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(-) Description

Title :  CRYSTAL STRUCTURE OF THE APAF-1 CARD
 
Authors :  D. E. Vaughn, L. Joshua-Tor
Date :  31 Aug 99  (Deposition) - 13 Sep 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Caspase Recruitment Domain, Death Fold, Six Alpha-Helix Bundle, Greek Key Topology, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. E. Vaughn, J. Rodriguez, Y. Lazebnik, L. Joshua-Tor
Crystal Structure Of Apaf-1 Caspase Recruitment Domain: An Alpha-Helical Greek Key Fold For Apoptotic Signaling.
J. Mol. Biol. V. 293 439 1999
PubMed-ID: 10543941  |  Reference-DOI: 10.1006/JMBI.1999.3177
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (APOPTOTIC PROTEASE ACTIVATING FACTOR 1)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCASPASE RECRUITMENT DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAPAF-1 CARD

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2ZN5Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:17 , GLN A:50 , ASP A:64 , ASP A:66 , HOH A:201 , HOH A:290BINDING SITE FOR RESIDUE ZN A 101
2AC2SOFTWAREASP A:27 , ILE A:30 , GLU A:40 , HIS A:88 , HOH A:282BINDING SITE FOR RESIDUE ZN A 102
3AC3SOFTWAREHIS A:28 , ASP A:32 , HOH A:299BINDING SITE FOR RESIDUE ZN A 103
4AC4SOFTWAREGLU A:41 , HIS A:77BINDING SITE FOR RESIDUE ZN A 104
5AC5SOFTWAREHIS A:28 , GLU A:78 , HOH A:305 , HOH A:306BINDING SITE FOR RESIDUE ZN A 105
6AC6SOFTWARECYS A:8 , HIS A:12 , ASP A:82 , LEU A:86 , GLY A:90 , HOH A:207BINDING SITE FOR RESIDUE BME A 99

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CY5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1CY5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CY5)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARDPS50209 CARD caspase recruitment domain profile.APAF_HUMAN1-90  1A:1-90

(-) Exons   (0, 0)

(no "Exon" information available for 1CY5)

(-) 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:93
 aligned with APAF_HUMAN | O14727 from UniProtKB/Swiss-Prot  Length:1248

    Alignment length:93
                                    10        20        30        40        50        60        70        80        90   
            APAF_HUMAN    1 MDAKARNCLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAAMLIKMILKKDNDSYVSFYNALLHEGYKDLAALLHDGIPV 93
               SCOP domains d1cy5a_ A: Apoptotic protease activating factor 1, APAF-1                                     SCOP domains
               CATH domains 1cy5A00 A:1-93 Death Domain, Fas                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CARD  PDB: A:1-90 UniProt: 1-90                                                           --- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                  1cy5 A  1 MDAKARNCLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAAMLIKMILKKDNDSYVSFYNALLHEGYKDLAALLHDGIPV 93
                                    10        20        30        40        50        60        70        80        90   

   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 1CY5)

(-) Gene Ontology  (37, 37)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (APAF_HUMAN | O14727)
molecular function
    GO:0043531    ADP binding    Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008656    cysteine-type endopeptidase activator activity involved in apoptotic process    Increases the rate of proteolysis catalyzed by a cysteine-type endopeptidase involved in the apoptotic process.
    GO:0031072    heat shock protein binding    Interacting selectively and non-covalently with a heat shock protein, any protein synthesized or activated in response to heat shock.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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: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:0008635    activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process and is mediated by cytochrome c.
    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:0097190    apoptotic signaling pathway    A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
    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:0010659    cardiac muscle cell apoptotic process    A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a cardiac muscle cell and result in its death. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0071560    cellular response to transforming growth factor beta 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 a transforming growth factor beta stimulus.
    GO:0030900    forebrain development    The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
    GO:0034349    glial cell apoptotic process    Any apoptotic process in a glial cell, a non-neuronal cell of the nervous system.
    GO:0097193    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).
    GO:0070059    intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to a stimulus indicating endoplasmic reticulum (ER) stress, and ends when the execution phase of apoptosis is triggered. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0001843    neural tube closure    The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
    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:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:2001235    positive regulation of apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of apoptotic signaling pathway.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:1902510    regulation of apoptotic DNA fragmentation    Any process that modulates the frequency, rate or extent of apoptotic DNA fragmentation.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0072432    response to G1 DNA damage checkpoint signaling    A process that occurs in response to signals generated as a result of G1/S transition DNA damage checkpoint signaling.
    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:0007584    response to nutrient    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 nutrient stimulus.
cellular component
    GO:0043293    apoptosome    A multisubunit protein complex involved in the signaling phase of the apoptotic process. In mammals it is typically composed of seven Apaf-1 subunits bound to cytochrome c and caspase-9. A similar complex to promote apoptosis is formed from homologous gene products in other eukaryotic organisms.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        APAF_HUMAN | O147271c15 1cww 1z6t 2p1h 2ygs 3j2t 3jbt 3ygs 4rhw 5juy 5wvc 5wve

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1CY5)