[English] 日本語
Yorodumi
- PDB-7w9u: Crystal Structure of Zn bound human Focal Adhesion Targeting (FAT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7w9u
TitleCrystal Structure of Zn bound human Focal Adhesion Targeting (FAT) domain of the Focal Adhesion Kinase
ComponentsIsoform 5 of Focal adhesion kinase 1
KeywordsTRANSFERASE / Focal adhesion kinase / Protein tyrosine kinase 2
Function / homology
Function and homology information


netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / detection of muscle stretch / JUN kinase binding / signal complex assembly / positive regulation of ubiquitin-dependent protein catabolic process / positive regulation of macrophage proliferation / DCC mediated attractive signaling ...netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / detection of muscle stretch / JUN kinase binding / signal complex assembly / positive regulation of ubiquitin-dependent protein catabolic process / positive regulation of macrophage proliferation / DCC mediated attractive signaling / positive regulation of fibroblast migration / Signal regulatory protein family interactions / regulation of GTPase activity / growth hormone receptor signaling pathway / MET activates PTK2 signaling / regulation of focal adhesion assembly / negative regulation of cell-cell adhesion / positive regulation of wound healing / p130Cas linkage to MAPK signaling for integrins / regulation of osteoblast differentiation / Apoptotic cleavage of cellular proteins / establishment of cell polarity / positive regulation of macrophage chemotaxis / regulation of cytoskeleton organization / regulation of cell adhesion mediated by integrin / Fc-gamma receptor signaling pathway involved in phagocytosis / vascular endothelial cell response to oscillatory fluid shear stress / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of protein phosphorylation / negative regulation of anoikis / positive regulation of epithelial cell migration / ephrin receptor signaling pathway / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / RHO GTPases Activate WASPs and WAVEs / positive regulation of protein kinase activity / vascular endothelial growth factor receptor signaling pathway / regulation of cell adhesion / positive regulation of epithelial to mesenchymal transition / heart morphogenesis / stress fiber / EPHB-mediated forward signaling / Integrin signaling / protein tyrosine phosphatase activity / NCAM signaling for neurite out-growth / transforming growth factor beta receptor signaling pathway / SH2 domain binding / axon guidance / molecular function activator activity / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / integrin-mediated signaling pathway / non-membrane spanning protein tyrosine kinase activity / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / cell motility / placenta development / peptidyl-tyrosine phosphorylation / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / epidermal growth factor receptor signaling pathway / integrin binding / cell migration / regulation of cell shape / regulation of cell population proliferation / positive regulation of protein phosphorylation / actin binding / RAF/MAP kinase cascade / cell cortex / protein autophosphorylation / protein tyrosine kinase activity / protein phosphatase binding / angiogenesis / cytoskeleton / Extra-nuclear estrogen signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / ciliary basal body / cilium / positive regulation of cell migration / focal adhesion / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / centrosome / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
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 ...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 / 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
Similarity search - Domain/homology
Focal adhesion kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.163 Å
AuthorsMomin, A.A. / Sandholu, A.S. / Arold, S.T.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
King Abdullah University of Science and TechnologyURF/1/2602-01-01 Saudi Arabia
CitationJournal: To Be Published
Title: Crystal Structure of Zn bound human Focal Adhesion Targeting (FAT) domain of the Focal Adhesion Kinase
Authors: Momin, A.A. / Sandholu, A.S. / Arold, S.T.
History
DepositionDec 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Isoform 5 of Focal adhesion kinase 1
B: Isoform 5 of Focal adhesion kinase 1
C: Isoform 5 of Focal adhesion kinase 1
D: Isoform 5 of Focal adhesion kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,63212
Polymers73,1084
Non-polymers5238
Water1,72996
1
A: Isoform 5 of Focal adhesion kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4083
Polymers18,2771
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-36 kcal/mol
Surface area8110 Å2
MethodPISA
2
B: Isoform 5 of Focal adhesion kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3422
Polymers18,2771
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-34 kcal/mol
Surface area7970 Å2
MethodPISA
3
C: Isoform 5 of Focal adhesion kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4734
Polymers18,2771
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-35 kcal/mol
Surface area8060 Å2
MethodPISA
4
D: Isoform 5 of Focal adhesion kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4083
Polymers18,2771
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-35 kcal/mol
Surface area8060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.200, 52.450, 53.370
Angle α, β, γ (deg.)90.020, 90.000, 90.000
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Isoform 5 of Focal adhesion kinase 1 / FADK 1 / Focal adhesion kinase-related nonkinase / FRNK / Protein phosphatase 1 regulatory subunit ...FADK 1 / Focal adhesion kinase-related nonkinase / FRNK / Protein phosphatase 1 regulatory subunit 71 / PPP1R71 / Protein-tyrosine kinase 2 / p125FAK / pp125FAK


Mass: 18277.059 Da / Num. of mol.: 4 / Fragment: Focal Adhesion Targeting domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTK2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q05397, non-specific protein-tyrosine kinase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Zinc acetate dihydrate, 20% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.15→49.2 Å / Num. obs: 28719 / % possible obs: 96 % / Redundancy: 3.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.149 / Net I/σ(I): 6.8
Reflection shellResolution: 2.15→2.21 Å / Rmerge(I) obs: 1.124 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1627 / CC1/2: 0.197

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSVersion Jan 31, 2020data reduction
Aimless0.7.4data scaling
MoRDa1.4.01phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ow6

1ow6


Resolution: 2.163→49.2 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.915 / SU B: 9.89 / SU ML: 0.232 / Cross valid method: FREE R-VALUE / ESU R: 0.317 / ESU R Free: 0.244 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.275 1388 5.001 %
Rwork0.2148 26369 -
all0.218 --
obs-27757 97.27 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 50.538 Å2
Baniso -1Baniso -2Baniso -3
1--2.339 Å20.201 Å2-0.481 Å2
2---0.828 Å2-0.536 Å2
3---3.167 Å2
Refinement stepCycle: LAST / Resolution: 2.163→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4105 0 8 96 4209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124154
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.6395617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6875522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.85424.889180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.78215827
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0681516
X-RAY DIFFRACTIONr_chiral_restr0.1240.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022952
X-RAY DIFFRACTIONr_nbd_refined0.2460.22067
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22860
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2141
X-RAY DIFFRACTIONr_metal_ion_refined0.1290.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.280.2108
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1610.24
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0510.26
X-RAY DIFFRACTIONr_mcbond_it4.3264.5992103
X-RAY DIFFRACTIONr_mcangle_it6.5146.8562620
X-RAY DIFFRACTIONr_scbond_it6.7175.4462051
X-RAY DIFFRACTIONr_scangle_it9.9697.8252997
X-RAY DIFFRACTIONr_lrange_it12.85787.00417744
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.163-2.2190.449980.42618690.42721310.5790.60392.30410.432
2.219-2.280.393990.34618730.34920380.6440.65296.76150.348
2.28-2.3460.345980.32218720.32320220.7060.71597.42830.322
2.346-2.4180.343960.29918130.30119560.7540.77997.59710.292
2.418-2.4970.291900.24417260.24618640.7770.83897.42490.235
2.497-2.5840.306900.25717000.25918360.8290.84797.49460.244
2.584-2.6820.303840.25416010.25717230.8420.85297.79450.24
2.682-2.7910.298840.23515850.23817080.8270.8597.71660.222
2.791-2.9140.343780.23514930.24116070.8080.86397.75980.22
2.914-3.0560.268750.20314120.20615170.8940.91598.02240.194
3.056-3.2210.266720.22213840.22414810.8970.92498.3120.219
3.221-3.4150.312690.22212970.22613870.880.92298.48590.22
3.415-3.650.259640.20512250.20713170.9140.92697.8740.201
3.65-3.940.277600.1711370.17612250.9080.94197.71430.176
3.94-4.3140.176550.14410390.14511110.9550.95998.46980.154
4.314-4.8180.197500.1439610.14610360.9530.96297.58690.163
4.818-5.5550.297440.1878310.1918970.8680.94297.54740.207
5.555-6.7810.222370.276950.2677510.940.91997.470.288
6.781-9.5010.207280.1655360.1675760.9630.97897.91670.201
9.501-49.20.368170.1783200.1833430.9380.97498.25070.244

+
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