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Crystallographic structure of BCL-xL domain-swapped dimer in complex with PUMA BH3 peptide at 2.9A resolution
Biology and Chemistry Report
4HNJ
  •   Structure Details   Hide

    Structure Keywords

    Keywords Apoptosis/PROTEIN BINDING
    Text BCL2-family, domain-swapped dimer, apoptosis regulation, BCL-xL, PUMA, Apoptosis-PROTEIN BINDING complex

    Polymeric Molecules

    Chain A,B
    Description Bcl-2-like protein 1 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 23670.1 
    Source Method genetically manipulated  
    Entity Name Bcl2-L-1, Apoptosis regulator Bcl-X 
    Chain C
    Description Bcl-2-binding component 3 
    Fragment BH3 domain peptide 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 3053.4 
    Source Method synthetic  
    Entity Name JFY-1, p53 up-regulated modulator of apoptosis 

     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B B2CL1_HUMAN Q07817     
    C BBC3_HUMAN Q9BXH1     

    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    910   Cytokinesis  The Division of the Cytoplasm and the Plasma Membrane of a Cell and Its Partitioning Into Two Daughter Cells. 
    1541   Ovarian Follicle Development  The Process Whose Specific Outcome Is the Progression of the Ovarian Follicle Over Time From Its Formation to the Mature Structure. 
    1701   In Utero Embryonic Development  The Process Whose Specific Outcome Is the Progression of the Embryo in the Uterus Over Time From Formation of the Zygote in the Oviduct to Birth. an Example of This Process Is Found in Mus Musculus. 
    1836   Release of Cytochrome C From Mitochondria  The Process That Results in the Movement of Cytochrome C From the Mitochondrial Intermembrane Space Into the Cytosol Which Is Part of the Apoptotic Signaling Pathway and Leads to Caspase Activation. 
    6897   Endocytosis  A Vesicle Mediated Transport Process in Which Cells Take Up External Materials or Membrane Constituents by the Invagination of a Small Region of the Plasma Membrane to Form a New Membrane Bounded Vesicle. 
    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. 
    7093   Mitotic Cell Cycle Checkpoint  A Cell Cycle Checkpoint That Ensures Accurate Chromosome Replication and Segregation by Preventing Progression Through a Mitotic Cell Cycle Until Conditions Are Suitable For the Cell to Proceed to the Next Stage. 
    7281   Germ Cell Development  The Process Whose Specific Outcome Is the Progression of an Immature Germ Cell Over Time From Its Formation to the Mature Structure (gamete). a Germ Cell Is Any Reproductive Cell in a Multicellular Organism. 
    7283   Spermatogenesis  The Process of Formation of Spermatozoa Including Spermatocytogenesis and Spermiogenesis. 
    8283   Cell Proliferation  The Multiplication or Reproduction of Cells Resulting in the Expansion of a Cell Population. 
    8284   Positive Regulation of Cell Proliferation  Any Process That Activates or Increases the Rate or Extent of Cell Proliferation. 
    8584   Male Gonad Development  The Process Whose Specific Outcome Is the Progression of the Male Gonad Over Time From Its Formation to the Mature Structure. 
    8630   Intrinsic Apoptotic Signaling Pathway in Response to DNA Damage  A Series of Molecular Signals in Which an Intracellular Signal Is Conveyed to Trigger the Apoptotic Death of a Cell. the Pathway Is Induced by the Detection of DNA Damage and Ends When the Execution Phase of Apoptosis Is Triggered. 
    8637   Apoptotic Mitochondrial Changes  The Morphological and Physiological Alterations Undergone by Mitochondria During Apoptosis. 
    9314   Response to Radiation  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 an Electromagnetic Radiation Stimulus. Electromagnetic Radiation Is a Propagating Wave in Space with Electric and Magnetic Components. These Components Oscillate At Right Angles to Each Other and to the Direction of Propagation. 
    9566   Fertilization  The Union of Gametes of Opposite Sexes During the Process of Sexual Reproduction to Form a Zygote. It Involves the Fusion of the Gametic Nuclei (karyogamy) and Cytoplasm (plasmogamy). 
    9615   Response to Virus  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 Stimulus From a Virus. 
    12501   Programmed Cell Death  A Process Which Begins When a Cell Receives an Internal or External Signal and Activates a Series of Biochemical Events (signaling Pathway). the Process Ends with the Death of the Cell. 
    19050   Suppression by Virus of Host Apoptotic Process  Any Viral Process That Inhibits Apoptosis of Infected Host Cells Facilitating Prolonged Cell Survival During Viral Replication. 
    34097   Response to Cytokine  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 Cytokine Stimulus. 
    35872   Nucleotide Binding Domain Leucine Rich Repeat Containing Receptor Signaling Pathway  A Series of Molecular Signals Generated As a Consequence of a Nucleotide Binding Domain Leucine Rich Repeat Containing Receptor (nlr) Binding to One of Its Physiological Ligands. Nlrs Are Cytoplasmic Receptors Defined by Their Tripartite Domain Architecture That Contains: a Variable C Terminus a Middle Nucleotide Binding Domain and a Lrr Domain That Is Variable in the Repeats Composition and Number. the Nlr Signaling Pathway Begins with Binding of a Ligand to a Nlr Receptor and Ends with Regulation of a Downstream Cellular Process. 
    40007   Growth  The Increase in Size or Mass of an Entire Organism a Part of an Organism or a Cell. 
    42981   Regulation of Apoptotic Process  Any Process That Modulates the Occurrence or Rate of Cell Death by Apoptotic Process. 
    43065   Positive Regulation of Apoptotic Process  Any Process That Activates or Increases the Frequency Rate or Extent of Cell Death by Apoptotic Process. 
    43066   Negative Regulation of Apoptotic Process  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Cell Death by Apoptotic Process. 
    43524   Negative Regulation of Neuron Apoptotic Process  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Cell Death by Apoptotic Process in Neurons. 
    45087   Innate Immune Response  Innate Immune Responses Are Defense Responses Mediated by Germline Encoded Components That Directly Recognize Components of Potential Pathogens. 
    46898   Response to Cycloheximide  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 Cycloheximide Stimulus. Cycloheximide (actidione) Is an Antibiotic Produced by Some Streptomyces Species Which Interferes with Protein Synthesis in Eukaryotes. 
    46902   Regulation of Mitochondrial Membrane Permeability  Any Process That Modulates the Frequency Rate or Extent of the Passage or Uptake of Molecules by the Mitochondrial Membrane. 
    51402   Neuron Apoptotic Process  Any Apoptotic Process in a Neuron the Basic Cellular Unit of Nervous Tissue. Each Neuron Consists of a Body an Axon and Dendrites. Their Purpose Is to Receive Conduct and Transmit Impulses in the Nervous System. 
    51881   Regulation of Mitochondrial Membrane Potential  Any Process That Modulates the Establishment or Extent of the Mitochondrial Membrane Potential the Electric Potential Existing Across the Mitochondrial Membrane Arising From Charges in the Membrane Itself and From the Charges Present in the Media On Either Side of the Membrane. 
    60154   Cellular Process Regulating Host Cell Cycle in Response to Virus  Any Cellular Process That Modulates the Rate or Extent of Progression Through the Cell Cycle in Response to a Virus. 
    70584   Mitochondrion Morphogenesis  The Process in Which the Anatomical Structures of a Mitochondrion Are Generated and Organized. 
    71230   Cellular Response to Amino Acid Stimulus  Any Process That Results in a Change in State or Activity of a Cell (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of an Amino Acid Stimulus. an Amino Acid Is a Carboxylic Acids Containing One or More Amino Groups. 
    71312   Cellular Response to Alkaloid  Any Process That Results in a Change in State or Activity of a Cell (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of an Alkaloid Stimulus. Alkaloids Are a Large Group of Nitrogenous Substances Found in Naturally in Plants Many of Which Have Extracts That Are Pharmacologically Active. 
    71480   Cellular Response to Gamma Radiation  Any Process That Results in a Change in State or Activity of a Cell (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Gamma Radiation Stimulus. Gamma Radiation Is a Form of Electromagnetic Radiation (emr) or Light Emission of a Specific Frequency Produced From Sub Atomic Particle Interaction Such As Electron Positron Annihilation and Radioactive Decay. Gamma Rays Are Generally Characterized As Emr Having the Highest Frequency and Energy and Also the Shortest Wavelength Within the Electromagnetic Radiation Spectrum. 
    71839   Apoptotic Process in Bone Marrow  The Apoptotic Process in Cells in the Bone Marrow. 
    90005   Negative Regulation of Establishment of Protein Localization to Plasma Membrane  Any Process That Decreases the Frequency Rate or Extent of the Directed Movement of a Protein to a Specific Location in the Plasma Membrane. 
    90201   Negative Regulation of Release of Cytochrome C From Mitochondria  Any Process That Decreases the Rate Frequency or Extent of Release of Cytochrome C From Mitochondria the Process in Which Cytochrome C Is Enabled to Move From the Mitochondrial Intermembrane Space Into the Cytosol Which Is an Early Step in Apoptosis and Leads to Caspase Activation. 
    97192   Extrinsic Apoptotic Signaling Pathway in Absence of Ligand  A Series of Molecular Signals in Which a Signal Is Conveyed From the Cell Surface to Trigger the Apoptotic Death of a Cell. the Pathway Starts with Withdrawal of a Ligand From a Cell Surface Receptor and Ends When the Execution Phase of Apoptosis Is Triggered. 
    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). 
    97284   Hepatocyte Apoptotic Process  Any Apoptotic Process in a Hepatocyte the Main Structural Component of the Liver. 
    1900118   Negative Regulation of Execution Phase of Apoptosis  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Execution Phase of Apoptosis. 
    1902230   Negative Regulation of Intrinsic Apoptotic Signaling Pathway in Response to DNA Damage  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Intrinsic Apoptotic Signaling Pathway in Response to DNA Damage. 
    2001240   Negative Regulation of Extrinsic Apoptotic Signaling Pathway in Absence of Ligand  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Extrinsic Apoptotic Signaling Pathway in Absence of Ligand. 
    2001243   Negative Regulation of Intrinsic Apoptotic Signaling Pathway  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Intrinsic Apoptotic Signaling Pathway. 
    2001244   Positive Regulation of Intrinsic Apoptotic Signaling Pathway  Any Process That Activates or Increases the Frequency Rate or Extent of Intrinsic Apoptotic Signaling Pathway. 
    5622   Intracellular  The Living Contents of a Cell; the Matter Contained Within (but Not Including) the Plasma Membrane Usually Taken to Exclude Large Vacuoles and Masses of Secretory or Ingested Material. in Eukaryotes It Includes the Nucleus and Cytoplasm. 
    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. 
    5730   Nucleolus  A Small Dense Body One or More of Which Are Present in the Nucleus of Eukaryotic Cells. It Is Rich in RNA and Protein Is Not Bounded by a Limiting Membrane and Is Not Seen During Mitosis. Its Prime Function Is the Transcription of the Nucleolar DNA Into 45s Ribosomal Precursor RNA the Processing of This RNA Into 5.8s 18s and 28s Components of Ribosomal RNA and the Association of These Components with 5s RNA and Proteins Synthesized Outside the Nucleolus. This Association Results in the Formation of Ribonucleoprotein Precursors; These Pass Into the Cytoplasm and Mature Into the 40s and 60s Subunits of the Ribosome. 
    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. 
    5741   Mitochondrial Outer Membrane  The Outer I.e. Cytoplasm Facing Lipid Bilayer of the Mitochondrial Envelope. 
    5743   Mitochondrial Inner Membrane  The Inner I.e. Lumen Facing Lipid Bilayer of the Mitochondrial Envelope. It Is Highly Folded to Form Cristae. 
    5759   Mitochondrial Matrix  The Gel Like Material with Considerable Fine Structure That Lies in the Matrix Space or Lumen of a Mitochondrion. It Contains the Enzymes of the Tricarboxylic Acid Cycle and in Some Organisms the Enzymes Concerned with Fatty Acid Oxidation. 
    5813   Centrosome  A Structure Comprised of a Core Structure (in Most Organisms a Pair of Centrioles) and Peripheral Material From Which a Microtubule Based Structure Such As a Spindle Apparatus Is Organized. Centrosomes Occur Close to the Nucleus During Interphase in Many Eukaryotic Cells Though in Animal Cells It Changes Continually During the Cell Division Cycle. 
    5815   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. 
    5829   Cytosol  The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 
    5856   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. 
    16020   Membrane  A Lipid Bilayer Along with All the Proteins and Protein Complexes Embedded in It an Attached to It. 
    16021   Integral Component of Membrane  The Component of a Membrane Consisting of the Gene Products and Protein Complexes Having At Least Some Part of Their Peptide Sequence Embedded in the Hydrophobic Region of the Membrane. 
    30054   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. 
    30672   Synaptic Vesicle Membrane  The Lipid Bilayer Surrounding a Synaptic Vesicle. 
    31410   Cytoplasmic Vesicle  A Vesicle Formed of Membrane or Protein Found in the Cytoplasm of a Cell. 
    31965   Nuclear Membrane  Either of the Lipid Bilayers That Surround the Nucleus and Form the Nuclear Envelope; Excludes the Intermembrane Space. 
    31966   Mitochondrial Membrane  Either of the Lipid Bilayers That Surround the Mitochondrion and Form the Mitochondrial Envelope. 
    45202   Synapse  The Junction Between a Nerve Fiber of One Neuron and Another Neuron or Muscle Fiber or Glial Cell; the Site of Interneuronal Communication. As the Nerve Fiber Approaches the Synapse It Enlarges Into a Specialized Structure the Presynaptic Nerve Ending Which Contains Mitochondria and Synaptic Vesicles. At the Tip of the Nerve Ending Is the Presynaptic Membrane; Facing It and Separated From It by a Minute Cleft (the Synaptic Cleft) Is a Specialized Area of Membrane On the Receiving Cell Known As the Postsynaptic Membrane. in Response to the Arrival of Nerve Impulses the Presynaptic Nerve Ending Secretes Molecules of Neurotransmitters Into the Synaptic Cleft. These Diffuse Across the Cleft and Transmit the Signal to the Postsynaptic Membrane. 
    97136   Bcl 2 Family Protein Complex  A Protein Complex That Consists of Members of the Bcl 2 Family of Anti and Proapoptotic Regulators. Bcl 2 Proteins Respond to Cues From Various Forms of Intracellular Stress Such As DNA Damage or Cytokine Deprivation and Interact with Opposing Family Members to Determine Whether or Not the Caspase Proteolytic Cascade Should Be Unleashed. 
    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). 
    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. 
    42802   Identical Protein Binding  Interacting Selectively and Non Covalently with an Identical Protein or Proteins. 
    42803   Protein Homodimerization Activity  Interacting Selectively and Non Covalently with an Identical Protein to Form a Homodimer. 
    46982   Protein Heterodimerization Activity  Interacting Selectively and Non Covalently with a Nonidentical Protein to Form a Heterodimer. 
    51434   Bh3 Domain Binding  Interacting Selectively and Non Covalently with the Bh3 Domain of a Protein of the Bcl 2 Family. the Bh3 Domain Is a Potent Death Domain and Has an Important Role in Protein Protein Interactions and in Cell Death. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene bcl2l1, bcl2l, bclx
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pET-28


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    19 19q13.3-q13.4 27113     BCL2 binding component 3 BBC3    
    20 20q11.21 598     BCL2-like 1 BCL2L1