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(-) Description

Title :  LAMININ BETA1 LN-LE1-4 STRUCTURE
 
Authors :  F. Carafoli, S. Hussain, E. Hohenester
Date :  19 Apr 12  (Deposition) - 15 Aug 12  (Release) - 14 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.11
Chains :  Asym./Biol. Unit :  A
Keywords :  Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Carafoli, S. Hussain, E. Hohenester
Crystal Structures Of The Network-Forming Short-Arm Tips Of The Laminin Beta1 And Gamma1 Chains.
Plos One V. 7 42473 2012
PubMed-ID: 22860131  |  Reference-DOI: 10.1371/JOURNAL.PONE.0042473

(-) Compounds

Molecule 1 - LAMININ SUBUNIT BETA-1
    ChainsA
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293 C18
    Expression System CommonHUMAN
    Expression System PlasmidPCEP-PU
    Expression System Taxid9606
    FragmentLN-LEA1-4 FRAGMENT, RESIDUES 22-542
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymLAMININ B1 CHAIN, LAMININ-1 SUBUNIT BETA, LAMININ-10 SUBUNIT BETA, LAMININ-12 SUBUNIT BETA, LAMININ-2 SUBUNIT BETA, LAMININ-6 SUBUNIT BETA, LAMININ-8 SUBUNIT BETA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2FUL1Ligand/IonBETA-L-FUCOSE
3MAN1Ligand/IonALPHA-D-MANNOSE
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:120BINDING SITE FOR MONO-SACCHARIDE NAG A1001 BOUND TO ASN A 120
2AC2SOFTWAREARG A:322 , ASN A:356 , ARG A:436BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 356 RESIDUES 2001 TO 2005

(-) SS Bonds  (19, 19)

Asymmetric/Biological Unit
No.Residues
1A:30 -A:35
2A:56 -A:79
3A:65 -A:76
4A:170 -A:190
5A:271 -A:280
6A:273 -A:298
7A:300 -A:309
8A:312 -A:332
9A:335 -A:344
10A:337 -A:362
11A:365 -A:374
12A:377 -A:395
13A:398 -A:411
14A:400 -A:426
15A:428 -A:437
16A:440 -A:455
17A:458 -A:472
18A:460 -A:479
19A:481 -A:490

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AQS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AQS)

(-) PROSITE Motifs  (4, 12)

Asymmetric/Biological Unit (4, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LAMININ_NTERPS51117 Laminin N-terminal domain profile.LAMB1_MOUSE31-270  1A:31-270
2EGF_LAM_2PS50027 Laminin-type EGF-like (LE) domain profile.LAMB1_MOUSE271-334
335-397
398-457
458-509
510-555
773-820
821-866
867-916
917-975
976-1027
1028-1083
1084-1131
1132-1178
  4A:271-334
A:335-397
A:398-457
A:458-493
-
-
-
-
-
-
-
-
-
3EGF_1PS00022 EGF-like domain signature 1.LAMB1_MOUSE298-309
426-437
479-490
529-540
792-803
944-955
1054-1065
1103-1114
1151-1162
  3A:298-309
A:426-437
A:479-490
-
-
-
-
-
-
4EGF_LAM_1PS01248 Laminin-type EGF-like (LE) domain signature.LAMB1_MOUSE298-332
362-398
426-460
479-512
792-823
883-919
944-978
997-1030
1054-1086
1103-1134
1151-1182
  4A:298-332
A:362-398
A:426-460
A:479-493
-
-
-
-
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 4AQS)

(-) 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:454
 aligned with LAMB1_MOUSE | P02469 from UniProtKB/Swiss-Prot  Length:1786

    Alignment length:465
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488     
          LAMB1_MOUSE    29 GCAEGSCYPATGDLLIGRAQKLSVTSTCGLHKPEPYCIVSHLQEDKKCFICDSRDPYHETLNPDSHLIENVVTTFAPNRLKIWWQSENGVENVTIQLDLEAEFHFTHLIMTFKTFRPAAMLIERSSDFGKAWGVYRYFAYDCESSFPGISTGPMKKVDDIICDSRYSDIEPSTEGEVIFRALDPAFKIEDPYSPRIQNLLKITNLRIKFVKLHTLGDNLLDSRMEIREKYYYAVYDMVVRGNCFCYGHASECAPVDGVNEEVEGMVHGHCMCRHNTKGLNCELCMDFYHDLPWRPAEGRNSNACKKCNCNEHSSSCHFDMAVFLATGNVSGGVCDNCQHNTMGRNCEQCKPFYFQHPERDIRDPNLCEPCTCDPAGSENGGICDGYTDFSVGLIAGQCRCKLHVEGERCDVCKEGFYDLSAEDPYGCKSCACNPLGTIPGGNPCDSETGYCYCKRLVTGQRCDQC 493
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh......ee....hhh.ee..........eeeeee......eeeeee...............hhhhh...-----....ee........eeeeeeeeeeeeeeeeeee......eeeeeee.......eeeeeee......................ee............eeeee............hhhhhhhheeeeeeeeeee...........hhhhhh....eeeeeeeeee.........ee..------.......ee.....ee.....ee..............................eeeehhhhhhhh.....eeee.....ee.....ee...eee...........eee........hhhhh......hhhh...........ee.....ee...ee..........ee.................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --LAMININ_NTER  PDB: A:31-270 UniProt: 31-270                                                                                                                                                                                                     EGF_LAM_2  PDB: A:271-334 UniProt: 271-334                      EGF_LAM_2  PDB: A:335-397 UniProt: 335-397                     EGF_LAM_2  PDB: A:398-457 UniProt: 398-457                  EGF_LAM_2  PDB: A:458-493            PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EGF_LAM_1  PDB: A:298-332          -----------------------------EGF_LAM_1  PDB: A:362-398            ---------------------------EGF_LAM_1  PDB: A:426-460          ------------------EGF_LAM_1       PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EGF_1       --------------------------------------------------------------------------------------------------------------------EGF_1       -----------------------------------------EGF_1       --- PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aqs A  29 GCAEGSCYPATGDLLIGRAQKLSVTSTCGLHKPEPYCIVSHLQEDKKCFICDSRDPYHETLNPDSHLIENVVTT-----LKIWWQSENGVENVTIQLDLEAEFHFTHLIMTFKTFRPAAMLIERSSDFGKAWGVYRYFAYDCESSFPGISTGPMKKVDDIICDSRYSDIEPSTEGEVIFRALDPAFKIEDPYSPRIQNLLKITNLRIKFVKLHTLGDNLLDSRMEIREKYYYAVYDMVVRGNCFCYGHASECAPV------VEGMVHGHCMCRHNTKGLNCELCMDFYHDLPWRPAEGRNSNACKKCNCNEHSSSCHFDMAVFLATGNVSGGVCDNCQHNTMGRNCEQCKPFYFQHPERDIRDPNLCEPCTCDPAGSENGGICDGYTDFSVGLIAGQCRCKLHVEGERCDVCKEGFYDLSAEDPYGCKSCACNPLGTIPGGNPCDSETGYCYCKRLVTGQRCDQC 493
                                    38        48        58        68        78        88        98   |   108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278    |    - |     298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488     
                                                                                                   102   108                                                                                                                                                                            283    290                                                                                                                                                                                                           

   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 4AQS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AQS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AQS)

(-) Gene Ontology  (31, 31)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LAMB1_MOUSE | P02469)
molecular function
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    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:0007566    embryo implantation    Attachment of the blastocyst to the uterine lining.
    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:0007611    learning or memory    The acquisition and processing of information and/or the storage and retrieval of this information over time.
    GO:0007162    negative regulation of cell adhesion    Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion.
    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:0021812    neuronal-glial interaction involved in cerebral cortex radial glia guided migration    The changes in adhesion between neuronal cells and glial cells as a component of the process of cerebral cortex glial-mediated radial cell migration.
    GO:0042476    odontogenesis    The process whose specific outcome is the progression of a tooth or teeth over time, from formation to the mature structure(s). A tooth is any hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0043256    laminin complex    A large, extracellular glycoprotein complex composed of three different polypeptide chains, alpha, beta and gamma. Provides an integral part of the structural scaffolding of basement membranes.
    GO:0005606    laminin-1 complex    A laminin complex composed of alpha1, beta1 and gamma1 polypeptide chains.
    GO:0043259    laminin-10 complex    A laminin complex composed of alpha5, beta1 and gamma1 polypeptide chains.
    GO:0005607    laminin-2 complex    A laminin complex composed of alpha2, beta1 and gamma1 polypeptide chains.
    GO:0043257    laminin-8 complex    A laminin complex composed of alpha4, beta1 and gamma1 polypeptide chains.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LAMB1_MOUSE | P024695mc9

(-) Related Entries Specified in the PDB File

4aqt LAMININ GAMMA1 LN-LE1-2 STRUCTURE