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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 E1P5L6     
    C BBC3_HUMAN B9EGI3     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    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. 
    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. 
    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. 
    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  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. 
    16021   Integral Component of Membrane  The Component of a Membrane Consisting of Gene Products and Protein Complexes That Have Some Part That Penetrates At Least One Leaflet of the Membrane Bilayer. This Component Includes Gene Products That Are Buried in the Bilayer with No Exposure Outside the Bilayer. 
    30054   Cell Junction  A Cellular Component That Forms a Specialized Region of Connection Between Two 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. 
    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. 
    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. 
    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