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(-) Description

Title :  CRYSTAL STRUCTURE OF NEUROFASCIN ADHESION COMPLEX IN SPACE GROUP P3221
 
Authors :  H. Liu, X. He
Date :  05 Oct 10  (Deposition) - 03 Nov 10  (Release) - 19 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Ig Domains, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Liu, P. J. Focia, X. He
Homophilic Adhesion Mechanism Of Neurofascin, A Member Of The L1 Family Of Neural Cell Adhesion Molecules.
J. Biol. Chem. V. 286 797 2011
PubMed-ID: 21047790  |  Reference-DOI: 10.1074/JBC.M110.180281

(-) Compounds

Molecule 1 - NEUROFASCIN
    ChainsA
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System Cell LineHI5
    Expression System CommonCABBAGE LOOPER
    Expression System Taxid7111
    FragmentN-TERMINAL FOUR IG DOMAINS (UNP RESIDUES 25-428)
    GeneNFASC, KIAA0756
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:131 , ASN A:409 , SER A:411 , HOH A:582BINDING SITE FOR RESIDUE NAG A 1

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:63 -A:118
2A:162 -A:213
3A:268 -A:316
4A:358 -A:408

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:168 -Pro A:169
2Asn A:363 -Pro A:364

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_017251T159MNFASC_HUMANPolymorphism3795564AT159M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_017251T159MNFASC_HUMANPolymorphism3795564AT159M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P40)

(-) Exons   (0, 0)

(no "Exon" information available for 3P40)

(-) 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:390
 aligned with NFASC_HUMAN | O94856 from UniProtKB/Swiss-Prot  Length:1347

    Alignment length:390
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426
          NFASC_HUMAN    37 LTQPPTITKQSAKDHIVDPRDNILIECEAKGNPAPSFHWTRNSRFFNIAKDPRVSMRRRSGTLVIDFRSGGRPEEYEGEYQCFARNKFGTALSNRIRLQVSKSPLWPKENLDPVVVQEGAPLTLQCNPPPGLPSPVIFWMSSSMEPITQDKRVSQGHNGDLYFSNVMLQDMQTDYSCNARFHFTHTIQQKNPFTLKVLTTRGVAERTPSFMYPQGTASSQMVLRGMDLLLECIASGVPTPDIAWYKKGGDLPSDKAKFENFNKALRITNVSEEDSGEYFCLASNKMGSIRHTISVRVKAAPYWLDEPKNLILAPGEDGRLVCRANGNPKPTVQWMVNGEPLQSAPPNPNREVAGDTIIFRDTQISSRAVYQCNTSNEHGYLLANAFVSVL 426
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------Ig_2-3p40A03 A:140-233                                                                        -------------------------------------------------------------------------------------------------------I-set-3p40A01 A:337-425                                                                  - Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------Ig_2-3p40A04 A:140-233                                                                        -------------------------------------------------------------------------------------------------------I-set-3p40A02 A:337-425                                                                  - Pfam domains (2)
         Sec.struct. author ........ee...eeee.........ee.......ee..................................hhhhhheee..eee....eee...eeeee.............eeee....eee...........eeeee............eee.....eee.....hhhhh..eeeeee....eeee.....eeee..........ee......eeeeeee....eeee..ee.....eeeeee.........eee.....eeee........eeeeeeee....eeeeeeeeeeeeeeeeee....eee.....eeee.eeeee...eeeeee..ee.........eee...eeee........eeeeeeee......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------M--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p40 A  37 LTQPPTITKQSAKDHIVDPRDNILIECEAKGNPAPSFHWTRNSRFFNIAKDPRVSMRRRSGTLVIDFRSGGRPEEYEGEYQCFARNKFGTALSNRIRLQVSKSPLWPKENLDPVVVQEGAPLTLQCNPPPGLPSPVIFWMSSSMEPITQDKRVSQGHNGDLYFSNVMLQDMQTDYSCNARFHFTHTIQQKNPFTLKVLTTRGVAERTPSFMYPQGTASSQMVLRGMDLLLECIASGVPTPDIAWYKKGGDLPSDKAKFENFNKALRITNVSEEDSGEYFCLASNKMGSIRHTISVRVKAAPYWLDEPKNLILAPGEDGRLVCRANGNPKPTVQWMVNGEPLQSAPPNPNREVAGDTIIFRDTQISSRAVYQCNTSNEHGYLLANAFVSVL 426
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426

   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 3P40)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P40)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: Ig (577)
(-)
Family: I-set (67)
1aI-set-3p40A01A:337-425
1bI-set-3p40A02A:337-425
(-)
Family: Ig_2 (52)
2aIg_2-3p40A03A:140-233
2bIg_2-3p40A04A:140-233

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)
Chain A   (NFASC_HUMAN | O94856)
molecular function
    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:0086080    protein binding involved in heterotypic cell-cell adhesion    Interacting selectively and non-covalently with any protein or protein complex contributing to the adhesion of two different types of cells.
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
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:0045162    clustering of voltage-gated sodium channels    The process in which voltage-gated sodium channels become localized together in high densities. In animals, nodes of Ranvier differ dramatically from internodal axonal regions in very high densities of voltage-dependent sodium (Nav) channels responsible for the rapid, inward ionic currents that produce membrane depolarization.
    GO:0034113    heterotypic cell-cell adhesion    The attachment of a cell to a cell of a different type via adhesion molecules.
    GO:0042552    myelination    The process in which myelin sheaths are formed and maintained around neurons. Oligodendrocytes in the brain and spinal cord and Schwann cells in the peripheral nervous system wrap axons with compact layers of their plasma membrane. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier.
    GO:0030913    paranodal junction assembly    Formation of the junction between an axon and the glial cell that forms the myelin sheath. Paranodal junctions form at each paranode, i.e. at the ends of the unmyelinated nodes of Ranvier.
    GO:0007422    peripheral nervous system development    The process whose specific outcome is the progression of the peripheral nervous system over time, from its formation to the mature structure. The peripheral nervous system is one of the two major divisions of the nervous system. Nerves in the PNS connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
    GO:0071205    protein localization to juxtaparanode region of axon    Any process in which a protein is transported to, or maintained at, the juxtaparanode region of an axon.
    GO:0002175    protein localization to paranode region of axon    A cellular protein localization process in which a protein is transported to, or maintained at, the paranode region of an axon.
    GO:0072661    protein targeting to plasma membrane    The process of directing proteins towards the plasma membrane; usually uses signals contained within the protein.
    GO:0050808    synapse organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell).
    GO:0019226    transmission of nerve impulse    The neurological system process in which a signal is transmitted through the nervous system by a combination of action potential propagation and synaptic transmission.
cellular component
    GO:0097454    Schwann cell microvillus    Small finger-like extension of a Schwann cell that contacts the nodal membrane.
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0043194    axon initial segment    Portion of the axon proximal to the neuronal cell body, at the level of the axon hillock. The action potentials that propagate along the axon are generated at the level of this initial segment.
    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: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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    GO:0033268    node of Ranvier    An axon part that is a gap in the myelin where voltage-gated sodium channels cluster and saltatory conduction is executed.
    GO:0033010    paranodal junction    A highly specialized cell-cell junction found in vertebrates, which forms between a neuron and a glial cell, and has structural similarity to Drosophila septate junctions. It flanks the node of Ranvier in myelinated nerve and electrically isolates the myelinated from unmyelinated nerve segments and physically separates the voltage-gated sodium channels at the node from the cluster of potassium channels underneath the myelin sheath.
    GO:0033270    paranode region of axon    An axon part that is located adjacent to the nodes of Ranvier and surrounded by lateral loop portions of myelin sheath.
    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
        NFASC_HUMAN | O948563p3y

(-) Related Entries Specified in the PDB File

3p3y