[English] 日本語
Yorodumi
- PDB-1k40: crystal structure of the FAT domain of focal adhesion kinase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k40
Titlecrystal structure of the FAT domain of focal adhesion kinase
Componentsadhesion kinase
KeywordsTRANSFERASE / HELIX BUNDLE
Function / homology
Function and homology information


DCC mediated attractive signaling / Apoptotic cleavage of cellular proteins / MET activates PTK2 signaling / NCAM signaling for neurite out-growth / negative regulation of synapse assembly / central nervous system neuron axonogenesis / RHO GTPases Activate WASPs and WAVEs / regulation of substrate adhesion-dependent cell spreading / EPHB-mediated forward signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins ...DCC mediated attractive signaling / Apoptotic cleavage of cellular proteins / MET activates PTK2 signaling / NCAM signaling for neurite out-growth / negative regulation of synapse assembly / central nervous system neuron axonogenesis / RHO GTPases Activate WASPs and WAVEs / regulation of substrate adhesion-dependent cell spreading / EPHB-mediated forward signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / Extra-nuclear estrogen signaling / negative regulation of axonogenesis / intracellular chloride ion homeostasis / regulation of epithelial cell migration / RAF/MAP kinase cascade / negative regulation of organ growth / Regulation of actin dynamics for phagocytic cup formation / regulation of modification of postsynaptic actin cytoskeleton / JUN kinase binding / VEGFA-VEGFR2 Pathway / negative regulation of cell adhesion mediated by integrin / signal complex assembly / positive regulation of ubiquitin-dependent protein catabolic process / positive regulation of macrophage proliferation / positive regulation of fibroblast migration / positive regulation of smooth muscle cell migration / growth hormone receptor signaling pathway / regulation of focal adhesion assembly / negative regulation of cell-cell adhesion / regulation of cell adhesion mediated by integrin / nuclear migration / positive regulation of wound healing / regulation of osteoblast differentiation / positive regulation of cardiac muscle hypertrophy / blood vessel development / positive regulation of macrophage chemotaxis / negative regulation of anoikis / intercalated disc / positive regulation of epithelial cell migration / positive regulation of glial cell proliferation / ephrin receptor signaling pathway / positive regulation of epithelial to mesenchymal transition / cellular response to transforming growth factor beta stimulus / endothelial cell migration / positive regulation of synaptic transmission / vasculogenesis / phosphatase binding / regulation of cell adhesion / phosphatidylinositol 3-kinase binding / stress fiber / JNK cascade / extracellular matrix organization / positive regulation of smooth muscle cell proliferation / positive regulation of cell adhesion / transforming growth factor beta receptor signaling pathway / protein tyrosine phosphatase activity / negative regulation of autophagy / SH2 domain binding / negative regulation of cell migration / positive regulation of phagocytosis / molecular function activator activity / integrin-mediated signaling pathway / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / sarcolemma / vasodilation / integrin binding / microtubule cytoskeleton organization / epidermal growth factor receptor signaling pathway / neuron migration / cell migration / regulation of cell shape / MAPK cascade / lamellipodium / regulation of cell population proliferation / actin binding / positive regulation of cell growth / protein tyrosine kinase activity / angiogenesis / cell cortex / protein phosphatase binding / basolateral plasma membrane / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / apical plasma membrane / postsynapse / cilium / nuclear body / positive regulation of cell migration / ciliary basal body / focal adhesion / positive regulation of cell population proliferation / centrosome / protein kinase binding / negative regulation of apoptotic process / protein-containing complex binding / perinuclear region of cytoplasm / glutamatergic synapse
Similarity search - Function
Nucleotidyltransferases domain 2 / Focal adhesion kinase, targeting (FAT) domain / Focal adhesion kinase, targeting (FAT) domain superfamily / Focal adhesion kinase, N-terminal / FAK1/PYK2, FERM domain C-lobe / Focal adhesion targeting region / FERM N-terminal domain / : / FAK1/PYK2, FERM domain C-lobe / FERM domain signature 2. ...Nucleotidyltransferases domain 2 / Focal adhesion kinase, targeting (FAT) domain / Focal adhesion kinase, targeting (FAT) domain superfamily / Focal adhesion kinase, N-terminal / FAK1/PYK2, FERM domain C-lobe / Focal adhesion targeting region / FERM N-terminal domain / : / FAK1/PYK2, FERM domain C-lobe / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Four Helix Bundle (Hemerythrin (Met), subunit A) / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ubiquitin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Focal adhesion kinase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.25 Å
AuthorsHayashi, I. / Vuori, K. / Liddington, R.C.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: The focal adhesion targeting (FAT) region of focal adhesion kinase is a four-helix bundle that binds paxillin
Authors: Hayashi, I. / Vuori, K. / Liddington, R.C.
History
DepositionOct 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: adhesion kinase


Theoretical massNumber of molelcules
Total (without water)14,0061
Polymers14,0061
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.104, 40.163, 52.008
Angle α, β, γ (deg.)90.00, 103.82, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein adhesion kinase


Mass: 14006.386 Da / Num. of mol.: 1 / Fragment: FAT DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P34152, EC: 2.7.1.112
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7
Details: PEG10k, HEPES, pH 7.0, VAPOR DIFFUSION, temperature 295K
Crystal grow
*PLUS
Method: batch method / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH8.0
20.1 M1dropNaCl
31 mMdithiothreitol1drop
425 mg/mlprotein1drop
50.1 MHEPES1reservoirpH7.0
620 %(w/v)PEG100001reservoir

-
Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 8, 2001
RadiationMonochromator: Channel Cut Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionNum. all: 5618 / Num. obs: 5964 / Observed criterion σ(F): 1 / Biso Wilson estimate: 17.7 Å2
Reflection
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 20 Å / % possible obs: 98.2 % / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 91.9 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 6.05

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
DMmodel building
CNS1refinement
DMphasing
RefinementResolution: 2.25→18.66 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 1112998.34 / Data cutoff high rms absF: 1112998.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.294 318 5.7 %RANDOM
Rwork0.236 ---
obs0.236 5618 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.6602 Å2 / ksol: 0.399858 e/Å3
Displacement parametersBiso mean: 32.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.8 Å20 Å2-7.44 Å2
2--5.07 Å20 Å2
3---0.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.25→18.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 0 24 1001
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.7
X-RAY DIFFRACTIONc_improper_angle_d1.79
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scbond_it2.372
X-RAY DIFFRACTIONc_scangle_it3.612.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 53 5.9 %
Rwork0.242 850 -
obs--92.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 5300 / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.224 / Rfactor Rfree: 0.275
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.79
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_scbond_it2.372
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scangle_it3.612.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.356 / % reflection Rfree: 5.9 % / Rfactor Rwork: 0.242

+
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