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An Information Portal to 105025 Biological Macromolecular Structures

14-3-3 isoform zeta in complex with a diphoyphorylated C-RAF peptide
Biology and Chemistry Report
4FJ3
  •   Structure Details   Hide

    Structure Keywords

    Keywords PROTEIN BINDING/TRANSFERASE
    Text 14-3-3 fold, all alpha-helical, adapter protein, PROTEIN BINDING-TRANSFERASE complex

    Polymeric Molecules

    Chain A,B
    Description 14-3-3 protein zeta/delta 
    Fragment UNP residues 1-230 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 26720.4 
    Source Method genetically manipulated  
    Entity Name Protein kinase C inhibitor protein 1, KCIP-1 
    Chain P
    Description RAF proto-oncogene serine/threonine-protein kinase 
    Fragment UNP residues 229-264 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 4184.3 
    Source Method synthetic  
    Entity Name Proto-oncogene c-RAF, cRaf, Raf-1 

     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B 1433Z_HUMAN A8K1N0     
    P RAF1_HUMAN B0LPH8     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    2.7.11.1      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    2553   Histamine Secretion by Mast Cell  The Regulated Release of Histamine by a Mast Cell or Group of Mast Cells. 
    6605   Protein Targeting  The Process of Targeting Specific Proteins to Particular Membrane Bounded Subcellular Organelles. Usually Requires an Organelle Specific Protein Sequence Motif. 
    6626   Protein Targeting to Mitochondrion  The Process of Directing Proteins Towards and Into the Mitochondrion Usually Mediated by Mitochondrial Proteins That Recognize Signals Contained Within the Imported Protein. 
    6915   Apoptotic Process  A Programmed Cell Death Process Which Begins When a Cell Receives an Internal (e.g. DNA Damage) or External Signal (e.g. an Extracellular Death Ligand) and Proceeds Through a Series of Biochemical Events (signaling Pathway Phase) Which Trigger an Execution Phase. the Execution Phase Is the Last Step of an Apoptotic Process and Is Typically Characterized by Rounding Up of the Cell Retraction of Pseudopodes Reduction of Cellular Volume (pyknosis) Chromatin Condensation Nuclear Fragmentation (karyorrhexis) Plasma Membrane Blebbing and Fragmentation of the Cell Into Apoptotic Bodies. When the Execution Phase Is Completed the Cell Has Died. 
    7165   Signal Transduction  The Cellular Process in Which a Signal Is Conveyed to Trigger a Change in the Activity or State of a Cell. Signal Transduction Begins with Reception of a Signal (e.g. a Ligand Binding to a Receptor or Receptor Activation by a Stimulus Such As Light) or For Signal Transduction in the Absence of Ligand Signal Withdrawal or the Activity of a Constitutively Active Receptor. Signal Transduction Ends with Regulation of a Downstream Cellular Process E.g. Regulation of Transcription or Regulation of a Metabolic Process. Signal Transduction Covers Signaling From Receptors Located On the Surface of the Cell and Signaling Via Molecules Located Within the Cell. For Signaling Between Cells Signal Transduction Is Restricted to Events At and Within the Receiving Cell. 
    7596   Blood Coagulation  The Sequential Process in Which the Multiple Coagulation Factors of the Blood Interact Ultimately Resulting in the Formation of an Insoluble Fibrin Clot; It May Be Divided Into Three Stages: Stage 1 the Formation of Intrinsic and Extrinsic Prothrombin Converting Principle; Stage 2 the Formation of Thrombin; Stage 3 the Formation of Stable Fibrin Polymers. 
    10467   Gene Expression  The Process in Which a Gene's Sequence Is Converted Into a Mature Gene Product or Products (proteins or Rna). This Includes the Production of an RNA Transcript As Well As Any Processing to Produce a Mature RNA Product or an MRNA (for Protein Coding Genes) and the Translation of That MRNA Into Protein. Some Protein Processing Events May Be Included When They Are Required to Form an Active Form of a Product From an Inactive Precursor Form. 
    10941   Regulation of Cell Death  Any Process That Modulates the Rate or Frequency of Cell Death. Cell Death Is the Specific Activation or Halting of Processes Within a Cell So That Its Vital Functions Markedly Cease Rather Than Simply Deteriorating Gradually Over Time Which Culminates in Cell Death. 
    16070   RNA Metabolic Process  The Cellular Chemical Reactions and Pathways Involving RNA Ribonucleic Acid One of the Two Main Type of Nucleic Acid Consisting of a Long Unbranched Macromolecule Formed From Ribonucleotides Joined in 3' 5' Phosphodiester Linkage. 
    16071   MRNA Metabolic Process  The Chemical Reactions and Pathways Involving MRNA Messenger RNA Which Is Responsible For Carrying the Coded Genetic 'message' Transcribed From DNA to Sites of Protein Assembly At the Ribosomes. 
    30168   Platelet Activation  A Series of Progressive Overlapping Events Triggered by Exposure of the Platelets to Subendothelial Tissue. These Events Include Shape Change Adhesiveness Aggregation and Release Reactions. When Carried Through to Completion These Events Lead to the Formation of a Stable Hemostatic Plug. 
    42493   Response to Drug  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 Drug Stimulus. a Drug Is a Substance Used in the Diagnosis Treatment or Prevention of a Disease. 
    43066   Negative Regulation of Apoptotic Process  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Cell Death by Apoptotic Process. 
    61024   Membrane Organization  A Process Which Results in the Assembly Arrangement of Constituent Parts or Disassembly of a Membrane. a Membrane Is a Double Layer of Lipid Molecules That Encloses All Cells and in Eukaryotes Many Organelles; May Be a Single or Double Lipid Bilayer; Also Includes Associated Proteins. 
    97193   Intrinsic Apoptotic Signaling Pathway  A Series of Molecular Signals in Which an Intracellular Signal Is Conveyed to Trigger the Apoptotic Death of a Cell. the Pathway Starts with Reception of an Intracellular Signal (e.g. DNA Damage Endoplasmic Reticulum Stress Oxidative Stress Etc.) and Ends When the Execution Phase of Apoptosis Is Triggered. the Intrinsic Apoptotic Signaling Pathway Is Crucially Regulated by Permeabilization of the Mitochondrial Outer Membrane (momp). 
    1900740   Positive Regulation of Protein Insertion Into Mitochondrial Membrane Involved in Apoptotic Signaling Pathway  Any Process That Activates or Increases the Frequency Rate or Extent of Protein Insertion Into Mitochondrial Membrane Involved in Apoptotic Signaling Pathway. 
    5615   Extracellular Space  That Part of a Multicellular Organism Outside the Cells Proper Usually Taken to Be Outside the Plasma Membranes and Occupied by Fluid. 
    5634   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. 
    5654   Nucleoplasm  That Part of the Nuclear Content Other Than the Chromosomes or the Nucleolus. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5739   Mitochondrion  A Semiautonomous Self Replicating Organelle That Occurs in Varying Numbers Shapes and Sizes in the Cytoplasm of Virtually All Eukaryotic Cells. It Is Notably the Site of Tissue Respiration. 
    5829   Cytosol  The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 
    5925   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. 
    14069   Postsynaptic Density  The Postsynaptic Density Is a Region That Lies Adjacent to the Cytoplasmic Face of the Postsynaptic Membrane At Excitatory Synapse. It Forms a Disc That Consists of a Range of Proteins with Different Functions Some of Which Contact the Cytoplasmic Domains of Ion Channels in the Postsynaptic Membrane. the Proteins Making Up the Disc Include Receptors and Structural Proteins Linked to the Actin Cytoskeleton. They Also Include Signalling Machinery Such As Protein Kinases and Phosphatases. the Postsynaptic Density May Be Part of a Neuron or a Muscle Cell or a Glial Cell. 
    30659   Cytoplasmic Vesicle Membrane  The Lipid Bilayer Surrounding a Cytoplasmic Vesicle. 
    31252   Cell Leading Edge  The Area of a Motile Cell Closest to the Direction of Movement. 
    42470   Melanosome  A Tissue Specific Membrane Bounded Cytoplasmic Organelle Within Which Melanin Pigments Are Synthesized and Stored. Melanosomes Are Synthesized in Melanocyte Cells. 
    42629   Mast Cell Granule  Coarse Bluish Black Staining Cytoplasmic Granules Bounded by a Plasma Membrane and Found in Mast Cells and Basophils. Contents Include Histamine Heparin Chondroitin Sulfates Chymase and Tryptase. 
    43234   Protein Complex  Any Macromolecular Complex Composed (only) of Two or More Polypeptide Subunits Along with Any Covalently Attached Molecules (such As Lipid Anchors or Oligosaccharide) or Non Protein Prosthetic Groups (such As Nucleotides or Metal Ions). Prosthetic Group in This Context Refers to a Tightly Bound Cofactor. the Component Polypeptide Subunits May Be Identical. 
    48471   Perinuclear Region of Cytoplasm  Cytoplasm Situated Near or Occurring Around the Nucleus. 
    70062   Extracellular Vesicular Exosome  A Membrane Bounded Vesicle That Is Released Into the Extracellular Region by Fusion of the Limiting Endosomal Membrane of a Multivesicular Body with the Plasma Membrane. 
    72562   Blood Microparticle  A Phospholipid Microvesicle That Is Derived From Any of Several Cell Types Such As Platelets Blood Cells Endothelial Cells or Others and Contains Membrane Receptors As Well As Other Proteins Characteristic of the Parental Cell. Microparticles Are Heterogeneous in Size and Are Characterized As Microvesicles Free of Nucleic Acids. 
    5515   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). 
    8134   Transcription Factor Binding  Interacting Selectively and Non Covalently with a Transcription Factor Any Protein Required to Initiate or Regulate Transcription. 
    19901   Protein Kinase Binding  Interacting Selectively and Non Covalently with a Protein Kinase Any Enzyme That Catalyzes the Transfer of a Phosphate Group Usually From ATP to a Protein Substrate. 
    19904   Protein Domain Specific Binding  Interacting Selectively and Non Covalently with a Specific Domain of a Protein. 
    32403   Protein Complex Binding  Interacting Selectively and Non Covalently with Any Protein Complex (a Complex of Two or More Proteins That May Include Other Nonprotein Molecules). 
    42802   Identical Protein Binding  Interacting Selectively and Non Covalently with an Identical Protein or Proteins. 
    44822   Poly(a) RNA Binding  Interacting Non Covalently with a Poly(a) RNA a RNA Molecule Which Has a Tail of Adenine Bases. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene ywhaz
    Host Scientific Name Escherichia coli  


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    3 3p25 5894     Raf-1 proto-oncogene, serine/threonine kinase RAF1    
    8 8q23.1 7534     tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta YWHAZ    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs11551364 LS-SNP   dbSNP   A 22 M - > V Helix 0% (Buried) 8 101961054
    rs11551355 LS-SNP   dbSNP   A 27 K - > E Helix 30% (Intermediate) 8 101961039
    rs11551365 LS-SNP   dbSNP   A 76 Q - > R Helix 10% (Intermediate) 8 101960891
    rs137916988 LS-SNP   dbSNP   A 143 D - > N Helix 47% (Exposed) 8 101936518
    rs80338796 LS-SNP   dbSNP   P 257 S - > L Coil 15% (Intermediate) 3 12645699 SEP
    rs3730271 LS-SNP   dbSNP   P 259 S - > P Coil 25% (Intermediate) 3 12645694
    rs121434594 LS-SNP   dbSNP   P 261 P - > S Coil 46% (Exposed) 3 12645688 SEP