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(-) Description

Title :  STRUCTURE OF THE THIRD AND FOURTH SPECTRIN REPEATS OF THE PLAKIN DOMAIN OF PLECTIN
 
Authors :  E. Ortega, J. M. De Pereda
Date :  25 Oct 10  (Deposition) - 02 Feb 11  (Release) - 20 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Cytoskeleton, Plakin, Intermediate Filament, Spectrin Repeat, Structural Protein, Crosslinking (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Ortega, R. M. Buey, A. Sonnenberg, J. M. De Pereda
The Structure Of The Plakin Domain Of Plectin Reveals A Non-Canonical Sh3 Domain Interacting With Its Fourth Spectrin Repeat.
J. Biol. Chem. V. 286 12429 2011
PubMed-ID: 21288893  |  Reference-DOI: 10.1074/JBC.M110.197467

(-) Compounds

Molecule 1 - PLECTIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidMODIFIED PET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentSPECTRIN REPEATS 3 AND 4 (UNP RESIDUES 653-848)
    GenePLEC, PLEC1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPCN, PLTN, HEMIDESMOSOMAL PROTEIN 1, HD1, PLECTIN-1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:699 , GLN A:703 , GLN A:728 , TRP A:731BINDING SITE FOR RESIDUE EDO A 201
2AC2SOFTWARETRP A:571 , SER A:634 , ALA A:637 , ARG A:638 , SER A:641 , PRO A:715BINDING SITE FOR RESIDUE PEG A 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PDY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PDY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PDY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PDY)

(-) Exons   (5, 10)

Asymmetric Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.6ENST000003228106ENSE00001244239chr8:145025044-145024352693PLEC_HUMAN1-1751750--
1.12ENST0000032281012ENSE00001742500chr8:145012860-14501279962PLEC_HUMAN175-195210--
1.14ENST0000032281014ENSE00001685326chr8:145012408-14501231990PLEC_HUMAN196-225300--
1.16ENST0000032281016ENSE00001316545chr8:145011410-14501133378PLEC_HUMAN226-251260--
1.17ENST0000032281017ENSE00001741875chr8:145011239-14501114793PLEC_HUMAN252-282310--
1.18cENST0000032281018cENSE00001244172chr8:145010182-145010016167PLEC_HUMAN283-338560--
1.19bENST0000032281019bENSE00001244165chr8:145009481-145009366116PLEC_HUMAN338-377400--
1.20bENST0000032281020bENSE00001244160chr8:145009285-145009179107PLEC_HUMAN377-412360--
1.21ENST0000032281021ENSE00001244151chr8:145009097-145008978120PLEC_HUMAN413-452400--
1.22ENST0000032281022ENSE00001244144chr8:145008898-14500880396PLEC_HUMAN453-484320--
1.23ENST0000032281023ENSE00001244136chr8:145008613-145008486128PLEC_HUMAN485-527430--
1.24ENST0000032281024ENSE00001244129chr8:145008259-14500816694PLEC_HUMAN527-558320--
1.25ENST0000032281025ENSE00001244123chr8:145007519-145007365155PLEC_HUMAN559-610520--
1.26ENST0000032281026ENSE00001301489chr8:145007279-145006961319PLEC_HUMAN610-7161072A:545-606
B:541-606
62
66
1.27ENST0000032281027ENSE00001244070chr8:145006880-14500680378PLEC_HUMAN717-742262A:607-632
B:607-632
26
26
1.28ENST0000032281028ENSE00002173555chr8:145006729-145006568162PLEC_HUMAN743-796542A:633-686
B:633-686
54
54
1.29ENST0000032281029ENSE00001244050chr8:145006402-145006298105PLEC_HUMAN797-831352A:687-721
B:687-721
35
35
1.30ENST0000032281030ENSE00001244041chr8:145006200-14500610596PLEC_HUMAN832-863322A:722-746
B:722-745
25
24
1.31ENST0000032281031ENSE00001244034chr8:145005827-145005702126PLEC_HUMAN864-905420--
1.32ENST0000032281032ENSE00001244024chr8:145004704-145004552153PLEC_HUMAN906-956510--
1.33ENST0000032281033ENSE00001244019chr8:145004466-145004312155PLEC_HUMAN957-1008520--
1.34ENST0000032281034ENSE00001244010chr8:145004230-145004104127PLEC_HUMAN1008-1050430--
1.35ENST0000032281035ENSE00001244001chr8:145003997-145003814184PLEC_HUMAN1051-1112620--
1.36ENST0000032281036ENSE00001315328chr8:145003739-145003582158PLEC_HUMAN1112-1164530--
1.37ENST0000032281037ENSE00001295392chr8:145003449-145003271179PLEC_HUMAN1165-1224600--
1.38ENST0000032281038ENSE00001319048chr8:145002160-145002022139PLEC_HUMAN1224-1270470--
1.39ENST0000032281039ENSE00001243956chr8:145001934-145001578357PLEC_HUMAN1271-13891190--
1.40ENST0000032281040ENSE00001243948chr8:145001503-14500142084PLEC_HUMAN1390-1417280--
1.41aENST0000032281041aENSE00001243936chr8:145001249-145001145105PLEC_HUMAN1418-1452350--
1.42ENST0000032281042ENSE00001243927chr8:145001050-14500095299PLEC_HUMAN1453-1485330--
1.43ENST0000032281043ENSE00001309447chr8:145000052-1449966723381PLEC_HUMAN1486-261211270--
1.44cENST0000032281044cENSE00001244232chr8:144996563-1449893217243PLEC_HUMAN2613-468420720--

(-) 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:202
 aligned with PLEC_HUMAN | Q15149 from UniProtKB/Swiss-Prot  Length:4684

    Alignment length:202
                                   664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854  
           PLEC_HUMAN   655 EDSTLRYLQDLLAWVEENQHRVDGAEWGVDLPSVEAQLGSHRGLHQSIEEFRAKIERARSDEGQLSPATRGAYRDCLGRLDLQYAKLLNSSKARLRSLESLHSFVAAATKELMWLNEKEEEEVGFDWSDRNTNMTAKKESYSALMRELELKEKKIKELQNAGDRLLREDHPARPTVESFQAALQTQWSWMLQLCCCIEAHLK 856
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.26  PDB: A:545-606 UniProt: 610-716 [INCOMPLETE]       Exon 1.27  PDB: A:607-632 Exon 1.28  PDB: A:633-686 UniProt: 743-796            Exon 1.29  PDB: A:687-721          Exon 1.30  PDB: A:722-746 Transcript 1
                 3pdy A 545 EDSTLRYLQDLLAWVEENQHRVDGAEWGVDLPSVEAQLGSHRGLHQSIEEFRAKIERARSDEGQLSPATRGAYRDCLGRLDLQYAKLLNSSKARLRSLESLHSFVAAATKELMWLNEKEEEEVGFDWSDRNTNMTAKKESYSALMRELELKEKKIKELQNAGDRLLREDHPARPTVESFQAALQTQWSWMLQLCCCIEAHLK 746
                                   554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744  

Chain B from PDB  Type:PROTEIN  Length:205
 aligned with PLEC_HUMAN | Q15149 from UniProtKB/Swiss-Prot  Length:4684

    Alignment length:205
                                   660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850     
           PLEC_HUMAN   651 RPELEDSTLRYLQDLLAWVEENQHRVDGAEWGVDLPSVEAQLGSHRGLHQSIEEFRAKIERARSDEGQLSPATRGAYRDCLGRLDLQYAKLLNSSKARLRSLESLHSFVAAATKELMWLNEKEEEEVGFDWSDRNTNMTAKKESYSALMRELELKEKKIKELQNAGDRLLREDHPARPTVESFQAALQTQWSWMLQLCCCIEAHL 855
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.26  PDB: B:541-606 UniProt: 610-716 [INCOMPLETE]           Exon 1.27  PDB: B:607-632 Exon 1.28  PDB: B:633-686 UniProt: 743-796            Exon 1.29  PDB: B:687-721          Exon 1.30  PDB: B:722-74 Transcript 1
                 3pdy B 541 HMELEDSTLRYLQDLLAWVEENQHRVDGAEWGVDLPSVEAQLGSHRGLHQSIEEFRAKIERARSDEGQLSPATRGAYRDCLGRLDLQYAKLLNSSKARLRSLESLHSFVAAATKELMWLNEKEEEEVGFDWSDRNTNMTAKKESYSALMRELELKEKKIKELQNAGDRLLREDHPARPTVESFQAALQTQWSWMLQLCCCIEAHL 745
                                   550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740     

   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  (0, 0)

(no "SCOP Domain" information available for 3PDY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PDY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3PDY)

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PLEC_HUMAN | Q15149)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0030506    ankyrin binding    Interacting selectively and non-covalently with ankyrin, a 200 kDa cytoskeletal protein that attaches other cytoskeletal proteins to integral membrane proteins.
    GO:0008092    cytoskeletal protein binding    Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
    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:0008307    structural constituent of muscle    The action of a molecule that contributes to the structural integrity of a muscle fiber.
biological process
    GO:0031581    hemidesmosome assembly    Assembly of hemidesmosomes, integrin-containing protein complexes that bind to laminin in the basal lamina. Hemidesmosomes form the contact between the basal surface of epithelial cells and the underlying basal lamina.
cellular component
    GO:0005903    brush border    The dense covering of microvilli on the apical surface of a epithelial cells in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell.
    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:0043292    contractile fiber    Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle.
    GO:0043034    costamere    Regular periodic sub membranous arrays of vinculin in skeletal and cardiac muscle cells, these arrays link Z-discs to the sarcolemma and are associated with links to extracellular matrix.
    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: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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0030056    hemidesmosome    A cell-substrate junction (attachment structure) found in epithelial cells that links intermediate filaments to extracellular matrices via transmembrane complexes. In vertebrates, hemidesmosomes mediate contact between the basal side of epithelial cells and the basal lamina. In C. elegans, hemidesmosomes connect epithelial cells to distinct extracellular matrices on both the apical and basal cell surfaces.
    GO:0045111    intermediate filament cytoskeleton    Cytoskeletal structure made from intermediate filaments, typically organized in the cytosol as an extended system that stretches from the nuclear envelope to the plasma membrane. Some intermediate filaments run parallel to the cell surface, while others traverse the cytosol; together they form an internal framework that helps support the shape and resilience of the cell.
    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:0042383    sarcolemma    The outer membrane of a muscle cell, consisting of the plasma membrane, a covering basement membrane (about 100 nm thick and sometimes common to more than one fiber), and the associated loose network of collagen fibers.
    GO:0016528    sarcoplasm    The cytoplasm of a muscle cell; includes the sarcoplasmic reticulum.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PLEC_HUMAN | Q151491mb8 2n03 2odu 2odv 3f7p 3pe0 4gdo 4q58 4q59 5j1f 5j1g 5j1h 5j1i

(-) Related Entries Specified in the PDB File

2iak EQUIVALENT REGION OF THE PROTEIN BPAG1
2odu ANOTHER PAIR OF SPECTRIN REPEATS OF THE SAME PROTEIN
2odv ANOTHER PAIR OF SPECTRIN REPEATS OF THE SAME PROTEIN
3pe0 ANOTHER FRAGMENT OF THE PLAKIN DOMAIN WHICH SHARES THE SPECTRIN REPEAT 4 WITH THIS STRUCTURE