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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FIFTH LAMININ G-LIKE MODULE OF THE MOUSE LAMININ ALPHA2 CHAIN
 
Authors :  E. Hohenester, D. Tisi, J. F. Talts, R. Timpl
Date :  05 Jul 99  (Deposition) - 03 Dec 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  C,D  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Beta Sandwich, Calcium-Binding Protein, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Hohenester, D. Tisi, J. F. Talts, R. Timpl
The Crystal Structure Of A Laminin G-Like Module Reveals The Molecular Basis Of Alpha-Dystroglycan Binding To Laminins, Perlecan, And Agrin.
Mol. Cell V. 4 783 1999
PubMed-ID: 10619025  |  Reference-DOI: 10.1016/S1097-2765(00)80388-3
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LAMININ ALPHA2 CHAIN
    ChainsA, B, C, D
    EngineeredYES
    Expression System Common293-EBNA HUMAN AMBRYONIC KIDNEY CELLS
    FragmentLG5 MODULE
    MutationYES
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x) BC 
Biological Unit 3 (1x)  CD
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2SO47Ligand/IonSULFATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SO43Ligand/IonSULFATE ION
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SO44Ligand/IonSULFATE ION
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SO42Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESO4 A:801 , HOH A:975 , ASP A:2982 , ASN A:2999 , SER A:3053 , ASP A:3055BINDING SITE FOR RESIDUE CA A 701
02AC2SOFTWARECA A:701 , ALA A:3050 , SER A:3051 , THR A:3052 , SER A:3053BINDING SITE FOR RESIDUE SO4 A 801
03AC3SOFTWAREPRO A:3066 , GLY A:3067 , ARG A:3079 , ARG A:3108BINDING SITE FOR RESIDUE SO4 A 802
04AC4SOFTWARESO4 B:803 , HOH B:1035 , ASP B:2982 , ASN B:2999 , SER B:3053 , ASP B:3055BINDING SITE FOR RESIDUE CA B 702
05AC5SOFTWARECA B:702 , ASN B:2999 , SER B:3051 , THR B:3052 , SER B:3053 , LYS C:3027BINDING SITE FOR RESIDUE SO4 B 803
06AC6SOFTWARESO4 C:804 , HOH C:1133 , HOH C:1164 , ASP C:2982 , ASN C:2999 , SER C:3053 , ASP C:3055BINDING SITE FOR RESIDUE CA C 703
07AC7SOFTWARELYS B:3027 , CA C:703 , HOH C:1164 , ASN C:2999 , ALA C:3050 , SER C:3051 , THR C:3052 , SER C:3053BINDING SITE FOR RESIDUE SO4 C 804
08AC8SOFTWAREPRO C:3066 , GLY C:3067 , ARG C:3079 , ARG C:3108BINDING SITE FOR RESIDUE SO4 C 805
09AC9SOFTWARESO4 D:806 , ASP D:2982 , ASN D:2999 , SER D:3053 , ASP D:3055BINDING SITE FOR RESIDUE CA D 704
10BC1SOFTWARECA D:704 , ALA D:3050 , SER D:3051 , THR D:3052 , SER D:3053BINDING SITE FOR RESIDUE SO4 D 806
11BC2SOFTWAREPRO D:3066 , GLY D:3067 , ARG D:3079 , ARG D:3108BINDING SITE FOR RESIDUE SO4 D 807

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:3083 -A:3115
2B:3083 -B:3115
3C:3083 -C:3115
4D:3083 -D:3115

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QU0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QU0)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LAM_G_DOMAINPS50025 Laminin G domain profile.LAMA2_MOUSE2141-2324
2336-2517
2522-2706
2759-2930
2935-3115
  1-
-
-
-
C:2935-3115
Biological Unit 1 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LAM_G_DOMAINPS50025 Laminin G domain profile.LAMA2_MOUSE2141-2324
2336-2517
2522-2706
2759-2930
2935-3115
  0-
-
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LAM_G_DOMAINPS50025 Laminin G domain profile.LAMA2_MOUSE2141-2324
2336-2517
2522-2706
2759-2930
2935-3115
  1-
-
-
-
C:2935-3115
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LAM_G_DOMAINPS50025 Laminin G domain profile.LAMA2_MOUSE2141-2324
2336-2517
2522-2706
2759-2930
2935-3115
  1-
-
-
-
C:2935-3115
Biological Unit 4 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LAM_G_DOMAINPS50025 Laminin G domain profile.LAMA2_MOUSE2141-2324
2336-2517
2522-2706
2759-2930
2935-3115
  0-
-
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 1QU0)

(-) 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:181
 aligned with LAMA2_MOUSE | Q60675 from UniProtKB/Swiss-Prot  Length:3118

    Alignment length:181
                                  2945      2955      2965      2975      2985      2995      3005      3015      3025      3035      3045      3055      3065      3075      3085      3095      3105      3115 
         LAMA2_MOUSE   2936 SGTYFDGTGFAKAVGGFKVGLDLLVEFEFRTTRPTGVLLGVSSQKMDGMGIEMIDEKLMFHVDNGAGRFTAIYDAGIPGHMCNGQWHKVTAKKIKNRLELVVDGNQVDAQSPNSASTSADTNDPVFVGGFPGGLNQFGLTTNIRFRGCIRSLKLTKGTGKPLEVNFAKALELRGVQPVSCP 3116
               SCOP domains d1qu0a_ A: Laminin alpha2 chain                                                                                                                                                       SCOP domains
               CATH domains 1qu0A00 A:2936-3116  [code=2.60.120.200, no name defined]                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.........eeeeeeeeee....eeeeeee.....eeeeeee..eeeeeee....eeeeee.....hhhhh...eeeeeeee..eeeeee..eeeeee...............ee..................eeeeeeeeeee........hhhhh.eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE LAM_G_DOMAIN  PDB: - UniProt: 2935-3115                                                                                                                                             - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1qu0 A 2936 SGTYFDGTGFAKAVGGFKVGLDLLVEFEFRTTRPTGVLLGISSQKMDGMGIEMIDEKLMFHVDNGAGRFTAIYDAEIPGHMCNGQWHKVTAKKIKNRLELVVDGNQVDAQSPNSASTSADTNDPVFVGGFPGGLNQFGLTTNIRFRGCIRSLKLTKGTGKPLEVNFAKALELRGVQPVSCP 3116
                                  2945      2955      2965      2975      2985      2995      3005      3015      3025      3035      3045      3055      3065      3075      3085      3095      3105      3115 

Chain B from PDB  Type:PROTEIN  Length:181
 aligned with LAMA2_MOUSE | Q60675 from UniProtKB/Swiss-Prot  Length:3118

    Alignment length:181
                                  2945      2955      2965      2975      2985      2995      3005      3015      3025      3035      3045      3055      3065      3075      3085      3095      3105      3115 
         LAMA2_MOUSE   2936 SGTYFDGTGFAKAVGGFKVGLDLLVEFEFRTTRPTGVLLGVSSQKMDGMGIEMIDEKLMFHVDNGAGRFTAIYDAGIPGHMCNGQWHKVTAKKIKNRLELVVDGNQVDAQSPNSASTSADTNDPVFVGGFPGGLNQFGLTTNIRFRGCIRSLKLTKGTGKPLEVNFAKALELRGVQPVSCP 3116
               SCOP domains d1qu0b_ B: Laminin alpha2 chain                                                                                                                                                       SCOP domains
               CATH domains 1qu0B00 B:2936-3116  [code=2.60.120.200, no name defined]                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.........eeeeeeeeee....eeeeeee.....eeeeeee..eeeeeee....eeeeee.....hhhhh...eeeeeeee..eeeeee..eeeeee...............ee..................eeeeeeeeeee........hhhhh.eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE LAM_G_DOMAIN  PDB: - UniProt: 2935-3115                                                                                                                                             - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1qu0 B 2936 SGTYFDGTGFAKAVGGFKVGLDLLVEFEFRTTRPTGVLLGISSQKMDGMGIEMIDEKLMFHVDNGAGRFTAIYDAEIPGHMCNGQWHKVTAKKIKNRLELVVDGNQVDAQSPNSASTSADTNDPVFVGGFPGGLNQFGLTTNIRFRGCIRSLKLTKGTGKPLEVNFAKALELRGVQPVSCP 3116
                                  2945      2955      2965      2975      2985      2995      3005      3015      3025      3035      3045      3055      3065      3075      3085      3095      3105      3115 

Chain C from PDB  Type:PROTEIN  Length:183
 aligned with LAMA2_MOUSE | Q60675 from UniProtKB/Swiss-Prot  Length:3118

    Alignment length:183
                                  2944      2954      2964      2974      2984      2994      3004      3014      3024      3034      3044      3054      3064      3074      3084      3094      3104      3114   
         LAMA2_MOUSE   2935 ESGTYFDGTGFAKAVGGFKVGLDLLVEFEFRTTRPTGVLLGVSSQKMDGMGIEMIDEKLMFHVDNGAGRFTAIYDAGIPGHMCNGQWHKVTAKKIKNRLELVVDGNQVDAQSPNSASTSADTNDPVFVGGFPGGLNQFGLTTNIRFRGCIRSLKLTKGTGKPLEVNFAKALELRGVQPVSCPT 3117
               SCOP domains d1qu0c_ C: Laminin alpha2 chain                                                                                                                                                         SCOP domains
               CATH domains 1qu0C00 C:2935-3117  [code=2.60.120.200, no name defined]                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee.........eeeeeeeee.....eeeeeee.....eeeeeee..eeeeeee....eeeeee.....hhhhh...eeeeeeee..eeeeee..eeeeee...............ee..................eeeeeeeeeee.....ee.hhhhh.eeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE LAM_G_DOMAIN  PDB: C:2935-3115 UniProt: 2935-3115                                                                                                                                    -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1qu0 C 2935 ESGTYFDGTGFAKAVGGFKVGLDLLVEFEFRTTRPTGVLLGISSQKMDGMGIEMIDEKLMFHVDNGAGRFTAIYDAEIPGHMCNGQWHKVTAKKIKNRLELVVDGNQVDAQSPNSASTSADTNDPVFVGGFPGGLNQFGLTTNIRFRGCIRSLKLTKGTGKPLEVNFAKALELRGVQPVSCPT 3117
                                  2944      2954      2964      2974      2984      2994      3004      3014      3024      3034      3044      3054      3064      3074      3084      3094      3104      3114   

Chain D from PDB  Type:PROTEIN  Length:181
 aligned with LAMA2_MOUSE | Q60675 from UniProtKB/Swiss-Prot  Length:3118

    Alignment length:181
                                  2945      2955      2965      2975      2985      2995      3005      3015      3025      3035      3045      3055      3065      3075      3085      3095      3105      3115 
         LAMA2_MOUSE   2936 SGTYFDGTGFAKAVGGFKVGLDLLVEFEFRTTRPTGVLLGVSSQKMDGMGIEMIDEKLMFHVDNGAGRFTAIYDAGIPGHMCNGQWHKVTAKKIKNRLELVVDGNQVDAQSPNSASTSADTNDPVFVGGFPGGLNQFGLTTNIRFRGCIRSLKLTKGTGKPLEVNFAKALELRGVQPVSCP 3116
               SCOP domains d1qu0d_ D: Laminin alpha2 chain                                                                                                                                                       SCOP domains
               CATH domains 1qu0D00 D:2936-3116  [code=2.60.120.200, no name defined]                                                                                                                             CATH domains
           Pfam domains (1) ----------------------------Laminin_G_2-1qu0D01 D:2964-3092                                                                                                  ------------------------ Pfam domains (1)
           Pfam domains (2) ----------------------------Laminin_G_2-1qu0D02 D:2964-3092                                                                                                  ------------------------ Pfam domains (2)
           Pfam domains (3) ----------------------------Laminin_G_2-1qu0D03 D:2964-3092                                                                                                  ------------------------ Pfam domains (3)
           Pfam domains (4) ----------------------------Laminin_G_2-1qu0D04 D:2964-3092                                                                                                  ------------------------ Pfam domains (4)
         Sec.struct. author ..eeeeeeeeee.........eeeeeeeeee....eeeeeee.....eeeeeee..eeeeeee....eeeeee.....hhhhh...eeeeeeee..eeeeee..eeeeee...............ee..................eeeeeeeeeee.....ee.hhhhh.eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE LAM_G_DOMAIN  PDB: - UniProt: 2935-3115                                                                                                                                             - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1qu0 D 2936 SGTYFDGTGFAKAVGGFKVGLDLLVEFEFRTTRPTGVLLGISSQKMDGMGIEMIDEKLMFHVDNGAGRFTAIYDAEIPGHMCNGQWHKVTAKKIKNRLELVVDGNQVDAQSPNSASTSADTNDPVFVGGFPGGLNQFGLTTNIRFRGCIRSLKLTKGTGKPLEVNFAKALELRGVQPVSCP 3116
                                  2945      2955      2965      2975      2985      2995      3005      3015      3025      3035      3045      3055      3065      3075      3085      3095      3105      3115 

   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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 4)

Asymmetric Unit

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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.

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 Related Entries

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

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

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