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- PDB-2l6f: NMR Solution structure of FAT domain of FAK complexed with LD2 an... -

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Basic information

Entry
Database: PDB / ID: 2l6f
TitleNMR Solution structure of FAT domain of FAK complexed with LD2 and LD4 motifs of PAXILLIN
ComponentsFocal adhesion kinase 1, linker1, Paxillin, linker2, PaxillinPTK2
KeywordsTRANSFERASE / CELL ADHESION / FAT / FAK / LD2 / LD4 / PAXILLIN / Fusion protein / Chimera protein
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RHO GTPases Activate WASPs and WAVEs / RAF/MAP kinase cascade / Regulation of actin dynamics for phagocytic cup formation / radial glia-guided pyramidal neuron migration / negative regulation of protein autophosphorylation / calcium-dependent cysteine-type endopeptidase activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate / vinculin binding ...Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RHO GTPases Activate WASPs and WAVEs / RAF/MAP kinase cascade / Regulation of actin dynamics for phagocytic cup formation / radial glia-guided pyramidal neuron migration / negative regulation of protein autophosphorylation / calcium-dependent cysteine-type endopeptidase activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate / vinculin binding / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / angiogenesis involved in wound healing / signal complex assembly / response to pH / negative regulation of cell-substrate adhesion / wound healing, spreading of cells / positive regulation of focal adhesion assembly / negative regulation of anoikis / endothelial cell migration / positive regulation of protein tyrosine kinase activity / regulation of cell adhesion / stress fiber / response to muscle stretch / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / ciliary basal body / actin filament organization / molecular function activator activity / non-specific protein-tyrosine kinase / sarcolemma / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / integrin binding / cell cortex / positive regulation of protein binding / angiogenesis / protein tyrosine kinase activity / protease binding / dendritic spine / protein autophosphorylation / positive regulation of cell migration / focal adhesion / centrosome / positive regulation of cell population proliferation / perinuclear region of cytoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / plasma membrane / cytoplasm
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 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) / 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 / Mainly Alpha
Similarity search - Domain/homology
Paxillin / Focal adhesion kinase 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
unidentified (others)
MethodSOLUTION NMR / SIMULATED ANNEALING, TORSION ANGLE DYNAMICS
Model detailslowest energy, model 1
AuthorsBertolucci, C.M. / Guibao, C. / Zhang, C. / Zheng, J.
CitationJournal: To be Published
Title: NMR Solution Structure of Fat Domain of Fak Complexed with Ld2 and Ld4 Motifs of Paxillin
Authors: Bertolucci, C.M. / Guibao, C. / Zheng, J.
History
DepositionNov 19, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Source and taxonomy

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Focal adhesion kinase 1, linker1, Paxillin, linker2, Paxillin


Theoretical massNumber of molelcules
Total (without water)22,2551
Polymers22,2551
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Focal adhesion kinase 1, linker1, Paxillin, linker2, Paxillin / PTK2 / FADK 1 / Protein-tyrosine kinase 2 / PP125FAK


Mass: 22254.971 Da / Num. of mol.: 1
Fragment: FAT DOMAIN, UNP RESIDUES 916-1053, LINKER1, LD2, UNP RESIDUES 140-161, LINKER2, LD4, UNP RESIDUES 262-276
Source method: isolated from a genetically manipulated source
Details: Fat domain of focal adhesion kinase with the Ld2 motif of paxillin tethered via linker1 GSGGSGSGGSGGSG which is then linked to Ld4 motif of paxillin via linker 2 GSGSGSGSGGSGGSGGSGGSGGSGGS
Source: (gene. exp.) Gallus gallus, unidentified / Gene: PTK2, FAK, FAK1, PXN / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q00944, UniProt: P49024, non-specific protein-tyrosine kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1313D (H)CCH-TOCSY
1413D (H)CCH-COSY
1513D HNCA
1613D CBCA(CO)NH
1713D HNCO
1813D HN(CA)CB
1912D 1H-15N HSQC
11012D 1H-13C HSQC

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] FOCAL ADHESION KINASE 1, LINKER, 22-MERIC PEPTIDE FROM PAXILLIN, LINKER, 15-MERIC PEPTIDE FROM PAXILLIN-1, 10 mM potassium phosphate-2, 0.1 % sodium azide-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMFOCAL ADHESION KINASE 1, LINKER, 22-MERIC PEPTIDE FROM PAXILLIN, LINKER, 15-MERIC PEPTIDE FROM PAXILLIN-1[U-100% 13C; U-100% 15N]1
10 mMpotassium phosphate-21
0.1 %sodium azide-31
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: AMBIENT Pa / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
BRUKER AVANCEBrukerAvance8001
VARIAN INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
SPARKY3Goddardstructure solution
NMRPIPEDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure solution
MOLMOLKoradi, Billeter and Wuthrichstructure solution
RefinementMethod: SIMULATED ANNEALING, TORSION ANGLE DYNAMICS / Software ordinal: 1
Details: THE SAMPLES USED ARE CONSTRUCTS IN WHICH ONE MOTIF IS TETHERED TO THE C-TERMINUS OF THE FAT DOMAIN VIA A GGSX LINKER AND THE OTHER LD MOTIF IS BOUND AS A FREE PEPTIDE. THE GGS LINKERS ARE ...Details: THE SAMPLES USED ARE CONSTRUCTS IN WHICH ONE MOTIF IS TETHERED TO THE C-TERMINUS OF THE FAT DOMAIN VIA A GGSX LINKER AND THE OTHER LD MOTIF IS BOUND AS A FREE PEPTIDE. THE GGS LINKERS ARE UNSTRUCTURED AND COMPARISON OF SPECTRA LEAD US TO BELIEVE THEY DO NOT IMPOSE ANY CONSTRAINT UPON HOW THE TETHERED LD MOTIFS BIND TO FAT. HOWEVER WHEN ANALYZING THE STRUCTURE IN CYANA, THE PRESENCE OF THE GGS LINKER IN THE SEQUENCE INTERFERS WITH CYANA'S INITIAL ALIGNMENT OF THE 20 LOWEST ENERGY STRUCTURES AND THUS CONFUSES RMSD AND TARGET FUNCTION CALCULATIONS. WE FOUND THAT USING PSEUDO LINKERS IN CYANA RESOLVED THIS PROBLEM WITHOUT CHANGING THE STRUCTURES IN QUESTION AND SO WE CHOSE TO SUBMIT THE STRUCTURES IN THAT WAY. 2RP6 REPRESENTS A COMPOSITE STRUCTURE USING CONSTRAINTS OBTAINED FROM THE 2RP7 AND 2RP9 DATA SETS. IT DOES NOT REPRESENT A NEW CONSTRUCT IN ITSELF, BUT MOST ACCURATELY REPRESENTS THE COMPLETE COMPLEX STRUCTURE BETWEEN PAXILLIN AND FOCAL ADHESION KINASE.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 20

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