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(-) Description

Title :  SOLUTION STRUCTURE OF THE SYNDECAN-4 WHOLE CYTOPLASMIC DOMAIN
 
Authors :  D. Lee, E. S. Oh, A. Woods, J. R. Couchman, W. Lee
Date :  03 Mar 00  (Deposition) - 19 Sep 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (16x)
Keywords :  Symmetric-Parallel-Interwinded Dimer, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Shin, W. Lee, D. Lee, B. K. Koo, I. Han, Y. Lim, A. Woods, J. R. Couchman, E. S. Oh
Solution Structure Of The Dimeric Cytoplasmic Domain Of Syndecan-4.
Biochemistry V. 40 8471 2001
PubMed-ID: 11456484  |  Reference-DOI: 10.1021/BI002750R
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SYNDECAN-4
    ChainsA, B
    EngineeredYES
    FragmentWHOLE CYTOPLASMIC DOMAIN
    Other DetailsTHIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PETIDE OCCURS NATURALLY IN HUMANS (HOMO SAPIENS).
    SynonymAMPHIGLYCAN, RYUDOCAN CORE PROTEIN, SYND4
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (16x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1EJP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 2)

NMR Structure (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003727331ENSE00001458506chr20:43977064-43976965100SDC4_HUMAN1-20200--
1.2ENST000003727332ENSE00000906918chr20:43964560-43964422139SDC4_HUMAN21-67470--
1.3ENST000003727333ENSE00000844970chr20:43961709-4396166347SDC4_HUMAN67-82160--
1.4ENST000003727334ENSE00000844969chr20:43959204-43959006199SDC4_HUMAN83-149670--
1.5ENST000003727335ENSE00001458498chr20:43956055-439539282128SDC4_HUMAN149-198502A:1-28
B:1-28
28
28

(-) Sequences/Alignments

NMR Structure
   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:28
 aligned with SDC4_HUMAN | P31431 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:28
                                   180       190        
           SDC4_HUMAN   171 RMKKKDEGSYDLGKKPIYKKAPTNEFYA 198
               SCOP domains d1ejpa_ A:                   SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author ............................ Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
               Transcript 1 Exon 1.5  PDB: A:1-28        Transcript 1
                 1ejp A   1 RMKKKDEGSYDLGKKPIYKKAPTNEFYA  28
                                    10        20        

Chain B from PDB  Type:PROTEIN  Length:28
 aligned with SDC4_HUMAN | P31431 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:28
                                   180       190        
           SDC4_HUMAN   171 RMKKKDEGSYDLGKKPIYKKAPTNEFYA 198
               SCOP domains d1ejpb_ B:                   SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author ............................ Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
               Transcript 1 Exon 1.5  PDB: B:1-28        Transcript 1
                 1ejp B   1 RMKKKDEGSYDLGKKPIYKKAPTNEFYA  28
                                    10        20        

   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)

NMR Structure
(-)
Class: Peptides (792)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1EJP)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

NMR Structure(hide GO term definitions)
Chain A,B   (SDC4_HUMAN | P31431)
molecular function
    GO:0001968    fibronectin binding    Interacting selectively and non-covalently with a fibronectin, a group of related adhesive glycoproteins of high molecular weight found on the surface of animal cells, connective tissue matrices, and in extracellular fluids.
    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:0005080    protein kinase C binding    Interacting selectively and non-covalently with protein kinase C.
    GO:0070053    thrombospondin receptor activity    Combining with thrombospondin and transmitting the signal to initiate a change in cell activity.
biological process
    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:0006024    glycosaminoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of glycosaminoglycans, any of a group of polysaccharides that contain amino sugars.
    GO:0006027    glycosaminoglycan catabolic process    The chemical reactions and pathways resulting in the breakdown of glycosaminoglycans, any one of a group of polysaccharides that contain amino sugars.
    GO:0030203    glycosaminoglycan metabolic process    The chemical reactions and pathways involving glycosaminoglycans, any one of a group of polysaccharides that contain amino sugars. Formerly known as mucopolysaccharides, they include hyaluronic acid and chondroitin, which provide lubrication in joints and form part of the matrix of cartilage. The three-dimensional structure of these molecules enables them to trap water, which forms a gel and gives glycosaminoglycans their elastic properties.
    GO:0060122    inner ear receptor stereocilium organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a stereocilium. A stereocilium is an actin-based protrusion from the apical surface of inner ear receptor cells.
    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:1903543    positive regulation of exosomal secretion    Any process that activates or increases the frequency, rate or extent of exosomal secretion.
    GO:1903553    positive regulation of extracellular exosome assembly    Any process that activates or increases the frequency, rate or extent of extracellular vesicular exosome assembly.
    GO:0051894    positive regulation of focal adhesion assembly    Any process that activates or increases the frequency, rate or extent of focal adhesion assembly, the establishment and maturation of focal adhesions.
    GO:0045860    positive regulation of protein kinase activity    Any process that activates or increases the frequency, rate or extent of protein kinase activity.
    GO:0051496    positive regulation of stress fiber assembly    Any process that activates or increases the frequency, rate or extent of the assembly of a stress fiber, a bundle of microfilaments and other proteins found in fibroblasts.
    GO:0010762    regulation of fibroblast migration    Any process that modulates the rate, frequency or extent of fibroblast cell migration. Fibroblast cell migration is accomplished by extension and retraction of a pseudopodium.
    GO:0001523    retinoid metabolic process    The chemical reactions and pathways involving retinoids, any member of a class of isoprenoids that contain or are derived from four prenyl groups linked head-to-tail. Retinoids include retinol and retinal and structurally similar natural derivatives or synthetic compounds, but need not have vitamin A activity.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0001657    ureteric bud development    The process whose specific outcome is the progression of the ureteric bud over time, from its formation to the mature structure.
    GO:0042060    wound healing    The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
    GO:0005796    Golgi lumen    The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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: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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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: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:0005887    integral component of plasma membrane    The component of the plasma 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:0043202    lysosomal lumen    The volume enclosed within the lysosomal membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    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
        SDC4_HUMAN | P314311ejq 1oby 1ybo

(-) Related Entries Specified in the PDB File

1ejq SOLUTION STRUCTURE OF THE SYNDECAN-4 WHOLE CYTOPLASMIC DOMAIN IN THE PRESENCE OF PHOSPHATIDYLINOSITOL 4,5- BISPHOSPHATE