å °0.0669 Å °0.0378 Å °-0.0463 Å °-0.0226 Å °0.0669 Å °-0.0226 Å °0.1957 Å °
Refinement TLS groupSelection details: { A|* }

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