[English] 日本語
Yorodumi
- PDB-9d5h: Crystal structure of the ILK mutant (R371Q)/alpha-parvin core com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9d5h
TitleCrystal structure of the ILK mutant (R371Q)/alpha-parvin core complex bound to gefitinib
Components
  • Alpha-parvin
  • Integrin-linked protein kinase
KeywordsTRANSFERASE/INHIBITOR / Pseudokinase / Inhibitor / Complex / Scaffolding / Drug / CELL ADHESION / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


actin-mediated cell contraction / smooth muscle cell chemotaxis / establishment or maintenance of cell polarity regulating cell shape / protein localization to cell cortex / caveola assembly / 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 / nerve development ...actin-mediated cell contraction / smooth muscle cell chemotaxis / establishment or maintenance of cell polarity regulating cell shape / protein localization to cell cortex / caveola assembly / 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 / 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 / outflow tract septum morphogenesis / sprouting angiogenesis / neural precursor cell proliferation / heterotypic cell-cell adhesion / branching involved in ureteric bud morphogenesis / protein kinase inhibitor activity / establishment or maintenance of cell polarity / outflow tract morphogenesis / cilium assembly / 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 / platelet aggregation / integrin binding / Z disc / cell morphogenesis / positive regulation of canonical Wnt signaling pathway / lamellipodium / actin cytoskeleton / actin binding / actin cytoskeleton organization / cell cortex / protein-macromolecule adaptor activity / cell differentiation / positive regulation of canonical NF-kappaB signal transduction / protein kinase activity / protein stabilization / cadherin binding / signaling receptor binding / focal adhesion / positive regulation of cell population proliferation / centrosome / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / magnesium ion binding / nucleoplasm / ATP binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Integrin-linked protein kinase, pseudokinase domain / Parvin / 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. ...Integrin-linked protein kinase, pseudokinase domain / Parvin / 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 / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Gefitinib / Scaffold protein ILK / Alpha-parvin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFukuda, K. / Qin, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)2R01HL058758-23A1 United States
CitationJournal: To Be Published
Title: Crystal structure of the ILK mutant (R371Q)/alpha-parvin core complex bound to gefitinib
Authors: Fukdua, K. / Qin, J.
History
DepositionAug 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,5154
Polymers45,7862
Non-polymers7292
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-22 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.154, 118.355, 47.452
Angle α, β, γ (deg.)90.000, 100.820, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

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


Mass: 30942.947 Da / Num. of mol.: 1 / Mutation: C346S, R371Q, C422S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ILK, ILK1, ILK2 / Plasmid: pST39 / Details (production host): Coexpression / Production host: Escherichia coli (E. coli)
References: UniProt: Q13418, non-specific serine/threonine protein kinase
#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
Source method: isolated from a genetically manipulated source
Details: Vector sequence (GSHM) at the N-terminus / Source: (gene. exp.) Homo sapiens (human) / Gene: PARVA, MXRA2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NVD7
#3: Chemical ChemComp-IRE / Gefitinib


Mass: 446.902 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24ClFN4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: Bis-Tris Propane, PEG3350, 1-propanol, gefitinib, and DMSO

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 73604 / % possible obs: 99.2 % / Redundancy: 4.7 % / Biso Wilson estimate: 20.81 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 43.32
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.13 / Num. unique obs: 3608 / % possible all: 95

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→30.26 Å / SU ML: 0.1707 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.9682
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2239 3668 4.99 %
Rwork0.1954 69864 -
obs0.1968 73532 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.69 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3180 0 50 323 3553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00783314
X-RAY DIFFRACTIONf_angle_d1.04354492
X-RAY DIFFRACTIONf_chiral_restr0.0561488
X-RAY DIFFRACTIONf_plane_restr0.0077572
X-RAY DIFFRACTIONf_dihedral_angle_d15.33311269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.30291310.27662460X-RAY DIFFRACTION88.07
1.52-1.540.30191230.25852658X-RAY DIFFRACTION96.87
1.54-1.570.2961600.25412632X-RAY DIFFRACTION95.23
1.57-1.590.24961320.2362650X-RAY DIFFRACTION96.16
1.59-1.610.2411680.22132662X-RAY DIFFRACTION96.92
1.61-1.640.22951510.22012646X-RAY DIFFRACTION95.27
1.64-1.670.21021620.21422646X-RAY DIFFRACTION97.7
1.67-1.70.24831530.21162654X-RAY DIFFRACTION95.51
1.7-1.730.2761530.21422655X-RAY DIFFRACTION97.94
1.73-1.770.2261520.22072692X-RAY DIFFRACTION96.11
1.77-1.810.23051460.2052691X-RAY DIFFRACTION98.3
1.81-1.850.24221390.21162668X-RAY DIFFRACTION96.63
1.85-1.890.22821360.21142740X-RAY DIFFRACTION98.29
1.89-1.940.24471520.2092663X-RAY DIFFRACTION97.17
1.94-20.20721320.19992715X-RAY DIFFRACTION97.23
2-2.070.25171410.20012719X-RAY DIFFRACTION98.15
2.07-2.140.21791450.19872699X-RAY DIFFRACTION97.83
2.14-2.230.23111270.19312702X-RAY DIFFRACTION97.55
2.23-2.330.22521410.20162737X-RAY DIFFRACTION98.06
2.33-2.450.22781270.20092750X-RAY DIFFRACTION98.56
2.45-2.60.23611300.20652745X-RAY DIFFRACTION98.43
2.6-2.80.22431440.2042749X-RAY DIFFRACTION98.97
2.8-3.090.23811380.19322754X-RAY DIFFRACTION99.18
3.09-3.530.21881340.18732760X-RAY DIFFRACTION99.01
3.53-4.450.19631290.16172777X-RAY DIFFRACTION98.71
4.45-30.260.19981220.18942640X-RAY DIFFRACTION93.09

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more