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- PDB-4hi9: 1.2 structure of integrin-linked kinase ankyrin repeat domain in ... -

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Basic information

Entry
Database: PDB / ID: 4hi9
Title1.2 structure of integrin-linked kinase ankyrin repeat domain in complex with PINCH1 LIM1 domain collected at wavelength 0.91974
Components
  • Integrin-linked protein kinase
  • LIM and senescent cell antigen-like-containing domain protein 1
KeywordsSIGNALING PROTEIN / ANKYRIN REPEAT LIM DOMAIN / SIGNALING PROTEIN-SIGNALING PROTEIN COMPLEX / ILK-PINCH / Focal adhesion
Function / homology
Function and homology information


Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / negative regulation of neural precursor cell proliferation / positive regulation of signal transduction / positive regulation of integrin-mediated signaling pathway / nerve development / Cell-extracellular matrix interactions / fibroblast migration / myelination in peripheral nervous system / cell projection organization ...Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / negative regulation of neural precursor cell proliferation / positive regulation of signal transduction / positive regulation of integrin-mediated signaling pathway / nerve development / Cell-extracellular matrix interactions / fibroblast migration / myelination in peripheral nervous system / cell projection organization / cell-cell junction organization / positive regulation of BMP signaling pathway / neural precursor cell proliferation / establishment or maintenance of epithelial cell apical/basal polarity / positive regulation of cell-substrate adhesion / branching involved in ureteric bud morphogenesis / outflow tract morphogenesis / positive regulation of focal adhesion assembly / positive regulation of osteoblast differentiation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of phosphorylation / cellular response to transforming growth factor beta stimulus / tumor necrosis factor-mediated signaling pathway / sarcomere / phosphatidylinositol 3-kinase/protein kinase B signal transduction / substrate adhesion-dependent cell spreading / cell-matrix adhesion / positive regulation of GTPase activity / integrin-mediated signaling pathway / establishment of protein localization / cell morphogenesis / platelet aggregation / cell-cell adhesion / cell-cell junction / positive regulation of canonical Wnt signaling pathway / lamellipodium / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / positive regulation of protein phosphorylation / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of gene expression / protein kinase binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / zinc ion binding / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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. ...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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ribbon / Alpha Horseshoe / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / PHOSPHATE ION / LIM and senescent cell antigen-like-containing domain protein 1 / Integrin-linked protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.203 Å
AuthorsStiegler, A.L. / Jakoncic, J. / Stojanoff, V. / Chiswell, B.P. / Calderwood, D.A. / Boggon, T.J.
CitationJournal: To be Published
Title: 1.2 structure of integrin-linked kinase ankyrin repeat domain in complex with PINCH1 LIM1 domain collected at wavelength 0.91974
Authors: Stiegler, A.L. / Jakoncic, J. / Stojanoff, V. / Chiswell, B.P. / Calderwood, D.A. / Boggon, T.J.
History
DepositionOct 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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: Integrin-linked protein kinase
B: LIM and senescent cell antigen-like-containing domain protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,04015
Polymers28,5452
Non-polymers1,49513
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-18 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.144, 41.775, 46.798
Angle α, β, γ (deg.)78.670, 68.940, 85.810
Int Tables number1
Space group name H-MP1
Detailsbiological unit is the same as asym. unit

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Integrin-linked protein kinase / 59 kDa serine/threonine-protein kinase / ILK-1 / ILK-2 / 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: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: Q13418, non-specific serine/threonine protein kinase
#2: Protein LIM and senescent cell antigen-like-containing domain protein 1 / Particularly interesting new Cys-His protein 1 / PINCH-1 / Renal carcinoma antigen NY-REN-48


Mass: 8288.212 Da / Num. of mol.: 1 / Fragment: LIM1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIMS1, PINCH, PINCH1 / Plasmid: modified pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P48059

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Non-polymers , 4 types, 234 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 3350, 0.2M Sodium Formate, 0.5M Sodium Iodide, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.91974 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91974 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 75043 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 15.685
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.327 / Num. unique all: 7229 / Rsym value: 0.99 / % possible all: 90.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å24.19 Å
Translation2.5 Å24.19 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
Executordata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3F6Q

3f6q


Resolution: 1.203→34.662 Å / Occupancy max: 1 / Occupancy min: 0.05 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 17.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1982 3774 5.04 %random
Rwork0.1752 ---
all0.1763 74906 --
obs0.1763 74906 93.64 %-
Solvent computationShrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.822 Å2 / ksol: 0.259 e/Å3
Displacement parametersBiso max: 86.66 Å2 / Biso mean: 28.6533 Å2 / Biso min: 14.41 Å2
Baniso -1Baniso -2Baniso -3
1--2.9399 Å2-0.5317 Å20.3893 Å2
2---0.5341 Å2-3.0228 Å2
3---3.474 Å2
Refinement stepCycle: LAST / Resolution: 1.203→34.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1917 0 17 221 2155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112058
X-RAY DIFFRACTIONf_angle_d1.3122792
X-RAY DIFFRACTIONf_chiral_restr0.079280
X-RAY DIFFRACTIONf_plane_restr0.007379
X-RAY DIFFRACTIONf_dihedral_angle_d15.037761
LS refinement shellResolution: 1.2026→1.2178 Å / Total num. of bins used: 27
RfactorNum. reflection% reflection
Rfree0.3255 120 -
Rwork0.2858 2218 -
all-2338 -
obs-2338 80 %

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