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(-) Description

Title :  HUMAN NCAM, FN3 DOMAINS 1 AND 2
 
Authors :  F. Carafoli, J. L. Saffell, E. Hohenester
Date :  04 Jan 08  (Deposition) - 26 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Adhesion Receptor, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Carafoli, J. L. Saffell, E. Hohenester
Structure Of The Tandem Fibronectin Type 3 Domains Of Neural Cell Adhesion Molecule
J. Mol. Biol. V. 377 524 2008
PubMed-ID: 18261743  |  Reference-DOI: 10.1016/J.JMB.2008.01.030

(-) Compounds

Molecule 1 - NEURAL CELL ADHESION MOLECULE 1,140 KDA ISOFORM
    ChainsA, B
    EngineeredYES
    Expression SystemHUMAN
    Expression System Cell Line293-EBNA
    Expression System Taxid9606
    Expression System VectorPCEP-PU
    FragmentFN3 DOMAINS, RESIDUES 496-598,601-692
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymN-CAM 140, NCAM-140, CD56 ANTIGEN, NEURAL CELL ADHESION MOLECULE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:534 , TRP A:549 , ARG A:639 , LYS B:532 , ASP B:551 , HOH B:2044 , HOH B:2045BINDING SITE FOR RESIDUE SO4 B1692
2AC2SOFTWARELYS A:548 , TRP A:549 , LYS B:548 , TRP B:549 , HOH B:2046 , HOH B:2047BINDING SITE FOR RESIDUE SO4 B1693
3AC3SOFTWARELYS A:532 , ASP A:551 , HOH A:2051 , TRP B:549 , ARG B:639BINDING SITE FOR RESIDUE SO4 A1693
4AC4SOFTWAREARG B:637BINDING SITE FOR RESIDUE SO4 B1694
5AC5SOFTWAREHIS B:546 , SER B:547BINDING SITE FOR RESIDUE SO4 B1695

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049961E679DNCAM1_HUMANPolymorphism17115280A/BE668D

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

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FN3PS50853 Fibronectin type-III domain profile.NCAM1_HUMAN509-608
 
611-706
 
  4A:499-598
B:499-598
A:600-693
B:600-691

(-) Exons   (5, 10)

Asymmetric/Biological Unit (5, 10)
 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_HUMAN475-507332A:496-497
B:497-497
2
1
1.19bENST0000031685119bENSE00001680751chr11:113103869-113104039171NCAM1_HUMAN507-564582A:497-554
B:497-554
58
58
1.20bENST0000031685120bENSE00001127020chr11:113105755-113105890136NCAM1_HUMAN564-609462A:554-599
B:554-599
46
46
1.28cENST0000031685128cENSE00001127014chr11:113126600-113126723124NCAM1_HUMAN609-650422A:599-639 (gaps)
B:599-639 (gaps)
42
42
1.29eENST0000031685129eENSE00001795910chr11:113130868-113131045178NCAM1_HUMAN651-710602A:640-693
B:640-692
54
53
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:198
 aligned with NCAM1_HUMAN | P13591 from UniProtKB/Swiss-Prot  Length:858

    Alignment length:199
                                   515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695         
          NCAM1_HUMAN   506 QADTPSSPSIDQVEPYSSTAQVQFDEPEATGGVPILKYKAEWRAVGEEVWHSKWYDAKEASMEGIVTIVGLKPETTYAVRLAALNGKGLGEISAASEFKTQPVQGEPSAPKLEGQMGEDGNSIKVNLIKQDDGGSPIRHYLVRYRALSSEWKPEIRLPSGSDHVMLKSLDWNAEYEVYVVAENQQGKSKAAHFVFRTSA 704
               SCOP domains --d2vkwa1 A:498-598 Neural cell adhesion molecule 1, NCAM                                              ---d2vkwa2 A:601-693 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.....-.....eeeeee......eeeeee..........eeeeeeee........eee.....eeee.......eeeeeeeeee..ee...eeeeee... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------- SAPs(SNPs)
                    PROSITE ---FN3  PDB: A:499-598 UniProt: 509-608                                                                --FN3  PDB: A:600-693 UniProt: 611-706                                                           PROSITE
           Transcript 1 (1) 1.--------------------------------------------------------Exon 1.20b  PDB: A:554-599 UniProt: 564-609   -----------------------------------------Exon 1.29e  PDB: A:640-693 UniProt: 651-710            Transcript 1 (1)
           Transcript 1 (2) -Exon 1.19b  PDB: A:497-554 UniProt: 507-564               --------------------------------------------Exon 1.28c  PDB: A:599-639 (gaps)         ------------------------------------------------------ Transcript 1 (2)
                 2vkw A 496 QADTPSSPSIDQVEPYSSTAQVQFDEPEATGGVPILKYKAEWRAVGEEVWHSKWYDAKEASMEGIVTIVGLKPETTYAVRLAALNGKGLGEISAASEFKTQPVR-EPSAPKLEGQMGEDGNSIKVNLIKQDDGGSPIRHYLVRYRALSSEWKPEIRLPSGSDHVMLKSLDWNAEYEVYVVAENQQGKSKAAHFVFRTAA 693
                                   505       515       525       535       545       555       565       575       585       595   | | 604       614       624       634       644       654       664       674       684         
                                                                                                                                 599 |                                                                                             
                                                                                                                                   600                                                                                             

Chain B from PDB  Type:PROTEIN  Length:196
 aligned with NCAM1_HUMAN | P13591 from UniProtKB/Swiss-Prot  Length:858

    Alignment length:197
                                   516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       
          NCAM1_HUMAN   507 ADTPSSPSIDQVEPYSSTAQVQFDEPEATGGVPILKYKAEWRAVGEEVWHSKWYDAKEASMEGIVTIVGLKPETTYAVRLAALNGKGLGEISAASEFKTQPVQGEPSAPKLEGQMGEDGNSIKVNLIKQDDGGSPIRHYLVRYRALSSEWKPEIRLPSGSDHVMLKSLDWNAEYEVYVVAENQQGKSKAAHFVFRTS 703
               SCOP domains -d2vkwb1 B:498-598 Neural cell adhesion molecule 1, NCAM                                              ---d2vkwb2 B:601-692 Neural cell adhesion molecule 1, NCAM                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------fn3-2vkwB01 B:600-685                                                                 ------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------fn3-2vkwB02 B:600-685                                                                 ------- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------fn3-2vkwB03 B:600-685                                                                 ------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------fn3-2vkwB04 B:600-685                                                                 ------- Pfam domains (4)
         Sec.struct. author .......eeeeeee....eeeeee.........eeeeeeeeee......eeeeeehhhhhhhh.eee.......eeeeeeeeee..ee......eeee.....-.....eeeeee......eeeeee........eeeeeeeeee........eeee....eeee.......eeeeeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------ SAPs(SNPs)
                    PROSITE --FN3  PDB: B:499-598 UniProt: 509-608                                                                --FN3  PDB: B:600-691 UniProt: 611-706                                                          PROSITE
           Transcript 1 (1) 1--------------------------------------------------------Exon 1.20b  PDB: B:554-599 UniProt: 564-609   -----------------------------------------Exon 1.29e  PDB: B:640-692 UniProt: 651-710           Transcript 1 (1)
           Transcript 1 (2) Exon 1.19b  PDB: B:497-554 UniProt: 507-564               --------------------------------------------Exon 1.28c  PDB: B:599-639 (gaps)         ----------------------------------------------------- Transcript 1 (2)
                 2vkw B 497 ADTPSSPSIDQVEPYSSTAQVQFDEPEATGGVPILKYKAEWRAVGEEVWHSKWYDAKEASMEGIVTIVGLKPETTYAVRLAALNGKGLGEISAASEFKTQPVR-EPSAPKLEGQMGEDGNSIKVNLIKQDDGGSPIRHYLVRYRALSSEWKPEIRLPSGSDHVMLKSLDWNAEYEVYVVAENQQGKSKAAHFVFRTA 692
                                   506       516       526       536       546       556       566       576       586       596  | |  605       615       625       635       645       655       665       675       685       
                                                                                                                                599 |                                                                                            
                                                                                                                                  600                                                                                            

   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/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: E-set (290)
(-)
Family: fn3 (66)
1afn3-2vkwB01B:600-685
1bfn3-2vkwB02B:600-685
1cfn3-2vkwB03B:600-685
1dfn3-2vkwB04B:600-685

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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 2haz 2vkx 3mtr 5aea 5lkn

(-) Related Entries Specified in the PDB File

2vkx HUMAN NCAM, FN3 DOMAINS 1 AND 2, M610R MUTANT