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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TWO N-TERMINAL IMMUNOGLOBULIN DOMAINS OF THE NEURAL CELL ADHESION MOLECULE (NCAM)
 
Authors :  C. Kasper, H. Rasmussen, J. S. Kastrup, S. Ikemizu, E. Y. Jones, V. Berezin, E. Bock, I. K. Larsen
Date :  29 Mar 00  (Deposition) - 09 Oct 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Ncam, Immunoglobulin Fold, Glycoprotein, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Kasper, H. Rasmussen, J. S. Kastrup, S. Ikemizu, E. Y. Jones, V. Berezin, E. Bock, I. K. Larsen
Structural Basis Of Cell-Cell Adhesion By Ncam.
Nat. Struct. Biol. V. 7 389 2000
PubMed-ID: 10802736  |  Reference-DOI: 10.1038/75165
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (NEURAL CELL ADHESION MOLECULE)
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPHIL-S1
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL IG DOMAIN
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymNCAM

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU C:82 , HOH C:5140 , HOH C:5141 , HOH C:5270 , HOH C:5324BINDING SITE FOR RESIDUE CA C 5001

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:77
2A:120 -A:170
3B:22 -B:77
4B:120 -B:170
5C:22 -C:77
6C:120 -C:170
7D:22 -D:77
8D:120 -D:170

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Val A:6 -Pro A:7
2Thr A:106 -Pro A:107
3Val B:6 -Pro B:7
4Thr B:106 -Pro B:107
5Val C:6 -Pro C:7
6Thr C:106 -Pro C:107
7Val D:6 -Pro D:7
8Thr D:106 -Pro D:107

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1EPF)

(-) Exons   (0, 0)

(no "Exon" information available for 1EPF)

(-) 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:189
 aligned with NCAM1_RAT | P13596 from UniProtKB/Swiss-Prot  Length:858

    Alignment length:189
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199         
            NCAM1_RAT    20 LQVDIVPSQGEISVGESKFFLCQVAGDAKDKDISWFSPNGEKLSPNQQRISVVWNDDDSSTLTIYNANIDDAGIYKCVVTAEDGTQSEATVNVKIFQKLMFKNAPTPQEFKEGEDAVIVCDVVSSLPPTIIWKHKGRDVILKKDVRFIVLSNNYLQIRGIKKTDEGTYRCEGRILARGEINFKDIQVIV 208
               SCOP domains d1epfa1 A:1-97 Neural cell adhesion molecule (NCAM)                                              d1epfa2 A:98-189 Neural cell adhesion molecule (NCAM)                                        SCOP domains
               CATH domains 1epfA01 A:1-96 Immunoglobulins                                                                  1epfA02 A:97-189 Immunoglobulins                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeee....eeeeeee......eeeeee.....ee......eeeeeee..eeeeee...hhhhheeeeeeeee....eeeeeeeeeee...eeee....ee......eee..eee.....eeeeee..ee.hhhh...eee.....eee...hhhhheeeeeeeeehhhheeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1epf A   1 LQVDIVPSQGEISVGESKFFLCQVAGDAKDKDISWFSPNGEKLSPNQQRISVVWNDDDSSTLTIYNANIDDAGIYKCVVTAEDGTQSEATVNVKIFQKLMFKNAPTPQEFKEGEDAVIVCDVVSSLPPTIIWKHKGRDVILKKDVRFIVLSNNYLQIRGIKKTDEGTYRCEGRILARGEINFKDIQVIV 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         

Chain B from PDB  Type:PROTEIN  Length:191
 aligned with NCAM1_RAT | P13596 from UniProtKB/Swiss-Prot  Length:858

    Alignment length:191
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207 
            NCAM1_RAT    18 VSLQVDIVPSQGEISVGESKFFLCQVAGDAKDKDISWFSPNGEKLSPNQQRISVVWNDDDSSTLTIYNANIDDAGIYKCVVTAEDGTQSEATVNVKIFQKLMFKNAPTPQEFKEGEDAVIVCDVVSSLPPTIIWKHKGRDVILKKDVRFIVLSNNYLQIRGIKKTDEGTYRCEGRILARGEINFKDIQVIV 208
               SCOP domains d1epfb1 B:-1-97 Neural cell adhesion molecule (NCAM)                                               d1epfb2 B:98-189 Neural cell adhesion molecule (NCAM)                                        SCOP domains
               CATH domains --1epfB01 B:1-96 Immunoglobulins                                                                  1epfB02 B:97-189 Immunoglobulins                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..eeeee....eeeeeeee......eeeee.............eeeeeee..eeeeee...hhhhheeeeeeee.....eeeeeeeeeee...eeee....ee......eee..eee.....eeeeee..ee.hhhh...eee.....eee...hhhhheeeeeeee......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1epf B  -1 RVLQVDIVPSQGEISVGESKFFLCQVAGDAKDKDISWFSPNGEKLSPNQQRISVVWNDDDSSTLTIYNANIDDAGIYKCVVTAEDGTQSEATVNVKIFQKLMFKNAPTPQEFKEGEDAVIVCDVVSSLPPTIIWKHKGRDVILKKDVRFIVLSNNYLQIRGIKKTDEGTYRCEGRILARGEINFKDIQVIV 189
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188 

Chain C from PDB  Type:PROTEIN  Length:190
 aligned with NCAM1_RAT | P13596 from UniProtKB/Swiss-Prot  Length:858

    Alignment length:190
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208
            NCAM1_RAT    19 SLQVDIVPSQGEISVGESKFFLCQVAGDAKDKDISWFSPNGEKLSPNQQRISVVWNDDDSSTLTIYNANIDDAGIYKCVVTAEDGTQSEATVNVKIFQKLMFKNAPTPQEFKEGEDAVIVCDVVSSLPPTIIWKHKGRDVILKKDVRFIVLSNNYLQIRGIKKTDEGTYRCEGRILARGEINFKDIQVIV 208
               SCOP domains d1epfc1 C:0-97 Neural cell adhesion molecule (NCAM)                                               d1epfc2 C:98-189 Neural cell adhesion molecule (NCAM)                                        SCOP domains
               CATH domains -1epfC01 C:1-96 Immunoglobulins                                                                  1epfC02 C:97-189 Immunoglobulins                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeee..................eeeee...............................hhhhheeeeeeee.....eeeeeeeeeee...eeee............eee..eee................hhhh...eee.....eee...hhhhh........................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1epf C   0 VLQVDIVPSQGEISVGESKFFLCQVAGDAKDKDISWFSPNGEKLSPNQQRISVVWNDDDSSTLTIYNANIDDAGIYKCVVTAEDGTQSEATVNVKIFQKLMFKNAPTPQEFKEGEDAVIVCDVVSSLPPTIIWKHKGRDVILKKDVRFIVLSNNYLQIRGIKKTDEGTYRCEGRILARGEINFKDIQVIV 189
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189

Chain D from PDB  Type:PROTEIN  Length:191
 aligned with NCAM1_RAT | P13596 from UniProtKB/Swiss-Prot  Length:858

    Alignment length:191
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207 
            NCAM1_RAT    18 VSLQVDIVPSQGEISVGESKFFLCQVAGDAKDKDISWFSPNGEKLSPNQQRISVVWNDDDSSTLTIYNANIDDAGIYKCVVTAEDGTQSEATVNVKIFQKLMFKNAPTPQEFKEGEDAVIVCDVVSSLPPTIIWKHKGRDVILKKDVRFIVLSNNYLQIRGIKKTDEGTYRCEGRILARGEINFKDIQVIV 208
               SCOP domains d1epfd1 D:-1-97 Neural cell adhesion molecule (NCAM)                                               d1epfd2 D:98-189 Neural cell adhesion molecule (NCAM)                                        SCOP domains
               CATH domains --1epfD01 D:1-96 Immunoglobulins                                                                  1epfD02 D:97-189 Immunoglobulins                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee..................eeeee...............................hhhhheeeeeeee.....eeeeeeeeeee...eeee............eee..eee................hhhh...eee.....eee...hhhhh.........hhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1epf D  -1 RVLQVDIVPSQGEISVGESKFFLCQVAGDAKDKDISWFSPNGEKLSPNQQRISVVWNDDDSSTLTIYNANIDDAGIYKCVVTAEDGTQSEATVNVKIFQKLMFKNAPTPQEFKEGEDAVIVCDVVSSLPPTIIWKHKGRDVILKKDVRFIVLSNNYLQIRGIKKTDEGTYRCEGRILARGEINFKDIQVIV 189
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188 

   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, 8)

Asymmetric Unit

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
1a1epfA01A:1-96
1b1epfB01B:1-96
1c1epfC01C:1-96
1d1epfD01D:1-96
1e1epfA02A:97-189
1f1epfB02B:97-189
1g1epfC02C:97-189
1h1epfD02D:97-189

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EPF)

(-) Gene Ontology  (31, 31)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (NCAM1_RAT | P13596)
molecular function
    GO:0030275    LRR domain binding    Interacting selectively and non-covalently with a LRR domain (leucine rich repeats) of a protein.
    GO:0008092    cytoskeletal protein binding    Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
    GO:0005104    fibroblast growth factor receptor binding    Interacting selectively and non-covalently with the fibroblast growth factor receptor (FGFR).
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0019902    phosphatase binding    Interacting selectively and non-covalently with any phosphatase.
    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:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0031100    animal organ regeneration    The regrowth of a lost or destroyed animal organ.
    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:0016338    calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules    The attachment of one cell to another cell via adhesion molecules that do not require the presence of calcium for the interaction.
    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:0071241    cellular response to inorganic substance    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an inorganic substance stimulus.
    GO:0071219    cellular response to molecule of bacterial origin    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by molecules of bacterial origin such as peptides derived from bacterial flagellin.
    GO:0007611    learning or memory    The acquisition and processing of information and/or the storage and retrieval of this information over time.
    GO:0033555    multicellular organismal response to stress    Any process that results in a change in state or activity of a multicellular organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
    GO:0060548    negative regulation of cell death    Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
    GO:0048666    neuron development    The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
    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:0014012    peripheral nervous system axon regeneration    The regrowth of axons outside the central nervous system (outside the brain and spinal cord) following an axonal injury.
    GO:0060045    positive regulation of cardiac muscle cell proliferation    Any process that activates or increases the frequency, rate or extent of cardiac muscle cell proliferation.
    GO:0051930    regulation of sensory perception of pain    Any process that modulates the frequency, rate or extent of the sensory perception of pain, the series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal.
    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:0042220    response to cocaine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cocaine stimulus. Cocaine is a crystalline alkaloid obtained from the leaves of the coca plant.
    GO:0010035    response to inorganic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an inorganic substance stimulus.
    GO:0010288    response to lead ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lead ion stimulus.
    GO:0021794    thalamus development    The process in which the thalamus changes over time, from its initial formation to its mature state.
cellular component
    GO:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    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:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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_RAT | P135961lwr 1qz1

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1EPF)