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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FIRST FIBRONECTIN DOMAIN OF HUMAN NCAM1
 
Authors :  N. Sekulic, A. Lavie
Date :  13 Jun 06  (Deposition) - 03 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Fibronectin Type Iii Repeat, Fn1, Ncam, Beta Sandwich, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. S. Mendiratta, N. Sekulic, F. G. Hernandez-Guzman, B. E. Close, A. Lavie, K. J. Colley
A Novel Alpha-Helix In The First Fibronectin Type Iii Repeat Of The Neural Cell Adhesion Molecule Is Critical For N-Glycan Polysialylation.
J. Biol. Chem. V. 281 36052 2006
PubMed-ID: 17003032  |  Reference-DOI: 10.1074/JBC.M608073200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEURAL CELL ADHESION MOLECULE 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET14B
    Expression System StrainBL21-DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentFIRST FIBRONECTIN TYPE III REPEAT DOMAIN
    GeneNCAM1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymN-CAM 1

 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
1NA1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:497 , ASP A:511 , ASP A:542 , GLU A:545BINDING SITE FOR RESIDUE NA A 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HAZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2HAZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HAZ)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FN3PS50853 Fibronectin type-III domain profile.NCAM1_HUMAN509-608
611-706
  1A:490-589
-

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.6ENST000003168516ENSE00001530989chr11:113067915-11306793824NCAM1_HUMAN1-880--
1.7aENST000003168517aENSE00001530988chr11:113073076-113073175100NCAM1_HUMAN9-42340--
1.8aENST000003168518aENSE00001660707chr11:113075008-113075226219NCAM1_HUMAN42-115740--
1.9bENST000003168519bENSE00001659816chr11:113076245-113076388144NCAM1_HUMAN115-163490--
1.10ENST0000031685110ENSE00001338262chr11:113076765-113076902138NCAM1_HUMAN163-209470--
1.11ENST0000031685111ENSE00001338259chr11:113077983-113078100118NCAM1_HUMAN209-248400--
1.12ENST0000031685112ENSE00001338256chr11:113078555-113078724170NCAM1_HUMAN248-305580--
1.13ENST0000031685113ENSE00000989824chr11:113085091-113085233143NCAM1_HUMAN305-352480--
1.14aENST0000031685114aENSE00002168218chr11:113092018-11309204730NCAM1_HUMAN353-362100--
1.16bENST0000031685116bENSE00001725196chr11:113102367-113102517151NCAM1_HUMAN363-413510--
1.17bENST0000031685117bENSE00001701392chr11:113102892-113103076185NCAM1_HUMAN413-474620--
1.18bENST0000031685118bENSE00001742465chr11:113103440-11310353697NCAM1_HUMAN475-507331A:486-4883
1.19bENST0000031685119bENSE00001680751chr11:113103869-113104039171NCAM1_HUMAN507-564581A:488-54558
1.20bENST0000031685120bENSE00001127020chr11:113105755-113105890136NCAM1_HUMAN564-609461A:545-58945
1.28cENST0000031685128cENSE00001127014chr11:113126600-113126723124NCAM1_HUMAN609-650420--
1.29eENST0000031685129eENSE00001795910chr11:113130868-113131045178NCAM1_HUMAN651-710600--
1.31cENST0000031685131cENSE00001723448chr11:113140910-113141117208NCAM1_HUMAN710-779700--
1.32ENST0000031685132ENSE00001694365chr11:113142482-113142598117NCAM1_HUMAN779-818400--
1.34hENST0000031685134hENSE00001382162chr11:113145989-1131491333145NCAM1_HUMAN818-857400--

(-) 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:104
 aligned with NCAM1_HUMAN | P13591 from UniProtKB/Swiss-Prot  Length:858

    Alignment length:104
                                   514       524       534       544       554       564       574       584       594       604    
          NCAM1_HUMAN   505 VQADTPSSPSIDQVEPYSSTAQVQFDEPEATGGVPILKYKAEWRAVGEEVWHSKWYDAKEASMEGIVTIVGLKPETTYAVRLAALNGKGLGEISAASEFKTQPV 608
               SCOP domains ---d2haza1 A:489-589 Neural cell adhesion molecule 1, NCAM                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeee....eeeeee...........eeeeeeee......eeeeeehhhhhhhheeee.......eeeeeeeeee..ee......eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----FN3  PDB: A:490-589 UniProt: 509-608                                                                 PROSITE
           Transcript 1 (1) 1.1--------------------------------------------------------Exon 1.20b  PDB: A:545-589 UniProt: 564-609   Transcript 1 (1)
           Transcript 1 (2) --Exon 1.19b  PDB: A:488-545 UniProt: 507-564               -------------------------------------------- Transcript 1 (2)
                 2haz A 486 SHMDTPSSPSIDQVEPYSSTAQVQFDEPEATGGVPILKYKAEWRAVGEEVWHSKWYDAKEASMEGIVTIVGLKPETTYAVRLAALNGKGLGEISAASEFKTQPV 589
                                   495       505       515       525       535       545       555       565       575       585    

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2HAZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HAZ)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NCAM1_HUMAN | P13591)
molecular function
    GO:0005088    Ras guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0001618    virus receptor activity    Combining with a virus component and mediating entry of the virus into the cell.
biological process
    GO:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    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:0060333    interferon-gamma-mediated signaling pathway    A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
    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:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0048167    regulation of synaptic plasticity    A process that modulates synaptic plasticity, the ability of synapses to change as circumstances require. They may alter function, such as increasing or decreasing their sensitivity, or they may increase or decrease in actual numbers.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0031225    anchored component of membrane    The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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
        NCAM1_HUMAN | P135912e3v 2vkw 2vkx 3mtr 5aea 5lkn

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