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(-) Description

Title :  CRYSTAL STRUCTURE OF BCL-XL/BIM
 
Authors :  X. Liu, S. Dai, Y. Zhu, P. Marrack, J. W. Kappler
Date :  17 Jun 03  (Deposition) - 23 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bcl-Xl/Bim, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Liu, S. Dai, Y. Zhu, P. Marrack, J. W. Kappler
The Structure Of A Bcl-Xl/Bim Fragment Complex: Implications For Bim Function
Immunity V. 19 341 2003
PubMed-ID: 14499110  |  Reference-DOI: 10.1016/S1074-7613(03)00234-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - APOPTOSIS REGULATOR BCL-X
    ChainsA
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System CommonCABBAGE LOOPER
    Expression System StrainHI-FIVE
    Expression System Taxid7111
    Expression System VectorBACVECTOR 3000 (NOVAGEN)
    Expression System Vector TypeBACULOVIRUS
    FragmentBIM
    GeneBCL2L1 OR BCL2L OR BCLX
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymBCL2-LIKE 1 PROTEIN
 
Molecule 2 - BCL2-LIKE PROTEIN 11
    ChainsB
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System CommonCABBAGE LOOPER
    Expression System StrainHI-FIVE
    Expression System Taxid7111
    Expression System VectorBACVECTOR 3000 (NOVAGEN)
    Expression System Vector TypeBACULOVIRUS
    GeneBCL2L11 OR BIM
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymBCL2 INTERACTING MEDIATOR OF CELL DEATH

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1PQ1)

(-) Sites  (0, 0)

(no "Site" information available for 1PQ1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PQ1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PQ1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PQ1)

(-) PROSITE Motifs  (6, 6)

Asymmetric/Biological Unit (6, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BH4_1PS01260 Apoptosis regulator, Bcl-2 family BH4 motif signature.B2CL1_MOUSE4-24  1A:4-24
2BH4_2PS50063 Apoptosis regulator, Bcl-2 family BH4 motif profile.B2CL1_MOUSE5-24  1A:5-24
3BH3PS01259 Apoptosis regulator, Bcl-2 family BH3 motif signature.B2CL1_MOUSE86-100  1A:86-100
4BCL2_FAMILYPS50062 BCL2-like apoptosis inhibitors family profile.B2CL1_MOUSE90-190  1A:90-190
5BH1PS01080 Apoptosis regulator, Bcl-2 family BH1 motif signature.B2CL1_MOUSE130-148  1A:130-148
6BH2PS01258 Apoptosis regulator, Bcl-2 family BH2 motif signature.B2CL1_MOUSE181-192  1A:181-192

(-) Exons   (0, 0)

(no "Exon" information available for 1PQ1)

(-) Sequences/Alignments

Asymmetric/Biological 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:147
 aligned with B2CL1_MOUSE | Q64373 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:196
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190      
          B2CL1_MOUSE     1 MSQSNRELVVDFLSYKLSQKGYSWSQFSDVEENRTEAPEETEAERETPSAINGNPSWHLADSPAVNGATGHSSSLDAREVIPMAAVKQALREAGDEFELRYRRAFSDLTSQLHITPGTAYQSFEQVVNELFRDGVNWGRIVAFFSFGGALCVESVDKEMQVLVSRIASWMATYLNDHLEPWIQENGGWDTFVDLYG 196
               SCOP domains d1pq1a_ A: Apoptosis regulat                                                 or Bcl-xL                                                                                                               SCOP domains
               CATH domains 1pq1A00 A:1-196 Apoptosis Re                                                 gulator Bcl-x                                                                                                           CATH domains
               Pfam domains BH4-1pq1A01 A:1-27         --------------------------------------------------------------Bcl-2-1pq1A02 A:90-188                                                                             -------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh.........-------------------------------------------------....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---BH4_1  PDB: A:4-24   -------------------------------------------------------------BH3            -----------------------------BH1  PDB: A:130-148--------------------------------BH2         ---- PROSITE (1)
                PROSITE (2) ----BH4_2  PDB: A:5-24  -----------------------------------------------------------------BCL2_FAMILY  PDB: A:90-190 UniProt: 90-190                                                           ------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pq1 A   1 MSQSNRELVVDFLSYKLSQKGYSWSQFS-------------------------------------------------REVIPMAAVKQALREAGDEFELRYRRAFSDLTSQLHITPGTAYQSFEQVVNELFRDGVNWGRIVAFFSFGGALCVESVDKEMQVLVSRIASWMATYLNDHLEPWIQENGGWDTFVDLYG 196
                                    10        20       | -         -         -         -         -       |80        90       100       110       120       130       140       150       160       170       180       190      
                                                      28                                                78                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:33
 aligned with B2L11_MOUSE | O54918 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:33
                                   148       158       168   
          B2L11_MOUSE   139 DLRPEIRIAQELRRIGDEFNETYTRRVFANDYR 171
               SCOP domains --------------------------------- SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains Bclx_interact-1pq1B01      ------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------- PROSITE
                 Transcript --------------------------------- Transcript
                 1pq1 B  83 DLRPEIRIAQELRRIGDEFNETYTRRVFANDYR 115
                                    92       102       112   

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit

(-) Gene Ontology  (108, 122)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (B2CL1_MOUSE | Q64373)
molecular function
    GO:0051434    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.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0019901    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.
biological process
    GO:0006915    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.
    GO:0071839    apoptotic process in bone marrow    The apoptotic process in cells in the bone marrow.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0060154    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.
    GO:0071312    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.
    GO:0071230    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.
    GO:0071480    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.
    GO:0000910    cytokinesis    The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells.
    GO:0097192    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.
    GO:0009566    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).
    GO:0007281    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.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0097284    hepatocyte apoptotic process    Any apoptotic process in a hepatocyte, the main structural component of the liver.
    GO:0001701    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.
    GO:0008630    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.
    GO:0008584    male gonad development    The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
    GO:0070584    mitochondrion morphogenesis    The process in which the anatomical structures of a mitochondrion are generated and organized.
    GO:0007093    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.
    GO:2000811    negative regulation of anoikis    Any process that stops, prevents or reduces the frequency, rate or extent of anoikis.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0090005    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.
    GO: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.
    GO: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.
    GO: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.
    GO:0043524    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.
    GO:0090201    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.
    GO:0051402    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.
    GO:0001541    ovarian follicle development    The process whose specific outcome is the progression of the ovarian follicle over time, from its formation to the mature structure.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0046902    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.
    GO:0051881    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.
    GO:0001836    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.
    GO:0046898    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.
    GO:0034097    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.
    GO:0009314    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.
    GO:0009615    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.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0019050    suppression by virus of host apoptotic process    Any viral process that inhibits apoptosis of infected host cells, facilitating prolonged cell survival during viral replication.
cellular component
    GO:0097136    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.
    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:0005813    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.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016021    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.
    GO:0005622    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.
    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:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005759    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.
    GO:0031966    mitochondrial membrane    Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.
    GO:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
    GO:0005739    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.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    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:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. 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.
    GO:0030672    synaptic vesicle membrane    The lipid bilayer surrounding a synaptic vesicle.

Chain B   (B2L11_MOUSE | O54918)
molecular function
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    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).
biological process
    GO:0001783    B cell apoptotic process    Any apoptotic process in a B cell, a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
    GO:0001782    B cell homeostasis    The process of regulating the proliferation and elimination of B cells such that the total number of B cells within a whole or part of an organism is stable over time in the absence of an outside stimulus.
    GO:0043029    T cell homeostasis    The process of regulating the proliferation and elimination of T cells such that the total number of T cells within a whole or part of an organism is stable over time in the absence of an outside stimulus.
    GO:0006919    activation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
    GO:0006915    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.
    GO:1902263    apoptotic process involved in embryonic digit morphogenesis    Any apoptotic process that is involved in embryonic digit morphogenesis.
    GO:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0007160    cell-matrix adhesion    The binding of a cell to the extracellular matrix via adhesion molecules.
    GO:0060154    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.
    GO:0048066    developmental pigmentation    The developmental process that results in the deposition of coloring matter in an organism, tissue or cell.
    GO:0043583    ear development    The process whose specific outcome is the progression of the ear over time, from its formation to the mature structure. The ear is the sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals.
    GO:0097192    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.
    GO:0001701    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.
    GO:0008630    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.
    GO:0001822    kidney development    The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
    GO:0001776    leukocyte homeostasis    The process of regulating the proliferation and elimination of cells of the immune system such that the total number of cells of a particular cell type within a whole or part of an organism is stable over time in the absence of an outside stimulus.
    GO:0002260    lymphocyte homeostasis    The process of regulating the proliferation and elimination of lymphocytes such that the total number of lymphocytes within a whole or part of an organism is stable over time in the absence of an outside stimulus.
    GO:0008584    male gonad development    The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
    GO:0030879    mammary gland development    The process whose specific outcome is the progression of the mammary gland over time, from its formation to the mature structure. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk. Its development starts with the formation of the mammary line and ends as the mature gland cycles between nursing and weaning stages.
    GO:0007127    meiosis I    The first meiotic nuclear division in which homologous chromosomes are paired and segregated from each other, producing two haploid daughter nuclei.
    GO:0002262    myeloid cell homeostasis    The process of regulating the proliferation and elimination of myeloid cells such that the total number of myeloid cells within a whole or part of an organism is stable over time in the absence of an outside stimulus.
    GO:0042475    odontogenesis of dentin-containing tooth    The process whose specific outcome is the progression of a dentin-containing tooth over time, from its formation to the mature structure. A dentin-containing tooth is a hard, bony organ borne on the jaw or other bone of a vertebrate, and is composed mainly of dentin, a dense calcified substance, covered by a layer of enamel.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0060139    positive regulation of apoptotic process by virus    Any viral process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0045787    positive regulation of cell cycle    Any process that activates or increases the rate or extent of progression through the cell cycle.
    GO:0010942    positive regulation of cell death    Any process that increases 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.
    GO:0043280    positive regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that activates or increases the activity of a cysteine-type endopeptidase involved in the apoptotic process.
    GO:2000271    positive regulation of fibroblast apoptotic process    Any process that activates or increases the frequency, rate or extent of fibroblast apoptotic process.
    GO:2001244    positive regulation of intrinsic apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of intrinsic apoptotic signaling pathway.
    GO:1902110    positive regulation of mitochondrial membrane permeability involved in apoptotic process    Any positive regulation of mitochondrial membrane permeability that is involved in apoptotic process.
    GO:0043525    positive regulation of neuron apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process.
    GO:0032464    positive regulation of protein homooligomerization    Any process that activates or increases the frequency, rate or extent of protein homooligomerization.
    GO:0090200    positive regulation of release of cytochrome c from mitochondria    Any process that increases 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.
    GO:0048563    post-embryonic animal organ morphogenesis    Morphogenesis, during the post-embryonic phase, of an animal tissue or tissues that work together to perform a specific function or functions. Morphogenesis pertains to process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0009791    post-embryonic development    The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0048070    regulation of developmental pigmentation    Any process that modulates the frequency, rate or extent of the developmental process that results in the deposition of coloring matter in an organism.
    GO:0046620    regulation of organ growth    Any process that modulates the frequency, rate or extent of growth of an organ of an organism.
    GO:0034976    response to endoplasmic reticulum stress    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 stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0048536    spleen development    The process whose specific outcome is the progression of the spleen over time, from its formation to the mature structure. The spleen is a large vascular lymphatic organ composed of white and red pulp, involved both in hemopoietic and immune system functions.
    GO:0070242    thymocyte apoptotic process    Any apoptotic process in a thymocyte, an immature T cell located in the thymus.
    GO:0048538    thymus development    The process whose specific outcome is the progression of the thymus over time, from its formation to the mature structure. The thymus is a symmetric bi-lobed organ involved primarily in the differentiation of immature to mature T cells, with unique vascular, nervous, epithelial, and lymphoid cell components.
    GO:0035148    tube formation    Creation of the central hole of a tube in an anatomical structure through which gases and/or liquids flow.
cellular component
    GO:0097141    BIM-BCL-2 complex    A heterodimeric protein complex consisting of BIM and BCL-2, members of the Bcl-2 family of anti- and proapoptotic regulators.
    GO:0097140    BIM-BCL-xl complex    A heterodimeric protein complex consisting of BIM and BCL-xl, members of the Bcl-2 family of anti- and proapoptotic regulators.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005868    cytoplasmic dynein complex    Any dynein complex with a homodimeric dynein heavy chain core that catalyzes movement along a microtubule. Cytoplasmic dynein complexes participate in many cytoplasmic transport activities in eukaryotes, such as mRNA localization, intermediate filament transport, nuclear envelope breakdown, apoptosis, transport of centrosomal proteins, mitotic spindle assembly, virus transport, kinetochore functions, and movement of signaling and spindle checkpoint proteins. Some complexes participate in intraflagellar transport. Subunits associated with the dynein heavy chain mediate association between dynein heavy chain and cargoes, and may include light chains and light intermediate chains.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0019898    extrinsic component of membrane    The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0005739    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.

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 Related Entries

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

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        B2CL1_MOUSE | Q643731pq0 2bzw 3ihc 3ihd 3ihe 3ihf 3iig 3iih 3ilb 3ilc 4yj4 4yk9 5c3g

(-) Related Entries Specified in the PDB File

1pq0 MONOMER