Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - model 1, sites
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - model 1, sites
NMR Structure - model 1, sites  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  LE (LAMININ-TYPE EGF-LIKE) MODULE GIII4 IN SOLUTION AT PH 3.5 AND 290 K, NMR, 14 STRUCTURES
 
Authors :  R. Baumgartner, M. Czisch, U. Mayer, E. P. Schl, R. Huber, R. Timpl, T. A. Holak
Date :  26 Jan 96  (Deposition) - 12 Feb 97  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (14x)
Keywords :  Glycoprotein, Extracellular Matrix Protein, Nidogen Binding, Le-Module (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Baumgartner, M. Czisch, U. Mayer, E. Poschl, R. Huber, R. Timpl, T. A. Holak
Structure Of The Nidogen Binding Le Module Of The Laminin Gamma1 Chain In Solution.
J. Mol. Biol. V. 257 658 1996
PubMed-ID: 8648631  |  Reference-DOI: 10.1006/JMBI.1996.0192
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LAMININ
    Chains: A
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Common: HOUSE MOUSE
    Expression System Gene: LAMC1
    Expression System Plasmid: PCEP4
    Expression System Taxid: 10090
    Fragment: NIDOGEN BINDING LE MODULE OF THE LAMININ GAMMA1 CHAIN, MODULE GIII4
    Gene: LAMC1
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: LAMININ-TYPE EGF-LIKE
    Tissue: BASEMENT MEMBRANE

 Structural Features

(-) Chains, Units

  
NMR Structure (14x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1BINUNKNOWNASN A:8 , ILE A:9 , ASP A:10 , PRO A:11 , ASN A:12 , ALA A:13 , VAL A:14BINDING SITE TO NIDOGEN.

(-) SS Bonds  (4, 4)

NMR Structure
No.Residues
1A:3 -A:17
2A:5 -A:24
3A:27 -A:36
4A:39 -A:56

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EGF_LAM_2PS50027 Laminin-type EGF-like (LE) domain profile.LAMC1_MOUSE284-329
340-395
396-442
443-492
722-770
771-825
826-881
882-932
933-980
981-1028		  1-
-
-
-
-
-
A:3-58
-
-
-
2EGF_LAM_1PS01248 Laminin-type EGF-like (LE) domain signature.LAMC1_MOUSE365-398
414-445
461-495
688-722
738-773
790-826
847-882
903-935
952-983
999-1032		  1-
-
-
-
-
-
A:24-58
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 1TLE)

(-) 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:58
 aligned with LAMC1_MOUSE | P02468 from UniProtKB/Swiss-Prot  Length:1607

    Alignment length:58
                                   833       843       853       863       873        
          LAMC1_MOUSE   824 RPCQCNDNIDPNAVGNCNRLTGECLKCIYNTAGFYCDRCKEGFFGNPLAPNPADKCKA 881
               SCOP domains d1tlea_ A: Laminin gamma1 chain                            SCOP domains
               CATH domains 1tleA00 A:1-58 Laminin                                     CATH domains
               Pfam domains --Laminin_EGF-1tleA01 A:3-56                            -- Pfam domains
         Sec.struct. author ..............................ee.....ee....ee......hhh.ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) EGEGF_LAM_2  PDB: A:3-58 UniProt: 826-881                  PROSITE (1)
                PROSITE (2) EGF--------------------EGF_LAM_1  PDB: A:24-58             PROSITE (2)
                 Transcript ---------------------------------------------------------- Transcript
                 1tle A   1 RPCQCNDNIDPNAVGNCNRLTGECLKCIYNTAGFYCDRCKEGFFGNPLAPNPADKCKA  58
                                    10        20        30        40        50
   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)

NMR Structure
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: EGF (60)

(-) Gene Ontology  (19, 19)

NMR Structure(hide GO term definitions)
Chain A   (LAMC1_MOUSE | P02468)
molecular function
    GO:0005201    extracellular matrix structural constituent    The action of a molecule that contributes to the structural integrity of the extracellular matrix.
    GO:0043208    glycosphingolipid binding    Interacting selectively and non-covalently with glycosphingolipid, a compound with residues of sphingoid and at least one monosaccharide.
    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:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    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: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:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    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.
    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:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0034446    substrate adhesion-dependent cell spreading    The morphogenetic process that results in flattening of a cell as a consequence of its adhesion to a substrate.
cellular component
    GO:0005605    basal lamina    A thin sheet of proteoglycans and glycoproteins, especially laminin, secreted by cells as an extracellular matrix.
    GO:0005604    basement membrane    A thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers.
    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:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    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:0043259    laminin-10 complex    A laminin complex composed of alpha5, beta1 and gamma1 polypeptide chains.
    GO:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1tle)
 
  Sites
    BIN  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1tle)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - model 1, sites PNG format | NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1tle
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  LAMC1_MOUSE | P02468
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  LAMC1_MOUSE | P02468
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        LAMC1_MOUSE | P02468: 1klo 1npe 4aqt 5mc9

(-) Related Entries Specified in the PDB File

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