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- PDB-8cis: The FERM domain of human moesin with two bound peptides identifie... -

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Basic information

Entry
Database: PDB / ID: 8cis
TitleThe FERM domain of human moesin with two bound peptides identified by phage display
Components
  • C3P
  • C3S1
  • Moesin
  • Unknown peptide
KeywordsPROTEIN BINDING / PIP / FERM domain
Function / homology
Function and homology information


regulation of lymphocyte migration / T cell aggregation / regulation of organelle assembly / 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 ...regulation of lymphocyte migration / T cell aggregation / regulation of organelle assembly / 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 / leukocyte migration / leukocyte cell-cell adhesion / regulation of cell size / microvillus membrane / pseudopodium / microvillus / Recycling pathway of L1 / T cell proliferation / T cell migration / cell adhesion molecule binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cell periphery / filopodium / adherens junction / structural constituent of cytoskeleton / apical part of cell / positive regulation of protein catabolic process / Signaling by ALK fusions and activated point mutants / regulation of cell shape / double-stranded RNA binding / actin binding / blood microparticle / basolateral plasma membrane / vesicle / 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 / cytoplasm / cytosol
Similarity search - Function
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 / Ezrin/radixin/moesin-like / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain ...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 / 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
ACETATE ION / Moesin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsBradshaw, W.J. / Katis, V.L. / Leisner, T.M. / Fairhead, M. / Bountra, C. / von Delft, F. / Pearce, K.H. / 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

Downloads & links

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Assembly

Deposited unit
A: Moesin
B: C3P
C: C3S1
D: Unknown peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,76613
Polymers45,1154
Non-polymers6529
Water8,287460
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.714, 37.263, 81.530
Angle α, β, γ (deg.)90.000, 108.150, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-657-

HOH

21A-883-

HOH

31A-907-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 41141.383 Da / Num. of mol.: 1
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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Protein/peptide , 3 types, 3 molecules BCD

#2: Protein/peptide C3P


Mass: 1758.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide C3S1


Mass: 1783.847 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Protein/peptide Unknown peptide


Mass: 430.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 469 molecules

#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 200 mM ammonium sulphate, 100 mM sodium acetate trihydrate, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.42→77.5 Å / Num. obs: 51601 / % possible obs: 59.7 % / Redundancy: 22.4 % / CC1/2: 0.997 / Net I/σ(I): 13.2
Reflection shellResolution: 1.42→1.56 Å / Redundancy: 25.3 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2581 / CC1/2: 0.707 / % possible all: 12.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DIALSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→77.473 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.495 / SU ML: 0.065 / Cross valid method: FREE R-VALUE / ESU R: 0.099 / ESU R Free: 0.104
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2272 1990 3.952 %
Rwork0.1823 48365 -
all0.184 --
obs-50355 71.167 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.463 Å2
Baniso -1Baniso -2Baniso -3
1-0.121 Å2-0 Å2-0.013 Å2
2--0.07 Å2-0 Å2
3----0.151 Å2
Refinement stepCycle: LAST / Resolution: 1.52→77.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2833 0 39 460 3332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123033
X-RAY DIFFRACTIONr_bond_other_d0.0530.0162814
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.654101
X-RAY DIFFRACTIONr_angle_other_deg1.1021.5666584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2945370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.687522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10110562
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.58610152
X-RAY DIFFRACTIONr_chiral_restr0.0870.2431
X-RAY DIFFRACTIONr_chiral_restr_other1.1380.21
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02619
X-RAY DIFFRACTIONr_nbd_refined0.2490.2545
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.22264
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21396
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21487
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2366
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0170.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.6990.283
X-RAY DIFFRACTIONr_nbd_other0.6220.2200
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2470.263
X-RAY DIFFRACTIONr_mcbond_it2.7471.7381414
X-RAY DIFFRACTIONr_mcbond_other2.7341.731410
X-RAY DIFFRACTIONr_mcangle_it4.2722.5641765
X-RAY DIFFRACTIONr_mcangle_other4.2722.5661766
X-RAY DIFFRACTIONr_scbond_it3.1952.0521619
X-RAY DIFFRACTIONr_scbond_other3.1942.0541620
X-RAY DIFFRACTIONr_scangle_it5.1412.8932323
X-RAY DIFFRACTIONr_scangle_other5.142.8952324
X-RAY DIFFRACTIONr_lrange_it8.81127.3833659
X-RAY DIFFRACTIONr_lrange_other8.69524.413498
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.52-1.5590.366450.31511810.31652080.9480.95323.54070.302
1.559-1.6020.267630.27615000.27550480.9660.96130.96280.261
1.602-1.6490.318760.27317640.27549010.9470.96237.54340.254
1.649-1.6990.267970.2621220.2648110.9520.96146.12350.236
1.699-1.7550.2621000.24124580.24246110.9570.96255.4760.209
1.755-1.8170.261150.2226900.22244830.9610.96862.56970.184
1.817-1.8850.2581190.21928910.22143290.9530.96769.53110.18
1.885-1.9620.2211460.20130750.20241830.970.97477.00220.163
1.962-2.0490.2641280.20632530.20940130.9530.97384.25120.174
2.049-2.1490.221360.19733130.19838350.9750.97789.93480.169
2.149-2.2650.2331220.17933280.1836300.9660.98195.04130.15
2.265-2.4030.21470.17332400.17534300.9740.98198.74640.146
2.403-2.5680.2261070.16531740.16732910.9690.98399.69610.145
2.568-2.7740.2191360.1728920.17230320.9680.98299.86810.153
2.774-3.0380.241110.16726980.1728110.9660.98399.92880.156
3.038-3.3960.221920.17124740.17325660.9730.9831000.165
3.396-3.920.227620.15721740.15822360.970.9851000.156
3.92-4.7980.175860.14118400.14319260.9860.9891000.14
4.798-6.7730.25610.18414560.18715170.9760.9831000.183
6.773-77.4730.236400.228380.2218780.9630.951000.241
Refinement TLS params.

Method: refined / 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)
10.3528-0.0721-0.00570.0577-0.03960.3558-0.009-0.01570.00560.0284-0.02610.0264-0.00710.01250.03510.0464-0.02360.0010.0493-0.01190.058227.200117.00115.4014
20.96560.57060.19512.5614-3.11814.74010.0617-0.06190.12470.30420.08820.1931-0.3726-0.1986-0.14990.09260.02910.04520.0699-0.03950.070812.783529.169122.8293
35.6865.0451-0.78626.5803-2.11811.0718-0.016-0.14740.33570.15910.00630.2352-0.1156-0.08970.00970.0190.01830.0010.0939-0.0690.09375.917627.34067.0164
425.321-0.0582-21.82460.8858-0.738821.398-0.33930.1542-0.10770.09980.1042-0.02090.5309-0.16890.23510.0927-0.00790.0290.0815-0.01240.012725.55269.545740.0588
Refinement TLS groupSelection: ALL

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