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- PDB-8cit: The FERM domain of human moesin mutant L281R -

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Basic information

Entry
Database: PDB / ID: 8cit
TitleThe FERM domain of human moesin mutant L281R
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 / 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
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: 2.536 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
B: Moesin
C: Moesin


Theoretical massNumber of molelcules
Total (without water)123,5563
Polymers123,5563
Non-polymers00
Water00
1
A: Moesin


Theoretical massNumber of molelcules
Total (without water)41,1851
Polymers41,1851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Moesin


Theoretical massNumber of molelcules
Total (without water)41,1851
Polymers41,1851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Moesin


Theoretical massNumber of molelcules
Total (without water)41,1851
Polymers41,1851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.704, 74.049, 115.075
Angle α, β, γ (deg.)90, 95.63, 90
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 41185.422 Da / Num. of mol.: 3 / Mutation: L281R
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

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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: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 200 mM sodium fluoride, 100 mM bris-tris-propane, 10% ethylene glycol, 20% PEG3350

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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: 2.536→62.2 Å / Num. obs: 23727 / % possible obs: 58.5 % / Redundancy: 7 % / CC1/2: 0.976 / Net I/σ(I): 4.3
Reflection shellResolution: 2.54→3.07 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3949 / CC1/2: 0.591

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
DIALSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.536→62.18 Å / Cor.coef. Fo:Fc: 0.842 / Cor.coef. Fo:Fc free: 0.802 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.492
RfactorNum. reflection% reflectionSelection details
Rfree0.2875 1173 -RANDOM
Rwork0.2439 ---
obs0.246 23727 58.5 %-
Displacement parametersBiso mean: 38.16 Å2
Baniso -1Baniso -2Baniso -3
1-15.0915 Å20 Å2-0.4746 Å2
2---7.3577 Å20 Å2
3----7.7338 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.536→62.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8245 0 0 0 8245
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0098435HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0311358HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3091SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1426HARMONIC5
X-RAY DIFFRACTIONt_it8435HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1059SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5944SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion20.09
LS refinement shellResolution: 2.54→2.7 Å
RfactorNum. reflection% reflection
Rfree0.3365 23 -
Rwork0.3309 --
obs0.3312 475 6.79 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.67550.083-0.49881.6473-0.40012.37570.0215-0.0056-0.2116-0.00560.0450.0415-0.21160.0415-0.06650.161-0.0331-0.1048-0.15750.0091-0.0527-4.9935-16.472-5.7556
20.31250.0859-0.22752.36810.45781.71480.06680.0556-0.21060.0556-0.0481-0.452-0.2106-0.452-0.01880.263-0.04970.0576-0.0644-0.043-0.1613-32.6464-28.01523.4421
30.978-0.26350.02032.1245-0.2741.59380.0586-0.4037-0.2118-0.40370.04810.1213-0.21180.1213-0.10670.3752-0.01940.0014-0.1308-0.0475-0.1919-19.9328-25.7739-46.3634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 341
2X-RAY DIFFRACTION2{ B|* }B3 - 343
3X-RAY DIFFRACTION3{ C|* }C0 - 327

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