[English] 日本語
Yorodumi
- PDB-4hi9: 1.2 structure of integrin-linked kinase ankyrin repeat domain in ... -

+
Open data


ID or keywords:

Loading...

-
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


caveola assembly / protein localization to cell cortex / 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 / fibroblast migration / establishment or maintenance of epithelial cell apical/basal polarity ...caveola assembly / protein localization to cell cortex / 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 / fibroblast migration / establishment or maintenance of epithelial cell apical/basal polarity / Cell-extracellular matrix interactions / cell projection organization / myelination in peripheral nervous system / cell-cell junction organization / positive regulation of BMP signaling pathway / positive regulation of cell-substrate adhesion / neural precursor cell proliferation / branching involved in ureteric bud morphogenesis / outflow tract morphogenesis / positive regulation of focal adhesion assembly / positive regulation of osteoblast differentiation / cellular response to transforming growth factor beta stimulus / tumor necrosis factor-mediated signaling pathway / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of GTPase activity / substrate adhesion-dependent cell spreading / sarcomere / cell-matrix adhesion / mitotic spindle organization / integrin-mediated signaling pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / establishment of protein localization / cell morphogenesis / cell-cell adhesion / platelet aggregation / integrin binding / positive regulation of canonical Wnt signaling pathway / cell-cell junction / lamellipodium / actin cytoskeleton / actin binding / cell cortex / protein-macromolecule adaptor activity / positive regulation of canonical NF-kappaB signal transduction / cell differentiation / protein kinase activity / signaling receptor binding / focal adhesion / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / centrosome / positive regulation of gene expression / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / magnesium ion binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Integrin-linked protein kinase, pseudokinase domain / LIM and senescent cell antigen-like-containing domain protein 1-like / : / : / 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 ...Integrin-linked protein kinase, pseudokinase domain / LIM and senescent cell antigen-like-containing domain protein 1-like / : / : / 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
IODIDE ION / PHOSPHATE ION / LIM and senescent cell antigen-like-containing domain protein 1 / Scaffold protein ILK
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
Phasing

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

-
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 %

+
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