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(-) Description

Title :  STRUCTURES OF TWO INTERMEDIATE FILAMENT-BINDING FRAGMENTS OF DESMOPLAKIN REVEAL A UNIQUE REPEAT MOTIF STRUCTURE
 
Authors :  H. J. Choi, S. Park-Snyder, L. T. Pascoe, K. J. Green, W. I. Weis
Date :  30 Apr 02  (Deposition) - 31 Jul 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Plakin Repeat, , Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. J. Choi, S. Park-Snyder, L. T. Pascoe, K. J. Green, W. I. Weis
Structures Of Two Intermediate Filament-Binding Fragments Of Desmoplakin Reveal A Unique Repeat Motif Structure.
Nat. Struct. Biol. V. 9 612 2002
PubMed-ID: 12101406
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUBDOMAIN OF DESMOPLAKIN CARBOXY-TERMINAL DOMAIN (DPCT)
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPPROEX HTC
    Expression System StrainDH5A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 2609-2822
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 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 1LM5)

(-) Sites  (0, 0)

(no "Site" information available for 1LM5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LM5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LM5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LM5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1LM5)

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003798021aENSE00002025723chr6:7541808-7542318511DESP_HUMAN1-57570--
1.2ENST000003798022ENSE00001155370chr6:7555951-7556053103DESP_HUMAN57-91350--
1.3ENST000003798023ENSE00001155361chr6:7558349-7558497149DESP_HUMAN92-141500--
1.4aENST000003798024aENSE00001155357chr6:7559459-7559633175DESP_HUMAN141-199590--
1.5ENST000003798025ENSE00001155350chr6:7562885-7563013129DESP_HUMAN200-242430--
1.6ENST000003798026ENSE00000683077chr6:7563969-756401951DESP_HUMAN243-259170--
1.7aENST000003798027aENSE00001155338chr6:7565592-7565753162DESP_HUMAN260-313540--
1.8ENST000003798028ENSE00001155330chr6:7566610-7566714105DESP_HUMAN314-348350--
1.9ENST000003798029ENSE00001155018chr6:7567587-756768296DESP_HUMAN349-380320--
1.10ENST0000037980210ENSE00001155013chr6:7568014-7568139126DESP_HUMAN381-422420--
1.11ENST0000037980211ENSE00001155008chr6:7568670-7568822153DESP_HUMAN423-473510--
1.12ENST0000037980212ENSE00001155002chr6:7569419-7569573155DESP_HUMAN474-525520--
1.13ENST0000037980213ENSE00001154996chr6:7570670-7570796127DESP_HUMAN525-567430--
1.14ENST0000037980214ENSE00001154992chr6:7571616-7571817202DESP_HUMAN568-635680--
1.15ENST0000037980215ENSE00001154985chr6:7572075-7572301227DESP_HUMAN635-710760--
1.16ENST0000037980216ENSE00001154981chr6:7574319-7574485167DESP_HUMAN711-766560--
1.17ENST0000037980217ENSE00001154978chr6:7574890-7575028139DESP_HUMAN766-812470--
1.18ENST0000037980218ENSE00001154975chr6:7575528-7575721194DESP_HUMAN813-877650--
1.19ENST0000037980219ENSE00001154968chr6:7576527-7576689163DESP_HUMAN877-931550--
1.20ENST0000037980220ENSE00001154962chr6:7577192-757727584DESP_HUMAN932-959280--
1.21ENST0000037980221ENSE00001154954chr6:7578012-7578119108DESP_HUMAN960-995360--
1.22ENST0000037980222ENSE00001154944chr6:7578697-757879599DESP_HUMAN996-1028330--
1.23bENST0000037980223bENSE00001154938chr6:7579508-75818022295DESP_HUMAN1029-17937650--
1.24bENST0000037980224bENSE00001482558chr6:7582875-75869504076DESP_HUMAN1794-287110782A:2616-2811 (gaps)
B:2613-2808 (gaps)
196
196

(-) 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:189
 aligned with DESP_HUMAN | P15924 from UniProtKB/Swiss-Prot  Length:2871

    Alignment length:196
                                  2625      2635      2645      2655      2665      2675      2685      2695      2705      2715      2725      2735      2745      2755      2765      2775      2785      2795      2805      
          DESP_HUMAN   2616 SSPIAAIFDTENLEKISITEGIERGIVDSITGQRLLEAQACTGGIIHPTTGQKLSLQDAVSQGVIDQDMATRLKPAQKAFIGFEGVKGKKKMSAAEAVKEKWLPYEAGQRFLEFQYLTGGLVDPEVHGRISTEEAIRKGFIDGRAAQRLQDTSSYAKILTCPKTKLKISYKDAINRSMVEDITGLRLLEAASVSSK 2811
               SCOP domains d1lm5a_ A: Desmoplakin intermediate filament-binding domains                                                                                                                                         SCOP domains
               CATH domains 1lm5A00 A:2616-2811 Plakin repeat                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....eeehhhhhhhh...hhhhhhhhhhhhhh...ee......eehhhhhhhh...hhhhhhhhhhhhhhhhh.-------..hhhhhhhh...hhhhhhhhhhhhhhh....hhhhh...hhhhhhhh...hhhhhhhhhhhhhh...ee......eehhhhhhhhhee......eeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.24b  PDB: A:2616-2811 (gaps) UniProt: 1794-2871 [INCOMPLETE]                                                                                                                                  Transcript 1
                1lm5 A 2616 SSPIAAIFDTENLEKISITEGIERGIVDSITGQRLLEAQACTGGIIHPTTGQKLSLQDAVSQGVIDQDMATRLKPAQKAFIGF-------KMSAAEAVKEKWLPYEAGQRFLEFQYLTGGLVDPEVHGRISTEEAIRKGFIDGRAAQRLQDTSSYAKILTCPKTKLKISYKDAINRSMVEDITGLRLLEAASVSSK 2811
                                  2625      2635      2645      2655      2665      2675      2685      2695  |      -|     2715      2725      2735      2745      2755      2765      2775      2785      2795      2805      
                                                                                                           2698    2706                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:193
 aligned with DESP_HUMAN | P15924 from UniProtKB/Swiss-Prot  Length:2871

    Alignment length:196
                                  2622      2632      2642      2652      2662      2672      2682      2692      2702      2712      2722      2732      2742      2752      2762      2772      2782      2792      2802      
          DESP_HUMAN   2613 LEESSPIAAIFDTENLEKISITEGIERGIVDSITGQRLLEAQACTGGIIHPTTGQKLSLQDAVSQGVIDQDMATRLKPAQKAFIGFEGVKGKKKMSAAEAVKEKWLPYEAGQRFLEFQYLTGGLVDPEVHGRISTEEAIRKGFIDGRAAQRLQDTSSYAKILTCPKTKLKISYKDAINRSMVEDITGLRLLEAASV 2808
               SCOP domains d1lm5b_ B: Desmoplakin intermediate filament-binding domains                                                                                                                                         SCOP domains
               CATH domains 1lm5B00 B:2613-2808 Plakin repeat                                                                                                                                                                    CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------Plectin-1lm5B01 B:2724-2768                  ---------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------Plectin-1lm5B02 B:2724-2768                  ---------------------------------------- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------Plectin-1lm5B03 B:2724-2768                  ---------------------------------------- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------Plectin-1lm5B04 B:2724-2768                  ---------------------------------------- Pfam domains (4)
         Sec.struct. author ......eeeeee....eeehhhhhhhh...hhhhhhhhhhhhhh...ee......eehhhhhhhh...hhhhhhhhhhhhhhhhh....---...hhhhhhhh...hhhhhhhhhhhhhhh...ee....ee.hhhhhhhh...hhhhhhhhhhhhhh...ee......eehhhhhhhhhee......eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.24b  PDB: B:2613-2808 (gaps) UniProt: 1794-2871 [INCOMPLETE]                                                                                                                                  Transcript 1
                1lm5 B 2613 LEESSPIAAIFDTENLEKISITEGIERGIVDSITGQRLLEAQACTGGIIHPTTGQKLSLQDAVSQGVIDQDMATRLKPAQKAFIGFEGV---KKMSAAEAVKEKWLPYEAGQRFLEFQYLTGGLVDPEVHGRISTEEAIRKGFIDGRAAQRLQDTSSYAKILTCPKTKLKISYKDAINRSMVEDITGLRLLEAASV 2808
                                  2622      2632      2642      2652      2662      2672      2682      2692        |-  |   2712      2722      2732      2742      2752      2762      2772      2782      2792      2802      
                                                                                                                 2701   |                                                                                                       
                                                                                                                     2705                                                                                                       

   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/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
1aPlectin-1lm5B01B:2724-2768
1bPlectin-1lm5B02B:2724-2768
1cPlectin-1lm5B03B:2724-2768
1dPlectin-1lm5B04B:2724-2768

(-) Gene Ontology  (37, 37)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DESP_HUMAN | P15924)
molecular function
    GO:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    GO:0086083    cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication    Interacting selectively and non-covalently with any protein or protein complex that results in the connection of a bundle of His cell with a Purkinje myocyte and contributes to the communication between the two cells.
    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:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
    GO:0005080    protein kinase C binding    Interacting selectively and non-covalently with protein kinase C.
    GO:0097110    scaffold protein binding    Interacting selectively and non-covalently with a scaffold protein. Scaffold proteins are crucial regulators of many key signaling pathways. Although not strictly defined in function, they are known to interact and/or bind with multiple members of a signaling pathway, tethering them into complexes.
    GO:0005200    structural constituent of cytoskeleton    The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0034332    adherens junction organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an adherens junction. An adherens junction is a cell junction at which the cytoplasmic face of the plasma membrane is attached to actin filaments.
    GO:0086073    bundle of His cell-Purkinje myocyte adhesion involved in cell communication    The attachment of a bundle of His cell to a Purkinje myocyte via adhesion molecules that results in the cells being juxtaposed so that they can communicate.
    GO:0002934    desmosome organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a desmosome. A desmosome is a patch-like intercellular junction found in vertebrate tissues, consisting of parallel zones of two cell membranes, separated by an space of 25-35 nm, and having dense fibrillar plaques in the subjacent cytoplasm.
    GO:0008544    epidermis development    The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species.
    GO:0045104    intermediate filament cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising intermediate filaments and their associated proteins.
    GO:0045109    intermediate filament organization    Control of the spatial distribution of intermediate filaments; includes organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
    GO:0030216    keratinocyte differentiation    The process in which a relatively unspecialized cell acquires specialized features of a keratinocyte.
    GO:0018149    peptide cross-linking    The formation of a covalent cross-link between or within protein chains.
    GO:0071896    protein localization to adherens junction    Any process in which a protein is transported to, and/or maintained at the adherens junction.
    GO:0086091    regulation of heart rate by cardiac conduction    A cardiac conduction process that modulates the frequency or rate of heart contraction.
    GO:0098911    regulation of ventricular cardiac muscle cell action potential    Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a ventricular cardiac muscle cell contributing to the regulation of its contraction. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
    GO:0016337    single organismal cell-cell adhesion    The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism.
    GO:0043588    skin development    The process whose specific outcome is the progression of the skin over time, from its formation to the mature structure. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner vascular dermis (cutis, corium or true skin) composed mostly of connective tissue.
    GO:0003223    ventricular compact myocardium morphogenesis    The process in which the anatomical structures of the compact cardiac ventricle muscle are generated and organized.
    GO:0042060    wound healing    The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
    GO:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    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:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    GO:0001533    cornified envelope    A type of plasma membrane that has been modified through addition of distinct intracellular and extracellular components, including ceramide, found in cornifying epithelial cells (corneocytes).
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0030057    desmosome    A cell-cell junction in which: on the cytoplasmic surface of each interacting plasma membrane is a dense plaque composed of a mixture of intracellular anchor proteins; a bundle of keratin intermediate filaments is attached to the surface of each plaque; transmembrane adhesion proteins of the cadherin family bind to the plaques and interact through their extracellular domains to hold the adjacent membranes together by a Ca2+-dependent mechanism.
    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:0005916    fascia adherens    A cell-cell adherens junction that contains the transmembrane protein N-cadherin, which interacts with identical molecules from neighboring cells to form a tight mechanical intercellular link; forms a large portion of the intercalated disc, the structure at which myofibrils terminate in cardiomyocytes.
    GO:0014704    intercalated disc    A complex cell-cell junction at which myofibrils terminate in cardiomyocytes; mediates mechanical and electrochemical integration between individual cardiomyocytes. The intercalated disc contains regions of tight mechanical attachment (fasciae adherentes and desmosomes) and electrical coupling (gap junctions) between adjacent cells.
    GO:0005882    intermediate filament    A cytoskeletal structure that forms a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: Type I, acidic keratins; Type II, basic keratins; Type III, including desmin, vimentin and others; Type IV, neurofilaments and related filaments; and Type V, lamins.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DESP_HUMAN | P159241lm7 3r6n 5dzz

(-) Related Entries Specified in the PDB File

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