[English] 日本語
Yorodumi
- PDB-3kmw: Crystal structure of the ILK/alpha-parvin core complex (MgATP) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kmw
TitleCrystal structure of the ILK/alpha-parvin core complex (MgATP)
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 / Alternative splicing / Cytoplasm / Cytoskeleton
Function / homology
Function and homology information


actin-mediated cell contraction / smooth muscle cell chemotaxis / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / negative regulation of neural precursor cell proliferation / positive regulation of signal transduction / nerve development / Cell-extracellular matrix interactions / fibroblast migration / myelination in peripheral nervous system ...actin-mediated cell contraction / smooth muscle cell chemotaxis / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / negative regulation of neural precursor cell proliferation / positive regulation of signal transduction / nerve development / Cell-extracellular matrix interactions / fibroblast migration / myelination in peripheral nervous system / cell projection organization / outflow tract septum morphogenesis / positive regulation of BMP signaling pathway / neural precursor cell proliferation / establishment or maintenance of epithelial cell apical/basal polarity / 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 / sarcomere / substrate adhesion-dependent cell spreading / cell-matrix adhesion / phosphatidylinositol 3-kinase/protein kinase B signal transduction / integrin-mediated signaling pathway / cell morphogenesis / platelet aggregation / Z disc / positive regulation of canonical Wnt signaling pathway / actin cytoskeleton / lamellipodium / actin binding / regulation of cell shape / actin cytoskeleton organization / positive regulation of canonical NF-kappaB signal transduction / protein stabilization / non-specific serine/threonine protein kinase / 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. / Ankyrin repeats (3 copies) ...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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFukuda, K. / Qin, J.
CitationJournal: Mol.Cell / Year: 2009
Title: The pseudoactive site of ILK is essential for its binding to alpha-Parvin and localization to focal adhesions.
Authors: Fukuda, K. / Gupta, S. / Chen, K. / Wu, C. / Qin, J.
History
DepositionNov 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,3474
Polymers45,8152
Non-polymers5312
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-11 kcal/mol
Surface area18590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.134, 117.103, 47.393
Angle α, β, γ (deg.)90.00, 101.96, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe heterodimeric complex observed in the asymmetric unit is relevant to the biological assembly unit in vivo.

-
Components

#1: Protein Integrin-linked kinase / / ILK


Mass: 30972.014 Da / Num. of mol.: 1
Fragment: C-terminal pseudokinase domain: UNP residues 183-452
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 / Calponin-like integrin-linked kinase-binding protein / CH-ILKBP / Matrix-remodeling-associated ...Calponin-like integrin-linked kinase-binding protein / CH-ILKBP / Matrix-remodeling-associated protein 2 / Actopaxin


Mass: 14843.072 Da / Num. of mol.: 1
Fragment: C-terminal 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine 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 / Water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.62 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 277 K / pH: 6.8
Details: 0.05 M Bis-Tris, 12% PEG 5000 MME, 5% 1-propyl alcohol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→46.36 Å / Num. obs: 31165 / % possible obs: 98.3 % / Redundancy: 5.53 % / Rsym value: 0.098 / Net I/σ(I): 12.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.09 % / Mean I/σ(I) obs: 7.8 / Rsym value: 0.136 / % possible all: 98.8

-
Processing

Software
NameClassification
StructureStudiodata collection
AMoREphasing
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KMU

3kmu


Resolution: 2→46.36 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1539 -RANDOM
Rwork0.199 ---
obs0.199 31052 98 %-
Refinement stepCycle: LAST / Resolution: 2→46.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3157 0 32 309 3498
LS refinement shellResolution: 2→2.02 Å /
RfactorNum. reflection
Rfree0.2475 51
Rwork0.2296 -

+
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