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- PDB-3rep: Crystal structure of the ILK/alpha-parvin core complex (MnATP) -

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Basic information

Entry
Database: PDB / ID: 3rep
TitleCrystal structure of the ILK/alpha-parvin core complex (MnATP)
Components
  • Alpha-parvin
  • Integrin-linked kinase
KeywordsCELL ADHESION / ANK REPEAT / ATP-BINDING / CELL JUNCTION / CELL MEMBRANE / INTEGRIN-BINDING PROTEIN / MEMBRANE / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN / PSEUDOKINASE / ACTIN-BINDING / CYTOSKELETON
Function / homology
Function and homology information


actin-mediated cell contraction / smooth muscle cell chemotaxis / 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 / outflow tract septum morphogenesis / nerve development / fibroblast migration / Cell-extracellular matrix interactions ...actin-mediated cell contraction / smooth muscle cell chemotaxis / 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 / outflow tract septum morphogenesis / nerve development / fibroblast migration / Cell-extracellular matrix interactions / myelination in peripheral nervous system / cell projection organization / positive regulation of BMP signaling pathway / establishment or maintenance of epithelial cell apical/basal polarity / neural precursor cell proliferation / heterotypic cell-cell adhesion / sprouting angiogenesis / branching involved in ureteric bud morphogenesis / establishment or maintenance of cell polarity / protein kinase inhibitor activity / outflow tract morphogenesis / cilium assembly / positive regulation of osteoblast differentiation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of phosphorylation / tumor necrosis factor-mediated signaling pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / sarcomere / cell-matrix adhesion / substrate adhesion-dependent cell spreading / integrin-mediated signaling pathway / cell morphogenesis / platelet aggregation / Z disc / positive regulation of canonical Wnt signaling pathway / actin cytoskeleton / lamellipodium / regulation of cell shape / actin binding / actin cytoskeleton organization / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / protein stabilization / cadherin binding / positive regulation of protein phosphorylation / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / positive regulation of cell population proliferation / protein kinase binding / positive regulation of DNA-templated transcription / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Integrin-linked protein kinase, pseudokinase domain / Parvin / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / : / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. ...Integrin-linked protein kinase, pseudokinase domain / Parvin / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / : / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / Integrin-linked protein kinase / Alpha-parvin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsFukuda, K. / Qin, J.
CitationJournal: To be Published
Title: Crystal structure of the ILK/alpha-parvin core complex (MnATP)
Authors: Fukuda, K. / Qin, J.
History
DepositionApr 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 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 / 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_asym_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

Downloads & links

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Assembly

Deposited unit
A: Integrin-linked kinase
B: Alpha-parvin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3774
Polymers45,8152
Non-polymers5622
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-11 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.022, 116.280, 47.284
Angle α, β, γ (deg.)90.00, 101.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Integrin-linked kinase / ILK


Mass: 30972.014 Da / Num. of mol.: 1 / Fragment: Pseudokinase domain, UNP residues 182-452 / Mutation: C346S, C422S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ILK, ILK1, ILK2 / Plasmid: pST39 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q13418
#2: Protein Alpha-parvin / Actopaxin / CH-ILKBP / Calponin-like integrin-linked kinase-binding protein / Matrix-remodeling- ...Actopaxin / CH-ILKBP / Calponin-like integrin-linked kinase-binding protein / Matrix-remodeling-associated protein 2


Mass: 14843.072 Da / Num. of mol.: 1 / Fragment: Calponin homology domain, UNP residues 248-372
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARVA, MXRA2 / Plasmid: pST39 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9NVD7
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 50 mM Bis-Tris Propane, 12.5 (w/v) PEG 5000 MME, 5% (v/v) 1-propyl alcohol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 22, 2011
RadiationMonochromator: Osmic VariMax optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→43.13 Å / Num. obs: 40605 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.15 % / Rmerge(I) obs: 0.034
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.22 % / Rmerge(I) obs: 0.136 / % possible all: 76.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
StructureStudiodata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3KMW

3kmw


Resolution: 1.8→34.64 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.692 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23783 1984 5 %RANDOM
Rwork0.20417 ---
obs0.20583 37526 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.042 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20.02 Å2
2--0.19 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3157 0 32 328 3517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223272
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9824445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7195390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38824.041146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86815572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7911519
X-RAY DIFFRACTIONr_chiral_restr0.0990.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022457
X-RAY DIFFRACTIONr_nbd_refined0.1970.21693
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22253
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.214
X-RAY DIFFRACTIONr_mcbond_it0.9721.52026
X-RAY DIFFRACTIONr_mcangle_it1.53723209
X-RAY DIFFRACTIONr_scbond_it2.32631416
X-RAY DIFFRACTIONr_scangle_it3.2854.51236
LS refinement shellResolution: 1.8→1.842 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.331 118
Rwork0.333 2002

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