[English] 日本語
Yorodumi
- PDB-3u3f: Structural basis for the interaction of Pyk2 PAT domain with paxi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3u3f
TitleStructural basis for the interaction of Pyk2 PAT domain with paxillin LD motifs
Components
  • Paxillin LD2 peptide
  • Protein-tyrosine kinase 2-beta
KeywordsTRANSFERASE/signaling protein / 4-helix bundle / focal adhesion / tyrosine kinase / paxillin / TRANSFERASE-signaling protein complex
Function / homology
Function and homology information


regulation of macrophage chemotaxis / response to cation stress / neurotransmitter receptor regulator activity / 3-phosphoinositide-dependent protein kinase binding / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / regulation of ubiquitin-dependent protein catabolic process / blood vessel endothelial cell migration ...regulation of macrophage chemotaxis / response to cation stress / neurotransmitter receptor regulator activity / 3-phosphoinositide-dependent protein kinase binding / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / regulation of ubiquitin-dependent protein catabolic process / blood vessel endothelial cell migration / endothelin receptor signaling pathway / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of myeloid cell differentiation / negative regulation of muscle cell apoptotic process / negative regulation of bone mineralization / cortical cytoskeleton organization / neuropilin binding / regulation of postsynaptic density assembly / vinculin binding / activation of Janus kinase activity / chemokine-mediated signaling pathway / apical dendrite / focal adhesion assembly / cellular response to fluid shear stress / regulation of release of sequestered calcium ion into cytosol / signal complex assembly / positive regulation of ubiquitin-dependent protein catabolic process / calcium/calmodulin-dependent protein kinase activity / Interleukin-2 signaling / long-term synaptic depression / oocyte maturation / sprouting angiogenesis / Signal regulatory protein family interactions / NMDA selective glutamate receptor complex / microtubule associated complex / growth hormone receptor signaling pathway / positive regulation of cell-matrix adhesion / positive regulation of DNA biosynthetic process / positive regulation of actin filament polymerization / stress fiber assembly / negative regulation of potassium ion transport / RHOU GTPase cycle / response to immobilization stress / positive regulation of excitatory postsynaptic potential / Smooth Muscle Contraction / positive regulation of protein kinase activity / GAB1 signalosome / postsynaptic density, intracellular component / glutamate receptor binding / vascular endothelial growth factor receptor signaling pathway / bone resorption / endothelial cell migration / postsynaptic modulation of chemical synaptic transmission / glial cell proliferation / cellular defense response / regulation of cell adhesion / response to glucose / peptidyl-tyrosine autophosphorylation / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / response to mechanical stimulus / stress fiber / response to cAMP / tumor necrosis factor-mediated signaling pathway / cellular response to retinoic acid / positive regulation of stress fiber assembly / response to hormone / positive regulation of endothelial cell migration / transforming growth factor beta receptor signaling pathway / ionotropic glutamate receptor signaling pathway / substrate adhesion-dependent cell spreading / positive regulation of synaptic transmission, glutamatergic / positive regulation of translation / response to ischemia / integrin-mediated signaling pathway / cellular response to reactive oxygen species / non-membrane spanning protein tyrosine kinase activity / regulation of actin cytoskeleton organization / non-specific protein-tyrosine kinase / positive regulation of JNK cascade / response to cocaine / peptidyl-tyrosine phosphorylation / Schaffer collateral - CA1 synapse / beta-catenin binding / regulation of synaptic plasticity / positive regulation of neuron projection development / response to hydrogen peroxide / VEGFA-VEGFR2 Pathway / long-term synaptic potentiation / epidermal growth factor receptor signaling pathway / response to calcium ion / positive regulation of angiogenesis / neuron projection development / positive regulation of reactive oxygen species metabolic process / positive regulation of nitric oxide biosynthetic process / MAPK cascade / cell-cell junction / cell migration / lamellipodium / regulation of cell shape / presynapse
Similarity search - Function
Paxillin / : / : / Paxillin family / 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 ...Paxillin / : / : / Paxillin family / 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 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. / Tyrosine-protein kinase, active site / PH-like domain superfamily / 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 / Protein-tyrosine kinase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.101 Å
AuthorsVanarotti, M. / Miller, D.J. / Guibao, C.C. / Zheng, J.J.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structural and Mechanistic Insights into the Interaction between Pyk2 and Paxillin LD Motifs.
Authors: Vanarotti, M.S. / Miller, D.J. / Guibao, C.D. / Nourse, A. / Zheng, J.J.
History
DepositionOct 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein-tyrosine kinase 2-beta
B: Protein-tyrosine kinase 2-beta
C: Protein-tyrosine kinase 2-beta
D: Protein-tyrosine kinase 2-beta
E: Paxillin LD2 peptide
F: Paxillin LD2 peptide
G: Paxillin LD2 peptide
H: Paxillin LD2 peptide
I: Paxillin LD2 peptide
J: Paxillin LD2 peptide


Theoretical massNumber of molelcules
Total (without water)72,53310
Polymers72,53310
Non-polymers00
Water543
1
A: Protein-tyrosine kinase 2-beta
E: Paxillin LD2 peptide
I: Paxillin LD2 peptide


Theoretical massNumber of molelcules
Total (without water)19,0913
Polymers19,0913
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-19 kcal/mol
Surface area7940 Å2
MethodPISA
2
B: Protein-tyrosine kinase 2-beta
F: Paxillin LD2 peptide
J: Paxillin LD2 peptide


Theoretical massNumber of molelcules
Total (without water)19,0913
Polymers19,0913
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-16 kcal/mol
Surface area7990 Å2
MethodPISA
3
C: Protein-tyrosine kinase 2-beta
G: Paxillin LD2 peptide


Theoretical massNumber of molelcules
Total (without water)17,1762
Polymers17,1762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-7 kcal/mol
Surface area7320 Å2
MethodPISA
4
D: Protein-tyrosine kinase 2-beta
H: Paxillin LD2 peptide


Theoretical massNumber of molelcules
Total (without water)17,1762
Polymers17,1762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-10 kcal/mol
Surface area7450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.599, 83.747, 170.545
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 15260.584 Da / Num. of mol.: 4 / Fragment: unp residues 871-1005 / Mutation: C899S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTK2B, FAK2, PYK2, RAFTK / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q14289, non-specific protein-tyrosine kinase
#2: Protein/peptide
Paxillin LD2 peptide


Mass: 1915.128 Da / Num. of mol.: 6 / Fragment: unp residues 261-277 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P49023
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.12 Å3/Da / Density % sol: 70.11 %
Crystal growTemperature: 291.2 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: The 4 ul drop contained 2 ul protein-LD4 peptide mixture (20mM Mes, pH6.2, 1mM protein, 2 mM peptide) and 2 ul ML (100 mM MES pH6.3, 4.2 M NaCl, 2%(v/v) glycerol., VAPOR DIFFUSION, SITTING ...Details: The 4 ul drop contained 2 ul protein-LD4 peptide mixture (20mM Mes, pH6.2, 1mM protein, 2 mM peptide) and 2 ul ML (100 mM MES pH6.3, 4.2 M NaCl, 2%(v/v) glycerol., VAPOR DIFFUSION, SITTING DROP, temperature 291.2K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 13, 2011 / Details: mirrors
RadiationMonochromator: Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. all: 22414 / Num. obs: 21900 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 106.2 Å2 / Rsym value: 0.06 / Net I/σ(I): 25.8
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 2076 / Rsym value: 0.647 / % possible all: 94.4

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERMolecular Replacementphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3GM1

3gm1


Resolution: 3.101→29.848 Å / SU ML: 0.3 / σ(F): 0.08 / Phase error: 29.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2659 1045 5.01 %Random
Rwork0.218 ---
obs0.2204 20847 93.3 %-
all-20847 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 78.391 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0616 Å20 Å2-0 Å2
2--3.1061 Å20 Å2
3----2.0445 Å2
Refinement stepCycle: LAST / Resolution: 3.101→29.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4289 0 0 3 4292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084307
X-RAY DIFFRACTIONf_angle_d1.0655844
X-RAY DIFFRACTIONf_dihedral_angle_d18.212738
X-RAY DIFFRACTIONf_chiral_restr0.061768
X-RAY DIFFRACTIONf_plane_restr0.004743
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.101-3.26430.35891090.31052385X-RAY DIFFRACTION81
3.2643-3.46860.33271550.26652783X-RAY DIFFRACTION93
3.4686-3.73590.28571370.24892822X-RAY DIFFRACTION94
3.7359-4.1110.25261560.20552875X-RAY DIFFRACTION96
4.111-4.70390.24551700.17512954X-RAY DIFFRACTION98
4.7039-5.91880.28781560.2172960X-RAY DIFFRACTION97
5.9188-29.84950.23841620.20433023X-RAY DIFFRACTION95

+
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