[English] 日本語
Yorodumi
- PDB-4xef: Pyk2-FAT complexed with Leupaxin LD motif LD1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xef
TitlePyk2-FAT complexed with Leupaxin LD motif LD1
Components
  • 20-mer peptide containing LD1 motif of leupaxin
  • Protein-tyrosine kinase 2-beta
KeywordsCELL ADHESION / 4-HELIX BUNDLE / FOCAL ADHESION / TYROSINE KINASE / LEUPAXIN
Function / homology
Function and homology information


regulation of macrophage chemotaxis / response to cation stress / neurotransmitter receptor regulator activity / 3-phosphoinositide-dependent protein kinase binding / negative regulation of B cell receptor signaling pathway / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / regulation of ubiquitin-dependent protein catabolic process / blood vessel endothelial cell migration / endothelin receptor signaling pathway ...regulation of macrophage chemotaxis / response to cation stress / neurotransmitter receptor regulator activity / 3-phosphoinositide-dependent protein kinase binding / negative regulation of B cell receptor signaling pathway / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / regulation of ubiquitin-dependent protein catabolic process / blood vessel endothelial cell migration / endothelin receptor signaling pathway / negative regulation of myeloid cell differentiation / negative regulation of muscle cell apoptotic process / negative regulation of bone mineralization / cortical cytoskeleton organization / regulation of postsynaptic density assembly / activation of Janus kinase activity / negative regulation of cell adhesion / 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 / podosome / positive regulation of cell-matrix adhesion / positive regulation of DNA biosynthetic process / positive regulation of actin filament polymerization / stress fiber assembly / regulation of cell adhesion mediated by integrin / negative regulation of potassium ion transport / RHOU GTPase cycle / response to immobilization stress / positive regulation of excitatory postsynaptic potential / positive regulation of protein kinase activity / 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 / response to mechanical stimulus / response to cAMP / tumor necrosis factor-mediated signaling pathway / cellular response to retinoic acid / response to hormone / positive regulation of endothelial cell migration / ionotropic glutamate receptor signaling pathway / transforming growth factor beta 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 / cell projection / non-membrane spanning protein tyrosine kinase activity / regulation of actin cytoskeleton organization / transcription coregulator activity / non-specific protein-tyrosine kinase / positive regulation of JNK cascade / response to cocaine / Schaffer collateral - CA1 synapse / peptidyl-tyrosine phosphorylation / 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 / lamellipodium / presynapse / regulation of cell shape / cell body / growth cone / positive regulation of cytosolic calcium ion concentration / positive regulation of cell growth / cell cortex / protein-containing complex assembly / protein autophosphorylation / protein tyrosine kinase activity / adaptive immune response / negative regulation of neuron apoptotic process
Similarity search - Function
Leupaxin/Paxillin/TGFB1I1 / 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 ...Leupaxin/Paxillin/TGFB1I1 / 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
Leupaxin / Protein-tyrosine kinase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMiller, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM100909-03 United States
CitationJournal: Biochemistry / Year: 2016
Title: Structural Basis for the Interaction between Pyk2-FAT Domain and Leupaxin LD Repeats.
Authors: Vanarotti, M.S. / Finkelstein, D.B. / Guibao, C.D. / Nourse, A. / Miller, D.J. / Zheng, J.J.
History
DepositionDec 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Mar 16, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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: Protein-tyrosine kinase 2-beta
B: 20-mer peptide containing LD1 motif of leupaxin
C: 20-mer peptide containing LD1 motif of leupaxin
D: Protein-tyrosine kinase 2-beta
E: 20-mer peptide containing LD1 motif of leupaxin
F: 20-mer peptide containing LD1 motif of leupaxin


Theoretical massNumber of molelcules
Total (without water)39,8076
Polymers39,8076
Non-polymers00
Water21612
1
A: Protein-tyrosine kinase 2-beta
B: 20-mer peptide containing LD1 motif of leupaxin
C: 20-mer peptide containing LD1 motif of leupaxin


Theoretical massNumber of molelcules
Total (without water)19,9043
Polymers19,9043
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-19 kcal/mol
Surface area8580 Å2
MethodPISA
2
D: Protein-tyrosine kinase 2-beta
E: 20-mer peptide containing LD1 motif of leupaxin
F: 20-mer peptide containing LD1 motif of leupaxin


Theoretical massNumber of molelcules
Total (without water)19,9043
Polymers19,9043
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-16 kcal/mol
Surface area8610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.482, 78.094, 165.418
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 / Calcium-dependent tyrosine kinase / CADTK / Calcium-regulated non-receptor proline-rich tyrosine ...Calcium-dependent tyrosine kinase / CADTK / Calcium-regulated non-receptor proline-rich tyrosine kinase / Cell adhesion kinase beta / CAKB / Focal adhesion kinase 2 / FADK 2 / Proline-rich tyrosine kinase 2 / Related adhesion focal tyrosine kinase / RAFTK


Mass: 15228.520 Da / Num. of mol.: 2 / Fragment: FAT domain (UNP residues 871-1005) / Mutation: C899S, C972A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTK2B, FAK2, PYK2, RAFTK / Production host: Escherichia coli (E. coli)
References: UniProt: Q14289, non-specific protein-tyrosine kinase
#2: Protein/peptide
20-mer peptide containing LD1 motif of leupaxin


Mass: 2337.492 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O60711*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.23 Å3/Da / Density % sol: 44.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 400 nl drop contained 200 nl protein/LD1 peptide mixture (20 mM MES, pH 6.2, 1 mM protein, and 2 mM peptide) and 200 nl well solution (100 mM Tris, pH 8.5, 0.2 M MgCl2, and 30% PEG 4000).

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9712 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9712 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 12937 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rsym value: 0.09 / Net I/σ(I): 20.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2.2 / % possible all: 91.7

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GM3

3gm3


Resolution: 2.5→24.83 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.266 690 5.36 %
Rwork0.224 --
obs0.227 12885 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→24.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2430 0 0 12 2442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092438
X-RAY DIFFRACTIONf_angle_d1.1383302
X-RAY DIFFRACTIONf_dihedral_angle_d15.632916
X-RAY DIFFRACTIONf_chiral_restr0.044431
X-RAY DIFFRACTIONf_plane_restr0.004421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.68770.2961250.25662181X-RAY DIFFRACTION91
2.6877-2.95780.28561290.25122439X-RAY DIFFRACTION100
2.9578-3.38480.26751500.24752451X-RAY DIFFRACTION100
3.3848-4.2610.28811440.21462475X-RAY DIFFRACTION100
4.261-24.83180.23721420.20682649X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7317-0.10520.09752.0501-0.29782.8096-0.0110.01280.01960.07350.0668-0.2027-0.29980.69890.03760.2649-0.05710.02610.276-0.00330.332815.42116.627518.0353
20.9987-0.47590.57560.999-0.50772.8883-0.0247-0.2140.10280.2364-0.00180.0964-0.5723-0.6820.02170.390.00780.02050.3855-0.03060.39874.938821.195623.8892
31.8071-0.592-0.07791.60050.18623.19880.18260.0082-0.19140.1499-0.0541-0.05820.629-0.3545-0.0260.2568-0.07970.04740.28440.01770.34396.50111.94619.7552
41.9392-0.0113-0.16162.5443-0.54852.07180.1044-0.1283-0.16150.0697-0.0788-0.2927-0.12840.6476-0.02620.1827-0.0509-0.00130.32150.00020.298127.061952.52711.4863
51.91360.081.18751.63270.39494.39890.0172-0.48850.05570.1053-0.20050.1623-0.6838-0.5603-0.08710.383-0.03920.0070.3505-0.01290.29116.877357.86918.2989
60.82940.14330.44952.12930.72974.45310.5156-0.3585-0.53270.2197-0.0471-0.25790.6133-0.3191-0.1090.2841-0.1007-0.00740.36160.03160.352619.243548.446716.3146
71.2657-0.3496-0.75550.27750.1670.3970.07570.4750.62310.9670.0861-0.3842-1.1060.08570.14870.89830.07490.02920.4438-0.01060.72129.359730.737121.3524
83.2783-0.0575-0.14931.75920.06834.06840.2616-0.2764-0.72810.063-0.138-0.32510.77440.3722-0.02460.59920.00780.05870.36780.13620.723515.53284.178620.6665
94.35251.7681-0.75267.66292.65395.20030.1465-0.32420.53420.2232-0.56390.4886-0.68440.28180.56520.5391-0.03280.06820.30960.00140.357220.312567.087814.3634
101.65120.38821.10532.16470.9491.22590.0056-0.6555-0.3116-0.00350.2261-0.06190.77340.3961-0.03720.5979-0.0728-0.05490.66350.18660.947827.75440.287917.485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 870 THROUGH 928 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 929 THROUGH 968 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 969 THROUGH 1005 )
4X-RAY DIFFRACTION4CHAIN 'D' AND (RESID 871 THROUGH 932 )
5X-RAY DIFFRACTION5CHAIN 'D' AND (RESID 933 THROUGH 966 )
6X-RAY DIFFRACTION6CHAIN 'D' AND (RESID 967 THROUGH 1004 )
7X-RAY DIFFRACTION7CHAIN 'C' AND (RESID 1 THROUGH 13 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 1 THROUGH 15 )
9X-RAY DIFFRACTION9CHAIN 'F' AND (RESID 2 THROUGH 13 )
10X-RAY DIFFRACTION10CHAIN 'E' AND (RESID 1 THROUGH 15 )

+
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