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- PDB-6txq: The high resolution structure of the FERM domain and helical link... -

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Basic information

Entry
Database: PDB / ID: 6txq
TitleThe high resolution structure of the FERM domain and helical linker of human moesin
ComponentsMoesin
KeywordsPROTEIN BINDING / PIP / FERM domain / Alzheimer's disease / CD44
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 / Recycling pathway of L1 / pseudopodium / microvillus / Signaling by ALK fusions and activated point mutants / T cell proliferation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cell adhesion molecule binding / filopodium / cell periphery / adherens junction / structural constituent of cytoskeleton / positive regulation of protein catabolic process / double-stranded RNA binding / apical part of cell / actin binding / regulation of cell shape / basolateral plasma membrane / blood microparticle / 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 / 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
ACETATE ION / Moesin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsBradshaw, W.J. / Katis, V.L. / Kelly, J.J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)1U54AG065187-01 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
DepositionJan 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / citation / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 1, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.3Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Moesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2002
Polymers41,1411
Non-polymers591
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-1 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.419, 112.419, 61.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11AAA-624-

HOH

21AAA-636-

HOH

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Components

#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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P26038
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.3547.6
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop8.50.1M ammonium acetate, 0.1M tris pH 8.5, 32% propan-2-ol
2772vapor diffusion, sitting drop8.50.2M ammonium acetate, 0.1M tris pH 8.5, 34% 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: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.73→112.42 Å / Num. obs: 41463 / % possible obs: 100 % / Redundancy: 88.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.26 / Rpim(I) all: 0.038 / Rrim(I) all: 0.262 / Χ2: 0.98 / Net I/σ(I): 15.6
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 51.5 % / Rmerge(I) obs: 16.039 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2210 / CC1/2: 0.377 / Rpim(I) all: 3.121 / Rrim(I) all: 16.345 / Χ2: 0.79 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E5W

1e5w


Resolution: 1.73→79.492 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.468 / SU ML: 0.104 / Cross valid method: FREE R-VALUE / ESU R: 0.113 / ESU R Free: 0.111
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.233 1912 4.619 %
Rwork0.1996 --
all0.201 --
obs-41394 99.976 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.457 Å2
Baniso -1Baniso -2Baniso -3
1-0.962 Å2-0 Å2-0 Å2
2--0.962 Å2-0 Å2
3----1.924 Å2
Refinement stepCycle: LAST / Resolution: 1.73→79.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2695 0 4 164 2863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132774
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172633
X-RAY DIFFRACTIONr_angle_refined_deg1.561.6473736
X-RAY DIFFRACTIONr_angle_other_deg1.3431.5836124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.865327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69322.778162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99515539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2711519
X-RAY DIFFRACTIONr_chiral_restr0.0720.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023048
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02589
X-RAY DIFFRACTIONr_nbd_refined0.2140.2499
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.22322
X-RAY DIFFRACTIONr_nbtor_refined0.170.21324
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21292
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2134
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2470.29
X-RAY DIFFRACTIONr_nbd_other0.270.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1690.211
X-RAY DIFFRACTIONr_mcbond_it3.3483.811300
X-RAY DIFFRACTIONr_mcbond_other3.3173.8051298
X-RAY DIFFRACTIONr_mcangle_it4.4865.6951623
X-RAY DIFFRACTIONr_mcangle_other4.4955.71624
X-RAY DIFFRACTIONr_scbond_it4.3224.4021474
X-RAY DIFFRACTIONr_scbond_other4.324.4031475
X-RAY DIFFRACTIONr_scangle_it6.5696.3522111
X-RAY DIFFRACTIONr_scangle_other6.5686.3532112
X-RAY DIFFRACTIONr_lrange_it8.23143.3063095
X-RAY DIFFRACTIONr_lrange_other8.23643.1973074
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
1.73-1.7750.3561220.35528680.35529920.4710.49699.93320.354
1.775-1.8240.3641430.32528020.32729500.6310.67299.83050.318
1.824-1.8760.41270.30327200.30728490.720.77499.92980.286
1.876-1.9340.3031270.27526520.27627790.8420.8531000.25
1.934-1.9970.3051270.25525690.25826960.8440.8761000.226
1.997-2.0680.2651270.23424830.23626100.8980.9021000.208
2.068-2.1460.291070.22424050.22725120.8910.9091000.201
2.146-2.2330.2561000.21423280.21624290.9160.91899.95880.192
2.233-2.3320.2491030.20922560.2123590.9160.9331000.192
2.332-2.4460.2351180.19121300.19322480.9240.941000.177
2.446-2.5780.2581020.19820180.20121200.910.9371000.187
2.578-2.7340.2911000.20419250.20920250.9050.9321000.197
2.734-2.9230.228910.19618240.19819150.9390.9441000.194
2.923-3.1570.23890.19916960.20117850.9330.9431000.201
3.157-3.4580.231730.20615920.20816650.9470.9441000.212
3.458-3.8650.206750.18914310.1915060.9460.9511000.202
3.865-4.4610.194640.1612700.16113340.9550.9671000.177
4.461-5.4590.172540.15710990.15811530.9740.9741000.176
5.459-7.7020.236340.198870.1919210.9610.9711000.206
7.702-79.4920.183290.1795260.185550.9730.9721000.196

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