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- PDB-5f28: Crystal structure of FAT domain of Focal Adhesion Kinase (FAK) bo... -

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Basic information

Entry
Database: PDB / ID: 5f28
TitleCrystal structure of FAT domain of Focal Adhesion Kinase (FAK) bound to the transcription factor MEF2C
Components
  • Focal adhesion kinase 1PTK2
  • MEF2C
KeywordsTranscription / protein binding / Transcription Factor / Kinase / Cardiovascular disease
Function / homology
Function and homology information


primary heart field specification / sinoatrial valve morphogenesis / positive regulation of alkaline phosphatase activity / nephron tubule epithelial cell differentiation / muscle cell fate determination / cartilage morphogenesis / regulation of sarcomere organization / cardiac ventricle formation / glomerulus morphogenesis / epithelial cell proliferation involved in renal tubule morphogenesis ...primary heart field specification / sinoatrial valve morphogenesis / positive regulation of alkaline phosphatase activity / nephron tubule epithelial cell differentiation / muscle cell fate determination / cartilage morphogenesis / regulation of sarcomere organization / cardiac ventricle formation / glomerulus morphogenesis / epithelial cell proliferation involved in renal tubule morphogenesis / positive regulation of skeletal muscle cell differentiation / DCC mediated attractive signaling / positive regulation of macrophage apoptotic process / Apoptotic cleavage of cellular proteins / DNA-binding transcription factor binding => GO:0140297 / MET activates PTK2 signaling / transdifferentiation / HMG box domain binding / NCAM signaling for neurite out-growth / regulation of synaptic activity / secondary heart field specification / cellular response to xenobiotic stimulus => GO:0071466 / negative regulation of synapse assembly / renal tubule morphogenesis / cellular response to trichostatin A / cell morphogenesis involved in neuron differentiation / EPHB-mediated forward signaling / central nervous system neuron axonogenesis / ventricular cardiac muscle cell differentiation / positive regulation of behavioral fear response / embryonic viscerocranium morphogenesis / RHO GTPases Activate WASPs and WAVEs / regulation of substrate adhesion-dependent cell spreading / positive regulation of cell proliferation in bone marrow / GRB2:SOS provides linkage to MAPK signaling for Integrins / positive regulation of cardiac muscle cell differentiation / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / RAF/MAP kinase cascade / Extra-nuclear estrogen signaling / regulation of dendritic spine development / intracellular chloride ion homeostasis / embryonic skeletal system morphogenesis / negative regulation of axonogenesis / regulation of epithelial cell migration / regulation of neurotransmitter secretion / Regulation of actin dynamics for phagocytic cup formation / negative regulation of organ growth / negative regulation of vascular associated smooth muscle cell migration / regulation of megakaryocyte differentiation / positive regulation of skeletal muscle tissue development / regulation of germinal center formation / smooth muscle cell differentiation / melanocyte differentiation / regulation of modification of postsynaptic actin cytoskeleton / cardiac muscle cell differentiation / germinal center formation / Myogenesis / regulation of AMPA receptor activity / endochondral ossification / positive regulation of ubiquitin-dependent protein catabolic process / JUN kinase binding / cellular response to fluid shear stress / VEGFA-VEGFR2 Pathway / cardiac muscle hypertrophy in response to stress / signal complex assembly / negative regulation of ossification / positive regulation of macrophage proliferation / neural crest cell differentiation / positive regulation of fibroblast migration / nuclear migration / cellular response to parathyroid hormone stimulus / negative regulation of vascular endothelial cell proliferation / regulation of NMDA receptor activity / growth hormone receptor signaling pathway / platelet formation / regulation of osteoblast differentiation / regulation of synapse assembly / regulation of focal adhesion assembly / organ growth / positive regulation of wound healing / positive regulation of macrophage chemotaxis / positive regulation of epithelial cell migration / roof of mouth development / negative regulation of cell-cell adhesion / positive regulation of cardiac muscle hypertrophy / heart looping / positive regulation of smooth muscle cell migration / blood vessel development / B cell proliferation / outflow tract morphogenesis / skeletal muscle cell differentiation / minor groove of adenine-thymine-rich DNA binding / negative regulation of vascular associated smooth muscle cell proliferation / regulation of cell adhesion mediated by integrin / monocyte differentiation / B cell homeostasis / humoral immune response / negative regulation of blood vessel endothelial cell migration / sarcoplasm
Similarity search - Function
SRF-like / Transcription factor, MADS-box / Holliday junction regulator protein family C-terminal / Holliday junction regulator protein family C-terminal repeat / MADS MEF2-like / Transcription factor, MADS-box / Transcription factor, MADS-box superfamily / SRF-type transcription factor (DNA-binding and dimerisation domain) / MADS-box domain signature. / MADS-box domain profile. ...SRF-like / Transcription factor, MADS-box / Holliday junction regulator protein family C-terminal / Holliday junction regulator protein family C-terminal repeat / MADS MEF2-like / Transcription factor, MADS-box / Transcription factor, MADS-box superfamily / SRF-type transcription factor (DNA-binding and dimerisation domain) / MADS-box domain signature. / MADS-box domain profile. / MADS / 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 / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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 / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Focal adhesion kinase 1 / Myocyte-specific enhancer factor 2C
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsCardoso, A.C. / Ambrosio, A.L.B. / Dessen, A. / Franchini, K.G.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2008/53519-5 Brazil
CitationJournal: Structure / Year: 2016
Title: FAK Forms a Complex with MEF2 to Couple Biomechanical Signaling to Transcription in Cardiomyocytes.
Authors: Cardoso, A.C. / Pereira, A.H.M. / Ambrosio, A.L.B. / Consonni, S.R. / Rocha de Oliveira, R. / Bajgelman, M.C. / Dias, S.M.G. / Franchini, K.G.
History
DepositionDec 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MEF2C
B: MEF2C
C: MEF2C
D: MEF2C
E: Focal adhesion kinase 1
F: Focal adhesion kinase 1
G: Focal adhesion kinase 1


Theoretical massNumber of molelcules
Total (without water)94,4057
Polymers94,4057
Non-polymers00
Water1,04558
1
A: MEF2C
B: MEF2C
F: Focal adhesion kinase 1


Theoretical massNumber of molelcules
Total (without water)38,9373
Polymers38,9373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: MEF2C
D: MEF2C
E: Focal adhesion kinase 1


Theoretical massNumber of molelcules
Total (without water)38,9373
Polymers38,9373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: MEF2C
B: MEF2C
C: MEF2C
D: MEF2C
E: Focal adhesion kinase 1
F: Focal adhesion kinase 1
G: Focal adhesion kinase 1

A: MEF2C
B: MEF2C
C: MEF2C
D: MEF2C
E: Focal adhesion kinase 1
F: Focal adhesion kinase 1
G: Focal adhesion kinase 1


Theoretical massNumber of molelcules
Total (without water)188,81114
Polymers188,81114
Non-polymers00
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area42370 Å2
ΔGint-317 kcal/mol
Surface area65140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.210, 139.210, 90.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein
MEF2C


Mass: 11202.983 Da / Num. of mol.: 4 / Fragment: UNP residues 1-95
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pETSUMO / Details (production host): Home-made / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: Q8CFN5
#2: Protein Focal adhesion kinase 1 / PTK2


Mass: 16531.158 Da / Num. of mol.: 3 / Fragment: UNP residues 935-1083
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET28a-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: P34152
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Magnseium acetate, 0.1M MES, pH 6.5, 12% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 11, 2013
RadiationMonochromator: Silicon 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.9→49.22 Å / Num. obs: 37566 / % possible obs: 100 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.344 / Net I/σ(I): 8.7
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.559 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2196)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1K40 (FAT) and 3KOV (MEF2)

1k40

3kov


Resolution: 2.9→43.221 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0.34 / Phase error: 25.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 1880 5 %Random selection
Rwork0.2084 ---
obs0.2097 37566 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→43.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5360 0 0 58 5418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045429
X-RAY DIFFRACTIONf_angle_d0.5937318
X-RAY DIFFRACTIONf_dihedral_angle_d16.1382095
X-RAY DIFFRACTIONf_chiral_restr0.038873
X-RAY DIFFRACTIONf_plane_restr0.004919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.97840.37621430.36162714X-RAY DIFFRACTION100
2.9784-3.06610.38341440.32382747X-RAY DIFFRACTION100
3.0661-3.1650.31261290.29732754X-RAY DIFFRACTION100
3.165-3.27810.32411440.27932758X-RAY DIFFRACTION100
3.2781-3.40930.27151430.26362751X-RAY DIFFRACTION100
3.4093-3.56440.25551480.23882761X-RAY DIFFRACTION100
3.5644-3.75220.26411740.20792721X-RAY DIFFRACTION100
3.7522-3.98710.24381410.192738X-RAY DIFFRACTION100
3.9871-4.29470.18571480.16522742X-RAY DIFFRACTION100
4.2947-4.72640.20471200.15632768X-RAY DIFFRACTION100
4.7264-5.40920.18321410.15152753X-RAY DIFFRACTION100
5.4092-6.81080.22311600.20962732X-RAY DIFFRACTION100
6.8108-43.2260.14711450.16072747X-RAY DIFFRACTION100

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