Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  LAMININ ALPHA 2 CHAIN LG4-5 DOMAIN PAIR, CA1 SITE MUTANT
 
Authors :  H. Wizemann, J. H. O. Garbe, M. V. K. Friedrich, R. Timpl, T. Sasaki, E. Hohenester
Date :  28 Jul 03  (Deposition) - 11 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Metal Binding Protein, Laminin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Wizemann, J. H. O. Garbe, M. V. K. Friedrich, R. Timpl, T. Sasaki, E. Hohenester
Distinct Requirements For Heparin And Alpha-Dystroglycan Binding Revealed By Structure-Based Mutagenesis Of The Laminin Alpha2 Lg4-Lg5 Domain Pair
J. Mol. Biol. V. 332 635 2003
PubMed-ID: 12963372  |  Reference-DOI: 10.1016/S0022-2836(03)00848-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LAMININ ALPHA 2 CHAIN
    CellEMRYONIC KIDNEY CELL
    Cell LineEBNA-293
    ChainsA
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineEBNA-293
    Expression System PlasmidPCEP-PU
    Expression System Taxid9606
    FragmentLAMININ G-LIKE DOMAIN 4-5 PAIR, RESIDUES 2729-3093
    MutationYES
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    StrainFVB/N
    TissueEMBRYO

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:2861 , ASP A:2982 , ASN A:2999 , SER A:3053 , ASP A:3055BINDING SITE FOR RESIDUE CA A4002

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:2747 -A:3017
2A:2905 -A:2930
3A:3083 -A:3115

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LAM_G_DOMAINPS50025 Laminin G domain profile.LAMA2_MOUSE2141-2324
2336-2517
2522-2706
2759-2930
2935-3115
  2-
-
-
A:2759-2930
A:2935-3115

(-) Exons   (0, 0)

(no "Exon" information available for 1OKQ)

(-) 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:374
 aligned with LAMA2_MOUSE | Q60675 from UniProtKB/Swiss-Prot  Length:3118

    Alignment length:374
                                  2753      2763      2773      2783      2793      2803      2813      2823      2833      2843      2853      2863      2873      2883      2893      2903      2913      2923      2933      2943      2953      2963      2973      2983      2993      3003      3013      3023      3033      3043      3053      3063      3073      3083      3093      3103      3113    
         LAMA2_MOUSE   2744 HGPCVAESEPALLTGSKQFGLSRNSHIAIAFDDTKVKNRLTIELEVRTEAESGLLFYMARINHADFATVQLRNGFPYFSYDLGSGDTSTMIPTKINDGQWHKIKIVRVKQEGILYVDDASSQTISPKKADILDVVGILYVGGLPINYTTRRIGPVTYSLDGCVRNLHMEQAPVDLDQPTSSFHVGTCFANAESGTYFDGTGFAKAVGGFKVGLDLLVEFEFRTTRPTGVLLGVSSQKMDGMGIEMIDEKLMFHVDNGAGRFTAIYDAGIPGHMCNGQWHKVTAKKIKNRLELVVDGNQVDAQSPNSASTSADTNDPVFVGGFPGGLNQFGLTTNIRFRGCIRSLKLTKGTGKPLEVNFAKALELRGVQPVSCPT 3117
               SCOP domains d1okqa1 A:2744-2932 Laminin alpha2 chain                                                                                                                                                     d1okqa2 A:2933-3117 Laminin alpha2 chain                                                                                                                                                  SCOP domains
               CATH domains 1okqA01     1okqA02 A:2756-2930  [code=2.60.120.200, no name defined]                                                                                                                      1okqA01 A:2744-2755,A:2931-3117  [code=2.60.120.200, no name defined]                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------Laminin_G_1-1okqA01 A:2789-2917                                                                                                  ----------------------------------------------Laminin_G_2-1okqA02 A:2964-3092                                                                                                  ------------------------- Pfam domains
         Sec.struct. author ................eee......eeeee........eeeeeeeeee....eeeeeee......eeeeeee..eeeeeee....eeeee.........eeeeeeeee..eeeeee..eeeeee............eeee....................eeeeeeee...........eee........eee.eeeeeeeeee.......................eeeeeee.....eeeeeee..eeeeeee....eeeeee....................................................ee..................eeeeeeeeeee........hhhhh.eeeeee..eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------LAM_G_DOMAIN  PDB: A:2759-2930 UniProt: 2759-2930                                                                                                                           ----LAM_G_DOMAIN  PDB: A:2935-3115 UniProt: 2935-3115                                                                                                                                    -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1okq A 2744 HGPCVAESEPALLTGSKQFGLSRNSHIAIAFDDTKVKNRLTIELEVRTEAESGLLFYMARINHAAFATVQLRNGFPYFSYDLGSGDTSTMIPTKINDGQWHKIKIVRVKQEGILYVDDASSQTISPKKADILAVVGILYVGGLPINYTTRRIGPVTYSLDGCVRNLHMEQAPVDLDQPTSSFHVGTCFANAESGTYFDGTGFAKAVGGFKVGLDLLVEFEFRTTRPTGVLLGVSSQKMDGMGIEMIDEKLMFHVDNGAGRFTAIYDAEIPGHMCNGQWHKVTAKKIKNRLELVVDGNQVDAQSPNSASTSADTNDPVFVGGFPGGLNQFGLTTNIRFRGCIRSLKLTKGTGKPLEVNFAKALELRGVQPVSCPT 3117
                                  2753      2763      2773      2783      2793      2803      2813      2823      2833      2843      2853      2863      2873      2883      2893      2903      2913      2923      2933      2943      2953      2963      2973      2983      2993      3003      3013      3023      3033      3043      3053      3063      3073      3083      3093      3103      3113    

   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: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LAMA2_MOUSE | Q60675)
molecular function
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
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: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:0022011    myelination in peripheral nervous system    The process in which neuronal axons and dendrites become coated with a segmented lipid-rich sheath (myelin) to enable faster and more energetically efficient conduction of electrical impulses. The sheath is formed by the cell membranes of Schwann cells in the peripheral nervous system. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier.
    GO:0032224    positive regulation of synaptic transmission, cholinergic    Any process that activates, maintains or increases the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine.
    GO:0030155    regulation of cell adhesion    Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix.
    GO:0030334    regulation of cell migration    Any process that modulates the frequency, rate or extent of cell migration.
    GO:0045995    regulation of embryonic development    Any process that modulates the frequency, rate or extent of embryonic development.
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:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
    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: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.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1okq)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1okq
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  LAMA2_MOUSE | Q60675
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  LAMA2_MOUSE | Q60675
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        LAMA2_MOUSE | Q606751dyk 1qu0 2wjs 5ik4 5ik5 5ik7 5ik8

(-) Related Entries Specified in the PDB File

1dyk CRYSTAL STRUCTURE OF LAMININ ALPHA 2 CHAIN LG4-5 DOMAIN PAIR
1qu0 CRYSTAL STRUCTURE OF THE FIFTH LAMININ G-LIKE MODULE OF THE MOUSE LAMININ ALPHA2 CHAIN