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(-) Description

Title :  RAT BCL-XL AN APOPTOSIS INHIBITORY PROTEIN
 
Authors :  M. Aritomi, N. Kunishima, N. Inohara, Y. Ishibashi, S. Ohta, K. Morikawa
Date :  21 Mar 97  (Deposition) - 07 Jul 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Bcl-Xl, Apoptosis, Mitochondrion, Alternative Splicing, Regulatory Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Aritomi, N. Kunishima, N. Inohara, Y. Ishibashi, S. Ohta, K. Morikawa
Crystal Structure Of Rat Bcl-Xl. Implications For The Function Of The Bcl-2 Protein Family.
J. Biol. Chem. V. 272 27886 1997
PubMed-ID: 9346936  |  Reference-DOI: 10.1074/JBC.272.44.27886
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - APOPTOSIS REGULATOR BCL-X
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentSOLUBLE REGION
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1AF3)

(-) Sites  (0, 0)

(no "Site" information available for 1AF3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1AF3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1AF3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1AF3)

(-) PROSITE Motifs  (6, 6)

Asymmetric/Biological Unit (6, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BH4_1PS01260 Apoptosis regulator, Bcl-2 family BH4 motif signature.B2CL1_RAT4-24  1A:4-24
2BH4_2PS50063 Apoptosis regulator, Bcl-2 family BH4 motif profile.B2CL1_RAT5-24  1A:5-24
3BH3PS01259 Apoptosis regulator, Bcl-2 family BH3 motif signature.B2CL1_RAT86-100  1A:86-100
4BCL2_FAMILYPS50062 BCL2-like apoptosis inhibitors family profile.B2CL1_RAT90-190  1A:90-190
5BH1PS01080 Apoptosis regulator, Bcl-2 family BH1 motif signature.B2CL1_RAT130-148  1A:130-148
6BH2PS01258 Apoptosis regulator, Bcl-2 family BH2 motif signature.B2CL1_RAT181-192  1A:181-192

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000107621ENSRNOE00000373917chr3:143180199-14318013466B2CL1_RAT-00--
1.3aENSRNOT000000107623aENSRNOE00000320159chr3:143178674-143177999676B2CL1_RAT1-1881881A:2-188 (gaps)187
1.4ENSRNOT000000107624ENSRNOE00000075458chr3:143130714-1431290891626B2CL1_RAT189-233451A:189-1968

(-) 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:145
 aligned with B2CL1_RAT | P53563 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:195
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191     
            B2CL1_RAT     2 SQSNRELVVDFLSYKLSQKGYSWSQFSDVEENRTEAPEETEPERETPSAINGNPSWHLADSPAVNGATGHSSSLDAREVIPMAAVKQALREAGDEFELRYRRAFSDLTSQLHITPGTAYQSFEQVVNELFRDGVNWGRIVAFFSFGGALCVESVDKEMQVLVSRIASWMATYLNDHLEPWIQENGGWDTFVDLYG 196
               SCOP domains d1af3a_ A: Apoptosis regulato                                                  r Bcl-xL                                                                                                             SCOP domains
               CATH domains 1af3A00 A:2-196 Apoptosis Reg                                                  ulator Bcl-x                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..........--------------------------------------------------..hhhhhhhhhhhhhhhhhhh...hhhhhhhhh.....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh 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 1 Exon 1.3a  PDB: A:2-188 (gaps) UniProt: 1-188 [INCOMPLETE]                                                                                                                                 Exon 1.4 Transcript 1
                 1af3 A   2 SQSNRELVVDFLSYKLSQKGYSWSQFSDV--------------------------------------------------IPMAAVKQALREAGDEFELRYRRAFSDLTSQLHITPGTAYQSFEQVVNELFRDGVNWGRIVAFFSFGGALCVESVDKEMQVLVSRIASWMATYLNDHLEPWIQENGGWDTFVDLYG 196
                                    11        21        |-         -         -         -         -        81        91       101       111       121       131       141       151       161       171       181       191     
                                                       30                                                 81                                                                                                                   

   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  (0, 0)

(no "Pfam Domain" information available for 1AF3)

(-) Gene Ontology  (47, 47)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (B2CL1_RAT | P53563)
molecular function
    GO:0051400    BH domain binding    Interacting selectively and non-covalently with the Bcl-2 homology (BH) domain of a protein. Bcl-2-related proteins share homology in one to four conserved regions designated the Bcl-2 homology (BH) domains BH1, BH2, BH3 and BH4. These domains contribute at multiple levels to the function of these proteins in cell death and survival. Anti-apoptotic members of the Bcl-2 family have four BH domains (BH1-BH4). Pro-apoptotic members have fewer BH domains.
    GO:0097371    MDM2/MDM4 family protein binding    Interacting selectively and non-covalently with any isoform of the MDM2/MDM4 protein family, comprising negative regulators of p53.
    GO:0043027    cysteine-type endopeptidase inhibitor activity involved in apoptotic process    Stops, prevents or reduces the activity of a cysteine-type endopeptidase involved in the apoptotic process.
    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.
biological process
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    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:0021987    cerebral cortex development    The progression of the cerebral cortex over time from its initial formation until its mature state. The cerebral cortex is the outer layered region of the telencephalon.
    GO:0000910    cytokinesis    The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells.
    GO:0006897    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.
    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: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: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: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:0043154    negative regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
    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: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:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0051602    response to electrical stimulus    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 electrical stimulus.
    GO:0042542    response to hydrogen peroxide    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 hydrogen peroxide (H2O2) stimulus.
    GO:0001666    response to hypoxia    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 indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0010035    response to inorganic substance    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 inorganic substance stimulus.
    GO:0002931    response to ischemia    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a inadequate blood supply.
    GO:0010288    response to lead ion    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 lead ion stimulus.
    GO:0014070    response to organic cyclic compound    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 organic cyclic compound stimulus.
    GO:0010243    response to organonitrogen compound    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 organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.
    GO:0006979    response to oxidative stress    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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0043434    response to peptide hormone    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 peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
cellular component
    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: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:0005740    mitochondrial envelope    The double lipid bilayer enclosing the mitochondrion and separating its contents from the cell cytoplasm; includes the intermembrane space.
    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: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.

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 Related Entries

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

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        B2CL1_RAT | P535634qnq

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