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- PDB-6xtj: The high resolution structure of the FERM domain of human FERMT2 -

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Basic information

Entry
Database: PDB / ID: 6xtj
TitleThe high resolution structure of the FERM domain of human FERMT2
ComponentsFermitin family homolog 2,Fermitin family homolog 2,Fermitin family homolog 2
KeywordsPROTEIN BINDING / Alzheimer's Disease / integrin binding / FERM domain
Function / homology
Function and homology information


adherens junction maintenance / positive regulation of myosin light chain kinase activity / protein localization to cell junction / positive regulation of mesenchymal stem cell proliferation / positive regulation of wound healing, spreading of epidermal cells / positive regulation of integrin activation / Cell-extracellular matrix interactions / type I transforming growth factor beta receptor binding / integrin activation / focal adhesion assembly ...adherens junction maintenance / positive regulation of myosin light chain kinase activity / protein localization to cell junction / positive regulation of mesenchymal stem cell proliferation / positive regulation of wound healing, spreading of epidermal cells / positive regulation of integrin activation / Cell-extracellular matrix interactions / type I transforming growth factor beta receptor binding / integrin activation / focal adhesion assembly / protein localization to membrane / negative regulation of vascular permeability / regulation of cell morphogenesis / I band / limb development / negative regulation of fat cell differentiation / SMAD binding / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of focal adhesion assembly / lamellipodium membrane / positive regulation of epithelial to mesenchymal transition / RAC3 GTPase cycle / positive regulation of osteoblast differentiation / positive regulation of substrate adhesion-dependent cell spreading / stress fiber / positive regulation of stress fiber assembly / RAC1 GTPase cycle / extrinsic component of cytoplasmic side of plasma membrane / substrate adhesion-dependent cell spreading / cell-matrix adhesion / transforming growth factor beta receptor signaling pathway / integrin-mediated signaling pathway / adherens junction / cytoplasmic side of plasma membrane / Wnt signaling pathway / positive regulation of GTPase activity / positive regulation of protein localization to nucleus / actin filament binding / integrin binding / cell junction / actin binding / cell cortex / regulation of cell shape / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / positive regulation of cell migration / focal adhesion / protein kinase binding / cell surface / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / FERM central domain / FERM central domain / FERM superfamily, second domain / Band 4.1 domain / Band 4.1 homologues / PH domain ...Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / FERM central domain / FERM central domain / FERM superfamily, second domain / Band 4.1 domain / Band 4.1 homologues / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
CITRIC ACID / Fermitin family homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBradshaw, W.J. / Katis, V.L. / Newman, J.A. / 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: To Be Published
Title: The high resolution structure of the FERM domain of human FERMT2
Authors: Bradshaw, W.J. / Katis, V.L. / Newman, J.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
History
DepositionJan 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Fermitin family homolog 2,Fermitin family homolog 2,Fermitin family homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1574
Polymers55,5811
Non-polymers5763
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint3 kcal/mol
Surface area24060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.172, 145.172, 59.633
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Fermitin family homolog 2,Fermitin family homolog 2,Fermitin family homolog 2 / Kindlin-2 / Mitogen-inducible gene 2 protein / MIG-2 / Pleckstrin homology domain-containing family ...Kindlin-2 / Mitogen-inducible gene 2 protein / MIG-2 / Pleckstrin homology domain-containing family C member 1 / PH domain-containing family C member 1


Mass: 55580.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FERMT2, KIND2, MIG2, PLEKHC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q96AC1
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES pH 7.0, 1.4M sodium citrate tribasic

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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: Feb 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→72.7 Å / Num. obs: 95151 / % possible obs: 100 % / Redundancy: 31.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.277 / Rpim(I) all: 0.071 / Rrim(I) all: 0.28 / Χ2: 0.93 / Net I/σ(I): 11
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 25.4 % / Rmerge(I) obs: 5.732 / Mean I/σ(I) obs: 1 / Num. unique obs: 4659 / CC1/2: 0.732 / Rpim(I) all: 1.638 / Rrim(I) all: 5.965 / Χ2: 0.86 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XPY

5xpy


Resolution: 1.6→72.7 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / Cross valid method: FREE R-VALUE / ESU R: 0.07 / ESU R Free: 0.071
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2037 1874 1.977 %
Rwork0.1807 --
all0.181 --
obs-94810 99.707 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.736 Å2
Baniso -1Baniso -2Baniso -3
1-0.782 Å20.391 Å20 Å2
2--0.782 Å2-0 Å2
3----2.536 Å2
Refinement stepCycle: LAST / Resolution: 1.6→72.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3694 0 39 377 4110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134068
X-RAY DIFFRACTIONr_bond_other_d0.0340.0173829
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.6365531
X-RAY DIFFRACTIONr_angle_other_deg2.2861.5798937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3225.205512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23423.592206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46315776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.291519
X-RAY DIFFRACTIONr_chiral_restr0.0740.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024677
X-RAY DIFFRACTIONr_gen_planes_other0.010.02828
X-RAY DIFFRACTIONr_nbd_refined0.270.2804
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2240.23268
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21834
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0660.21656
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2316
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.4590.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2560.254
X-RAY DIFFRACTIONr_nbd_other0.2530.2172
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1410.233
X-RAY DIFFRACTIONr_mcbond_it2.3762.8711915
X-RAY DIFFRACTIONr_mcbond_other2.3772.8691913
X-RAY DIFFRACTIONr_mcangle_it3.8344.3012407
X-RAY DIFFRACTIONr_mcangle_other3.8334.3022408
X-RAY DIFFRACTIONr_scbond_it3.0443.292153
X-RAY DIFFRACTIONr_scbond_other3.0263.2892152
X-RAY DIFFRACTIONr_scangle_it4.9474.793108
X-RAY DIFFRACTIONr_scangle_other4.9464.7923109
X-RAY DIFFRACTIONr_lrange_it7.29933.7774705
X-RAY DIFFRACTIONr_lrange_other7.24633.4484622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6420.3021170.2926869X-RAY DIFFRACTION99.8143
1.642-1.6870.3051490.2856653X-RAY DIFFRACTION99.6484
1.687-1.7350.2841230.2496458X-RAY DIFFRACTION99.4409
1.735-1.7890.2291300.2376240X-RAY DIFFRACTION99.314
1.789-1.8470.2411280.2226087X-RAY DIFFRACTION99.4082
1.847-1.9120.2411340.2185887X-RAY DIFFRACTION99.6195
1.912-1.9840.2561260.2035678X-RAY DIFFRACTION99.6053
1.984-2.0650.2071190.1925481X-RAY DIFFRACTION99.5556
2.065-2.1570.211990.1775249X-RAY DIFFRACTION99.6831
2.157-2.2630.182950.1665058X-RAY DIFFRACTION99.845
2.263-2.3850.199870.1634829X-RAY DIFFRACTION99.8375
2.385-2.530.165890.1644543X-RAY DIFFRACTION99.8922
2.53-2.7040.197940.1624274X-RAY DIFFRACTION99.8628
2.704-2.9210.247740.1753989X-RAY DIFFRACTION99.9262
2.921-3.1990.248650.1753697X-RAY DIFFRACTION99.9734
3.199-3.5770.164760.1643338X-RAY DIFFRACTION99.9415
3.577-4.1290.154580.1432976X-RAY DIFFRACTION100
4.129-5.0560.184440.1432529X-RAY DIFFRACTION100
5.056-7.1440.165420.2031967X-RAY DIFFRACTION100
7.144-72.690.174250.1841134X-RAY DIFFRACTION99.8277

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