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- PDB-4f7h: The crystal structure of kindlin-2 pleckstrin homology domain in ... -

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Basic information

Entry
Database: PDB / ID: 4f7h
TitleThe crystal structure of kindlin-2 pleckstrin homology domain in free form
ComponentsFermitin family homolog 2
KeywordsCELL ADHESION / beta-barrel / membrane binding / integrin activation / cytoplasmic membrane
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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / PH-domain like / FERM superfamily, second domain / Band 4.1 domain ...Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / FERM central domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / PH-domain like / 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 / Roll / Mainly Beta
Similarity search - Domain/homology
S,R MESO-TARTARIC ACID / Fermitin family homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLiu, Y. / Zhu, Y. / Qin, J. / Ye, S. / Zhang, R.
CitationJournal: Protein Cell / Year: 2012
Title: Crystal structure of kindlin-2 PH domain reveals a conformational transition for its membrane anchoring and regulation of integrin activation.
Authors: Liu, Y. / Zhu, Y. / Ye, S. / Zhang, R.
History
DepositionMay 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fermitin family homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7333
Polymers19,4331
Non-polymers3002
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.474, 58.474, 92.249
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-739-

HOH

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Components

#1: Protein 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: 19433.139 Da / Num. of mol.: 1 / Fragment: pleckstrin homology domain, UNP residues 328-499
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FERMT2, KIND2, MIG2, PLEKHC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96AC1
#2: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water / 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: 2.03 Å3/Da / Density % sol: 39.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.4 M ammonium tartrate dibasic, 0.1 M tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 7, 2012 / Details: mirrors
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→29.237 Å / Num. all: 13258 / Num. obs: 13245 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.4 %
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 6 % / Num. unique all: 848 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YS3

2ys3


Resolution: 1.9→29.237 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 21.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 652 4.94 %RANDOM
Rwork0.195 ---
all0.197 13258 --
obs0.1964 13195 99.96 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.96 Å2 / ksol: 0.381 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.28 Å20 Å2-0 Å2
2--2.28 Å2-0 Å2
3----4.5599 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1076 0 20 86 1182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131116
X-RAY DIFFRACTIONf_angle_d1.4861503
X-RAY DIFFRACTIONf_dihedral_angle_d17.15422
X-RAY DIFFRACTIONf_chiral_restr0.098166
X-RAY DIFFRACTIONf_plane_restr0.006189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8997-2.04640.28861380.24652417X-RAY DIFFRACTION100
2.0464-2.25220.22581350.20072475X-RAY DIFFRACTION100
2.2522-2.5780.25931250.20092465X-RAY DIFFRACTION100
2.578-3.24730.22551360.1952506X-RAY DIFFRACTION100
3.2473-29.24040.19781180.18382680X-RAY DIFFRACTION100
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)
11.03610.92750.21424.70270.97690.4290.20380.1268-0.08710.2486-0.2024-0.32360.17290.1529-0.06350.34590.01990.03420.20830.01560.216922.151110.212924.5856
21.2204-0.0261-0.49473.09660.39944.48550.0164-0.02150.1808-0.35070.0936-0.0046-0.66660.4504-0.05590.2864-0.06930.01460.1846-0.01140.186822.368911.23227.9062
33.1324-0.35220.49162.82440.05783.6402-0.0403-0.01170.16370.0238-0.04750.1163-0.3238-0.01870.05170.2302-0.01920.01990.1004-0.00620.186215.95546.119434.9868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 365:392)
2X-RAY DIFFRACTION2chain 'A' and (resseq 393:447)
3X-RAY DIFFRACTION3chain 'A' and (resseq 448:499)

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