[English] 日本語
Yorodumi
- PDB-1ow6: Paxillin LD4 motif bound to the Focal Adhesion Targeting (FAT) do... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ow6
TitlePaxillin LD4 motif bound to the Focal Adhesion Targeting (FAT) domain of the Focal Adhesion Kinase
Components
  • Focal adhesion kinase 1
  • Paxillin
KeywordsTRANSFERASE / 4 helical bundle / domain swapping / amphiphatic helix
Function / homology
Function and homology information


netrin-activated signaling pathway / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / detection of muscle stretch / vinculin binding / neuropilin binding / positive regulation of ubiquitin-dependent protein catabolic process ...netrin-activated signaling pathway / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / detection of muscle stretch / vinculin binding / neuropilin binding / positive regulation of ubiquitin-dependent protein catabolic process / JUN kinase binding / signal complex assembly / positive regulation of fibroblast migration / positive regulation of macrophage proliferation / DCC mediated attractive signaling / microtubule associated complex / growth hormone receptor signaling pathway / Signal regulatory protein family interactions / regulation of osteoblast differentiation / MET activates PTK2 signaling / regulation of focal adhesion assembly / regulation of GTPase activity / positive regulation of wound healing / Fc-gamma receptor signaling pathway involved in phagocytosis / establishment of cell polarity / negative regulation of cell-cell adhesion / positive regulation of macrophage chemotaxis / p130Cas linkage to MAPK signaling for integrins / positive regulation of epithelial cell migration / Apoptotic cleavage of cellular proteins / regulation of cytoskeleton organization / regulation of cell adhesion mediated by integrin / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of anoikis / endothelial cell migration / ephrin receptor signaling pathway / Smooth Muscle Contraction / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of protein kinase activity / RHO GTPases Activate WASPs and WAVEs / GAB1 signalosome / regulation of cell adhesion / vascular endothelial growth factor receptor signaling pathway / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of epithelial to mesenchymal transition / heart morphogenesis / stress fiber / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / NCAM signaling for neurite out-growth / Integrin signaling / SH2 domain binding / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / ciliary basal body / protein tyrosine phosphatase activity / molecular function activator activity / axon guidance / cell motility / integrin-mediated signaling pathway / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / regulation of protein phosphorylation / epidermal growth factor receptor signaling pathway / placenta development / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / beta-catenin binding / peptidyl-tyrosine phosphorylation / cellular response to reactive oxygen species / cell-cell junction / integrin binding / cell migration / lamellipodium / regulation of cell population proliferation / regulation of cell shape / actin binding / cell cortex / RAF/MAP kinase cascade / protein tyrosine kinase activity / protein phosphatase binding / angiogenesis / protein autophosphorylation / Extra-nuclear estrogen signaling / dendritic spine / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / cell adhesion / positive regulation of cell migration / positive regulation of protein phosphorylation / intracellular membrane-bounded organelle / focal adhesion / centrosome / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / signal transduction / ATP binding
Similarity search - Function
Paxillin / : / : / Paxillin family / Single helix bin / : / Nucleotidyltransferases domain 2 / Focal adhesion kinase, targeting (FAT) domain / Focal adhesion kinase, targeting (FAT) domain superfamily / Focal adhesion kinase, N-terminal ...Paxillin / : / : / Paxillin family / Single helix bin / : / 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 / 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. / 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) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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
Paxillin / Focal adhesion kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHoellerer, M.K. / Noble, M.E.M. / Labesse, G. / Campbell, I.D. / Werner, J.M. / Arold, S.T.
Citation
Journal: Structure / Year: 2003
Title: Molecular Recognition of Paxillin LD motifs by the Focal Adhesion Targeting Domain
Authors: Hoellerer, M.K. / Noble, M.E.M. / Labesse, G. / Campbell, I.D. / Werner, J.M. / Arold, S.T.
#1: Journal: Structure / Year: 2002
Title: The Structural Basis of Localization and Signaling by the Focal Adhesion Targeting Domain
Authors: Arold, S.T. / Hoellerer, M. / Noble, M.E.M.
History
DepositionMar 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 22, 2020Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_struct_special_symmetry / struct_biol
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Focal adhesion kinase 1
B: Focal adhesion kinase 1
C: Focal adhesion kinase 1
D: Paxillin
F: Paxillin


Theoretical massNumber of molelcules
Total (without water)56,3835
Polymers56,3835
Non-polymers00
Water2,144119
1
A: Focal adhesion kinase 1
D: Paxillin

A: Focal adhesion kinase 1
D: Paxillin


Theoretical massNumber of molelcules
Total (without water)38,5464
Polymers38,5464
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area6260 Å2
ΔGint-65 kcal/mol
Surface area16460 Å2
MethodPISA
2
B: Focal adhesion kinase 1

B: Focal adhesion kinase 1


Theoretical massNumber of molelcules
Total (without water)35,6732
Polymers35,6732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1520 Å2
ΔGint-14 kcal/mol
Surface area14570 Å2
MethodPISA
3
C: Focal adhesion kinase 1
F: Paxillin

C: Focal adhesion kinase 1
F: Paxillin


Theoretical massNumber of molelcules
Total (without water)38,5464
Polymers38,5464
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3200 Å2
ΔGint-28 kcal/mol
Surface area16020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.308, 223.274, 96.992
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-73-

HOH

21B-60-

HOH

31C-4-

HOH

41C-90-

HOH

-
Components

#1: Protein Focal adhesion kinase 1 / FADK 1 / pp125FAK / Protein- tyrosine kinase 2


Mass: 17836.539 Da / Num. of mol.: 3 / Fragment: Focal Adhesion Targeting Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTK2 OR FAK1 OR FAK / Plasmid: pGEX-6P2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q05397, EC: 2.7.1.112
#2: Protein/peptide Paxillin


Mass: 1436.609 Da / Num. of mol.: 2 / Fragment: Paxillin LD4 motif / Source method: obtained synthetically / Details: Sequence derived from human paxillin / References: UniProt: P49023*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 4.9 Å3/Da / Density % sol: 74.68 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: sodium chloride, glycerol, Hepes, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
13.9 M1reservoirNaCl
25 %glycerol1reservoir
3100 mMHEPES1reservoirpH6.3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 12, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.35→41.6 Å / Num. all: 39088 / Num. obs: 39088 / % possible obs: 97.3 % / Redundancy: 3 % / Biso Wilson estimate: 50.49 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.081 / Net I/σ(I): 7.2
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 1 / Num. unique all: 5762 / Rsym value: 0.749 / % possible all: 99.1
Reflection
*PLUS
Num. measured all: 116554 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 99.1 % / Rmerge(I) obs: 0.75

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K05

1k05


Resolution: 2.35→37.27 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.929 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The second LD4 motif (chain F, bound to molecule C) was fitted into the unbiased 3Fo-2Fc maps (CNS). Its position and orientation were inferred from homology with the well-defined other LD4 - ...Details: The second LD4 motif (chain F, bound to molecule C) was fitted into the unbiased 3Fo-2Fc maps (CNS). Its position and orientation were inferred from homology with the well-defined other LD4 - FAT interaction (chains A and C), and are supported by NMR data(see publication).
RfactorNum. reflection% reflectionSelection details
Rfree0.27357 1980 5.1 %RANDOM
Rwork0.24161 ---
all0.2432 39088 --
obs0.24326 39088 96.85 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.524 Å2
Baniso -1Baniso -2Baniso -3
1-7.69 Å20 Å20 Å2
2---5.3 Å20 Å2
3----2.38 Å2
Refinement stepCycle: LAST / Resolution: 2.35→37.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3369 0 0 119 3488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223410
X-RAY DIFFRACTIONr_bond_other_d0.0080.023274
X-RAY DIFFRACTIONr_angle_refined_deg2.2112.0094613
X-RAY DIFFRACTIONr_angle_other_deg1.00637678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3095430
X-RAY DIFFRACTIONr_chiral_restr0.1130.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023656
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02522
X-RAY DIFFRACTIONr_nbd_refined0.2430.21011
X-RAY DIFFRACTIONr_nbd_other0.2490.23934
X-RAY DIFFRACTIONr_nbtor_other0.0980.22009
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.298
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.2122
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.218
X-RAY DIFFRACTIONr_mcbond_it1.7211.52187
X-RAY DIFFRACTIONr_mcangle_it3.15723542
X-RAY DIFFRACTIONr_scbond_it3.95731223
X-RAY DIFFRACTIONr_scangle_it6.6414.51071
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.428 155
Rwork0.436 2747
Refinement
*PLUS
Lowest resolution: 41.6 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.21

+
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