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- PDB-3ixe: Structural basis of competition between PINCH1 and PINCH2 for bin... -

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Basic information

Entry
Database: PDB / ID: 3ixe
TitleStructural basis of competition between PINCH1 and PINCH2 for binding to the ankyrin repeat domain of integrin-linked kinase
Components
  • Integrin-linked protein kinase
  • LIM and senescent cell antigen-like-containing domain protein 2
KeywordsSIGNALING PROTEIN/SIGNALING PROTEIN / ILK / INTEGRIN-LINKED KINASE / PINCH / LIM / ANKYRIN REPEAT / ANK / IPP / INTEGRIN-MEDIATED SIGNALING / ANK REPEAT / LIM DOMAIN / ZINC / ATP-binding / Cell junction / Cell membrane / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Transferase / Alternative splicing / Metal-binding / Nucleus / SIGNALING PROTEIN-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


negative regulation of cholangiocyte proliferation / cholangiocyte proliferation / protein localization to cell cortex / negative regulation of hepatocyte proliferation / caveola assembly / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / negative regulation of neural precursor cell proliferation / positive regulation of integrin-mediated signaling pathway / positive regulation of signal transduction / nerve development ...negative regulation of cholangiocyte proliferation / cholangiocyte proliferation / protein localization to cell cortex / negative regulation of hepatocyte proliferation / caveola assembly / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / negative regulation of neural precursor cell proliferation / positive regulation of integrin-mediated signaling pathway / positive regulation of signal transduction / nerve development / fibroblast migration / establishment or maintenance of epithelial cell apical/basal polarity / myelination in peripheral nervous system / Cell-extracellular matrix interactions / positive regulation of BMP signaling pathway / cell projection organization / cell-cell junction organization / neural precursor cell proliferation / branching involved in ureteric bud morphogenesis / outflow tract morphogenesis / positive regulation of osteoblast differentiation / positive regulation of substrate adhesion-dependent cell spreading / substrate adhesion-dependent cell spreading / sarcomere / cell-matrix adhesion / tumor necrosis factor-mediated signaling pathway / mitotic spindle organization / integrin-mediated signaling pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell-cell adhesion / platelet aggregation / integrin binding / cell morphogenesis / cell-cell junction / positive regulation of canonical Wnt signaling pathway / lamellipodium / actin cytoskeleton / cell cortex / protein-macromolecule adaptor activity / cell differentiation / positive regulation of canonical NF-kappaB signal transduction / protein kinase activity / signaling receptor binding / focal adhesion / positive regulation of cell population proliferation / centrosome / protein kinase binding / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / magnesium ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
LIM and senescent cell antigen-like-containing domain protein 1-like / Integrin-linked protein kinase, pseudokinase domain / : / : / Cysteine Rich Protein / Cysteine Rich Protein / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type ...LIM and senescent cell antigen-like-containing domain protein 1-like / Integrin-linked protein kinase, pseudokinase domain / : / : / Cysteine Rich Protein / Cysteine Rich Protein / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Ankyrin repeat-containing domain / : / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ribbon / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Scaffold protein ILK / LIM and senescent cell antigen-like-containing domain protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChiswell, B.P. / Stiegler, A.L. / Boggon, T.J. / Calderwood, D.A.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Structural basis of competition between PINCH1 and PINCH2 for binding to the ankyrin repeat domain of integrin-linked kinase.
Authors: Chiswell, B.P. / Stiegler, A.L. / Razinia, Z. / Nalibotski, E. / Boggon, T.J. / Calderwood, D.A.
History
DepositionSep 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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

Downloads & links

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Assembly

Deposited unit
A: Integrin-linked protein kinase
B: LIM and senescent cell antigen-like-containing domain protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8654
Polymers28,7342
Non-polymers1312
Water6,648369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.416, 72.010, 83.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Integrin-linked protein kinase / ILK-1 / ILK-2 / 59 kDa serine/threonine-protein kinase / p59ILK


Mass: 20256.865 Da / Num. of mol.: 1 / Fragment: Ankyrin repeat domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ILK, ILK1, ILK2 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q13418, non-specific serine/threonine protein kinase
#2: Protein LIM and senescent cell antigen-like-containing domain protein 2 / Particularly interesting new Cys-His protein 2 / PINCH-2 / LIM-like protein 2


Mass: 8477.479 Da / Num. of mol.: 1 / Fragment: LIM1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIMS2, PINCH2 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q7Z4I7
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 8% PEG 550 MME, 0.1 M MES, pH 6.5, 0.2 uL 20% Benzamidine hydrochloride hydrate, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 6, 2009 / Details: Toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 20416 / Num. obs: 20416 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 12.403 Å2 / Rsym value: 0.136 / Net I/σ(I): 9.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 2002 / Rsym value: 0.414 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0093refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F6Q

3f6q


Resolution: 1.9→19.9 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.887 / SU B: 3.254 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21999 1040 5.1 %RANDOM
Rwork0.16957 ---
obs0.17207 19317 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.198 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 2 369 2370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212056
X-RAY DIFFRACTIONr_angle_refined_deg1.0711.9332792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3515261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.124.016122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91415346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2211519
X-RAY DIFFRACTIONr_chiral_restr0.0760.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211664
X-RAY DIFFRACTIONr_mcbond_it0.4431.51230
X-RAY DIFFRACTIONr_mcangle_it0.85621973
X-RAY DIFFRACTIONr_scbond_it1.3423826
X-RAY DIFFRACTIONr_scangle_it2.2534.5808
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 82 -
Rwork0.197 1373 -
obs--99.45 %

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