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(-) Description

Title :  CRYSTAL STRUCTURE OF BASIC PATCH MUTANT FAK FERM DOMAIN FAK31-405 K216A, K218A, R221A, K222A
 
Authors :  G. M. Goni, C. Epifano, J. Boskovic, M. Camacho-Artacho, J. Zhou, M. T. M M. J. Eck, L. Kremer, F. Graeter, F. L. Gervasio, M. Perez-Moreno, D. Li
Date :  30 Nov 12  (Deposition) - 12 Dec 12  (Release) - 20 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. M. Goni, C. Epifano, J. Boskovic, M. Camacho-Artacho, J. Zhou, A. Bronowska, M. T. Martin, M. J. Eck, L. Kremer, F. Grater, F. L. Gervasio, M. Perez-Moreno, D. Lietha
Phosphatidylinositol 4, 5-Bisphosphate Triggers Activation Of Focal Adhesion Kinase By Inducing Clustering And Conformational Changes.
Proc. Natl. Acad. Sci. Usa V. 111 E3177 2014
PubMed-ID: 25049397  |  Reference-DOI: 10.1073/PNAS.1317022111

(-) Compounds

Molecule 1 - FOCAL ADHESION KINASE 1
    ChainsA, B
    EC Number2.7.10.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET
    Expression System Vector TypePLASMID
    FragmentFERM DOMAIN, RESIDUES 31-405
    MutationYES
    Organism CommonCHICKEN
    Organism ScientificGALLUS GALLUS
    Organism Taxid9031
    SynonymFAK, FADK 1, FOCAL ADHESION KINASE-RELATED NONKINASE, FRNK, P41/P43FRNK, PROTEIN-TYROSINE KINASE 2, P125FAK, PP125FAK

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3ZDT)

(-) Sites  (0, 0)

(no "Site" information available for 3ZDT)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZDT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZDT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZDT)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FERM_3PS50057 FERM domain profile.FAK1_CHICK35-355
 
  2A:35-355
B:35-355
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FERM_3PS50057 FERM domain profile.FAK1_CHICK35-355
 
  1A:35-355
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FERM_3PS50057 FERM domain profile.FAK1_CHICK35-355
 
  1-
B:35-355

(-) Exons   (0, 0)

(no "Exon" information available for 3ZDT)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:326
 aligned with FAK1_CHICK | Q00944 from UniProtKB/Swiss-Prot  Length:1053

    Alignment length:368
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393        
           FAK1_CHICK    34 ERVLKVFHYFENSSEPTTWASIIRHGDATDVRGIIQKIVDCHKVKNVACYGLRLSHLQSEEVHWLHLDMGVSNVREKFELAHPPEEWKYELRIRYLPKGFLNQFTEDKPTLNFFYQQVKNDYMLEIADQVDQEIALKLGCLEIRRSYGEMRGNALEKKSNYEVLEKDVGLRRFFPKSLLDSVKAKTLRKLIQQTFRQFANLNREESILKFFEILSPVYRFDKECFKCALGSSWIISVELAIGPEEGISYLTDKGANPTHLADFNQVQTIQYSNSEDKDRKGMLQLKIAGAPEPLTVTAPSLTIAENMADLIDGYCRLVNGATQSFIIRPQKEGERALPSIPKLANNEKQGVRSHTVSVSETDDYAEII 401
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......hhhh.eeeeee....hhhhhhhhhhhhh...hhh.eeeeeee.....eeee....hhhhhhhhhhh......eeeeeee.....hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh---------hhhhhhhhhh..hhhhh.hhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.......eeeeeee.....eeeeeeee...eeee........eeeehhh.eeeeeeee.......eeeeeee......eeeee.hhhhhhhhhhhhhhhhhhhh......ee..---------------------------------...ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -FERM_3  PDB: A:35-355 UniProt: 35-355                                                                                                                                                                                                                                                                                            ---------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zdt A  34 ERVLKVFHYFENSSEPTTWASIIRHGDATDVRGIIQKIVDCHKVKNVACYGLRLSHLQSEEVHWLHLDMGVSNVREKFELAHPPEEWKYELRIRYLPKGFLNQFTEDKPTLNFFYQQVKNDYMLEIADQVDQEIALKLGCLEIRRSY---------KKSNYEVLEKDVGLRRFFPKSLLDSVAAATLAALIQQTFRQFANLNREESILKFFEILSPVYRFDKECFKCALGSSWIISVELAIGPEEGISYLTDKGANPTHLADFNQVQTIQYSNSEDKDRKGMLQLKIAGAPEPLTVTAPSLTIAENMADLIDGYCRLVNGATQSFIIRP---------------------------------DYAEII 401
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173      |  -      |193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353        |-         -         -         -  |     
                                                                                                                                                                            180       190                                                                                                                                                                         362                               396     

Chain B from PDB  Type:PROTEIN  Length:317
 aligned with FAK1_CHICK | Q00944 from UniProtKB/Swiss-Prot  Length:1053

    Alignment length:328
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354        
           FAK1_CHICK    35 RVLKVFHYFENSSEPTTWASIIRHGDATDVRGIIQKIVDCHKVKNVACYGLRLSHLQSEEVHWLHLDMGVSNVREKFELAHPPEEWKYELRIRYLPKGFLNQFTEDKPTLNFFYQQVKNDYMLEIADQVDQEIALKLGCLEIRRSYGEMRGNALEKKSNYEVLEKDVGLRRFFPKSLLDSVKAKTLRKLIQQTFRQFANLNREESILKFFEILSPVYRFDKECFKCALGSSWIISVELAIGPEEGISYLTDKGANPTHLADFNQVQTIQYSNSEDKDRKGMLQLKIAGAPEPLTVTAPSLTIAENMADLIDGYCRLVNGATQSFIIRP 362
               SCOP domains d3zdtb1 B:35-130 automated matches                                                              d3zdtb2 B:131-253 automated matches                                                                                        d3zdtb3 B:254-362 automated matches                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.......hhhh.eeeee.....hhhhhhhhhhhh....hhh.eeeeeee.....eeee....hhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-----------hhhhhhhh..hhhhh.hhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......eeeeeee.....eeeeeeee...eeee........eeeehhh.eeeeeeee.......eeeeeee......eeeee.hhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE FERM_3  PDB: B:35-355 UniProt: 35-355                                                                                                                                                                                                                                                                                            ------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zdt B  35 RVLKVFHYFENSSEPTTWASIIRHGDATDVRGIIQKIVDCHKVKNVACYGLRLSHLQSEEVHWLHLDMGVSNVREKFELAHPPEEWKYELRIRYLPKGFLNQFTEDKPTLNFFYQQVKNDYMLEIADQVDQEIALKLGCLEIRRSY-----------SNYEVLEKDVGLRRFFPKSLLDSVAAATLAALIQQTFRQFANLNREESILKFFEILSPVYRFDKECFKCALGSSWIISVELAIGPEEGISYLTDKGANPTHLADFNQVQTIQYSNSEDKDRKGMLQLKIAGAPEPLTVTAPSLTIAENMADLIDGYCRLVNGATQSFIIRP 362
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174     |   -       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354        
                                                                                                                                                                           180         192                                                                                                                                                                          

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (3, 3)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZDT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZDT)

(-) Gene Ontology  (50, 50)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FAK1_CHICK | Q00944)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004198    calcium-dependent cysteine-type endopeptidase activity    Catalysis of the hydrolysis of nonterminal peptide bonds in a polypeptide chain by a mechanism using a cysteine residue at the enzyme active center, and requiring the presence of calcium.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0004715    non-membrane spanning protein tyrosine kinase activity    Catalysis of the reaction: ATP + protein L-tyrosine = ADP + protein L-tyrosine phosphate by a non-membrane spanning protein.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0007015    actin filament organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0060055    angiogenesis involved in wound healing    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels and contribute to the series of events that restore integrity to a damaged tissue, following an injury.
    GO:0007173    epidermal growth factor receptor signaling pathway    A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:2000811    negative regulation of anoikis    Any process that stops, prevents or reduces the frequency, rate or extent of anoikis.
    GO:0010812    negative regulation of cell-substrate adhesion    Any process that decreases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules.
    GO:0031953    negative regulation of protein autophosphorylation    Any process that stops, prevents or decreases the rate of the phosphorylation by a protein of one or more of its own residues.
    GO:0038083    peptidyl-tyrosine autophosphorylation    The phosphorylation by a protein of one or more of its own tyrosine amino acid residues, or a tyrosine residue on an identical protein.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0051894    positive regulation of focal adhesion assembly    Any process that activates or increases the frequency, rate or extent of focal adhesion assembly, the establishment and maturation of focal adhesions.
    GO:0032092    positive regulation of protein binding    Any process that activates or increases the frequency, rate or extent of protein binding.
    GO:0061098    positive regulation of protein tyrosine kinase activity    Any process that increases the rate, frequency, or extent of protein tyrosine kinase activity.
    GO:1904237    positive regulation of substrate-dependent cell migration, cell attachment to substrate    Any process that activates or increases the frequency, rate or extent of substrate-dependent cell migration, cell attachment to substrate.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0021852    pyramidal neuron migration    The migration of pyramidal a neuron precursor from the ventricular zone to the correct layer of the cerebral cortex.
    GO:0035994    response to muscle stretch    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a myofibril being extended beyond its slack length.
    GO:0009268    response to pH    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus. pH is a measure of the acidity or basicity of an aqueous solution.
    GO:0007172    signal complex assembly    The aggregation, arrangement and bonding together of a set of components to form a complex capable of relaying a signal within a cell.
    GO:0044319    wound healing, spreading of cells    The migration of a cell along or through a wound gap that contributes to the reestablishment of a continuous surface.
cellular component
    GO:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0031234    extrinsic component of cytoplasmic side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0042383    sarcolemma    The outer membrane of a muscle cell, consisting of the plasma membrane, a covering basement membrane (about 100 nm thick and sometimes common to more than one fiber), and the associated loose network of collagen fibers.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        FAK1_CHICK | Q009441ktm 1pv3 1qvx 2aeh 2al6 2j0j 2j0k 2j0l 2j0m 2jkk 2jkm 2jko 2jkq 2l6f 2l6g 2l6h 4brx 4c7t 4cye 4d4r 4d4s 4d4v 4d4y 4d55 4d58 4d5h 4d5k

(-) Related Entries Specified in the PDB File

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