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(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-TERMINAL COILED COIL DOMAIN FROM APC
 
Authors :  C. L. Day, T. Alber
Date :  14 Nov 99  (Deposition) - 06 Sep 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (2x)
Biol. Unit 4:  A,B  (1x)
Biol. Unit 5:  A  (2x)
Keywords :  Apc, Coiled Coil, Tumor Suppressor, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. L. Day, T. Alber
Crystal Structure Of The Amino-Terminal Coiled-Coil Domain Of The Apc Tumor Suppressor.
J. Mol. Biol. V. 301 147 2000
PubMed-ID: 10926498  |  Reference-DOI: 10.1006/JMBI.2000.3895
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADENOMATOUS POLYPOSIS COLI PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPAED4
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL COILED COIL DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAPC PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (2x)AB
Biological Unit 4 (1x)AB
Biological Unit 5 (2x)A 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:17 , GLN B:50 , HOH B:213BINDING SITE FOR RESIDUE SO4 B 423

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1DEB)

(-) Exons   (2, 4)

Asymmetric Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2cENST000002574302cENSE00001913252chr5:112073585-11207362238APC_HUMAN-00--
1.4ENST000002574304ENSE00002144134chr5:112090570-112090722153APC_HUMAN1-45452A:2-45
B:3-45
44
43
1.5bENST000002574305bENSE00000917796chr5:112102023-11210210785APC_HUMAN46-74292A:46-55
B:46-55
10
10
1.6bENST000002574306bENSE00000972225chr5:112102886-112103087202APC_HUMAN74-141680--
1.7ENST000002574307ENSE00000917798chr5:112111326-112111434109APC_HUMAN141-177370--
1.8aENST000002574308aENSE00000972226chr5:112116487-112116600114APC_HUMAN178-215380--
1.9ENST000002574309ENSE00000972227chr5:112128143-11212822684APC_HUMAN216-243280--
1.10ENST0000025743010ENSE00000972228chr5:112136976-112137080105APC_HUMAN244-278350--
1.12ENST0000025743012ENSE00000917801chr5:112151192-11215129099APC_HUMAN279-311330--
1.13bENST0000025743013bENSE00000917803chr5:112154663-112155041379APC_HUMAN312-4381270--
1.14aENST0000025743014aENSE00000917804chr5:112157593-11215768896APC_HUMAN438-470330--
1.16aENST0000025743016aENSE00000917807chr5:112162805-112162944140APC_HUMAN470-516470--
1.17ENST0000025743017ENSE00000760099chr5:112163626-11216370378APC_HUMAN517-542260--
1.18bENST0000025743018bENSE00000917809chr5:112164553-112164669117APC_HUMAN543-581390--
1.19ENST0000025743019ENSE00000972229chr5:112170648-112170862215APC_HUMAN582-653720--
1.20gENST0000025743020gENSE00000972230chr5:112173250-1121819368687APC_HUMAN653-284321910--

(-) Sequences/Alignments

Asymmetric 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:54
 aligned with APC_HUMAN | P25054 from UniProtKB/Swiss-Prot  Length:2843

    Alignment length:54
                                    11        21        31        41        51    
             APC_HUMAN    2 AAASYDQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQLQGSI 55
               SCOP domains d1deba_ A: N-terminal coiled coil domain from apc      SCOP domains
               CATH domains 1debA00 A:2-55  [code=1.20.5.10, no name defined]      CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.4  PDB: A:2-45 UniProt: 1-45         Exon 1.5b  Transcript 1
                  1deb A  2 AAASYDQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQLQGSI 55
                                    11        21        31        41        51    

Chain B from PDB  Type:PROTEIN  Length:53
 aligned with APC_HUMAN | P25054 from UniProtKB/Swiss-Prot  Length:2843

    Alignment length:53
                                    12        22        32        42        52   
             APC_HUMAN    3 AASYDQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQLQGSI 55
               SCOP domains d1debb_ B: N-terminal coiled coil domain from apc     SCOP domains
               CATH domains 1debB00 B:3-55  [code=1.20.5.10, no name defined]     CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
               Transcript 1 Exon 1.4  PDB: B:3-45 UniProt: 1-45        Exon 1.5b  Transcript 1
                  1deb B  3 AASYDQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQLQGSI 55
                                    12        22        32        42        52   

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (77, 77)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (APC_HUMAN | P25054)
molecular function
    GO:0008013    beta-catenin binding    Interacting selectively and non-covalently with the beta subunit of the catenin complex.
    GO:0045296    cadherin binding    Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion.
    GO:0045295    gamma-catenin binding    Interacting selectively and non-covalently with the gamma subunit of the catenin complex.
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    GO:0051010    microtubule plus-end binding    Interacting selectively and non-covalently with the plus end of a microtubule.
    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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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.
    GO:0019887    protein kinase regulator activity    Modulates the activity of a protein kinase, an enzyme which phosphorylates a protein.
biological process
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:1904885    beta-catenin destruction complex assembly    The aggregation, arrangement and bonding together of a set of components to form a beta-catenin destruction complex.
    GO:1904886    beta-catenin destruction complex disassembly    The disaggregation of a beta-catenin destruction complex into its constituent components.
    GO:0070830    bicellular tight junction assembly    The aggregation, arrangement and bonding together of a set of components to form a tight junction, an occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet.
    GO:0060070    canonical Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0001708    cell fate specification    The process involved in the specification of cell identity. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0006921    cellular component disassembly involved in execution phase of apoptosis    The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis.
    GO:0006974    cellular response to DNA damage 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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:1990090    cellular response to nerve growth factor stimulus    A 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 nerve growth factor stimulus.
    GO:0007163    establishment or maintenance of cell polarity    Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns.
    GO:0000281    mitotic cytokinesis    A cell cycle process that results in the division of the cytoplasm of a cell after mitosis, resulting in the separation of the original cell into two daughter cells.
    GO:0007094    mitotic spindle assembly checkpoint    A cell cycle checkpoint that delays the metaphase/anaphase transition of a mitotic nuclear division until the spindle is correctly assembled and chromosomes are attached to the spindle.
    GO:0030178    negative regulation of Wnt signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the Wnt signaling pathway.
    GO:0090090    negative regulation of canonical Wnt signaling pathway    Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0045736    negative regulation of cyclin-dependent protein serine/threonine kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity.
    GO:0007026    negative regulation of microtubule depolymerization    Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule depolymerization; prevention of depolymerization of a microtubule can result from binding by 'capping' at the plus end (e.g. by interaction with another cellular protein of structure) or by exposing microtubules to a stabilizing drug such as taxol.
    GO:0031175    neuron projection development    The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0031016    pancreas development    The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes.
    GO:0007389    pattern specification process    Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate.
    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:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0045732    positive regulation of protein catabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0031274    positive regulation of pseudopodium assembly    Any process that activates or increases the frequency, rate or extent of the assembly of pseudopodia.
    GO:0043161    proteasome-mediated ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0051988    regulation of attachment of spindle microtubules to kinetochore    Any process that modulates the frequency, rate or extent of the attachment of spindle microtubules to the kinetochore.
    GO:0045595    regulation of cell differentiation    Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features.
    GO:2000211    regulation of glutamate metabolic process    Any process that modulates the frequency, rate or extent of glutamate metabolic process.
    GO:0032886    regulation of microtubule-based process    Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the microtubule cytoskeleton.
    GO:0097305    response to alcohol    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 alcohol stimulus.
    GO:0042493    response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
cellular component
    GO:1990909    Wnt signalosome    A multiprotein protein complex containing membrane-localized Wnt receptors and cytosolic protein complexes, which is capable of transmitting the Wnt signal. Contains at least a Wnt protein, LRP5 or LRP6, a member of the Frizzled (Fz) family, Axin and and a Dishevelled (DVL) protein.
    GO:0005912    adherens junction    A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
    GO:0044295    axonal growth cone    The migrating motile tip of a growing nerve cell axon.
    GO:0030877    beta-catenin destruction complex    A cytoplasmic protein complex containing glycogen synthase kinase-3-beta (GSK-3-beta), the adenomatous polyposis coli protein (APC), and the scaffolding protein axin, among others; phosphorylates beta-catenin, targets it for degradation by the proteasome.
    GO:0005923    bicellular tight junction    An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes.
    GO:0016342    catenin complex    Complex of peripheral cytoplasmic proteins (alpha-, beta- and gamma-catenin) that interact with the cytoplasmic region of uvomorulin/E-cadherin to connect it to the actin cytoskeleton.
    GO:0070852    cell body fiber    A neuron projection that is found in unipolar neurons and corresponds to the region between the cell body and the point at which the single projection branches.
    GO:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    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:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005913    cell-cell adherens junction    An adherens junction which connects a cell to another cell.
    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:0005881    cytoplasmic microtubule    Any microtubule 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:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    GO:0000776    kinetochore    A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
    GO:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    GO:0016328    lateral plasma membrane    The portion of the plasma membrane at the lateral side of the cell. In epithelial cells, lateral plasma membranes are on the sides of cells which lie at the interface of adjacent cells.
    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:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0044306    neuron projection terminus    The specialized, terminal region of a neuron projection such as an axon or a dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.
    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.

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  APC_HUMAN | P25054
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        APC_HUMAN | P250541emu 1jpp 1m5i 1t08 1th1 1v18 2rqu 3au3 3nmw 3nmx 3nmz 3qhe 3rl7 3rl8 3t7u 4g69 4yje 4yjl 4yk6 5b6g 5iz6 5iz8 5iz9 5iza

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