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(-) Description

Title :  CRYSTAL STRUCTURE OF RECOMBINANT BOVINE NEUROCALCIN DELTA AT 2.4 ANGSTROMS
 
Authors :  S. Vijay-Kumar, V. D. Kumar
Date :  25 Jun 98  (Deposition) - 22 Jul 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Calcium-Binding, Myristoylation, Neuronal Specific Guanylate Cyclase Activator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Vijay-Kumar, V. D. Kumar
Crystal Structure Of Recombinant Bovine Neurocalcin.
Nat. Struct. Biol. V. 6 80 1999
PubMed-ID: 9886296  |  Reference-DOI: 10.1038/4956
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEUROCALCIN DELTA
    Cellular Location: CYTOPLASM
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-C
    Expression System Taxid: 562
    Organism Common: CATTLE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Strain: DH5-ALPHA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:73 , ASN A:75 , ASP A:77 , THR A:79 , GLU A:84 , HOH A:505BINDING SITE FOR RESIDUE CA A 402
2AC2SOFTWAREASP A:109 , ASP A:111 , ASN A:113 , TYR A:115 , GLU A:120 , HOH A:587BINDING SITE FOR RESIDUE CA A 403
3AC3SOFTWAREASP A:157 , ASN A:159 , ASP A:161 , LYS A:163 , GLU A:168 , HOH A:513BINDING SITE FOR RESIDUE CA A 404
4AC4SOFTWAREASP B:73 , ASN B:75 , ASP B:77 , THR B:79 , GLU B:84 , HOH B:506BINDING SITE FOR RESIDUE CA B 406
5AC5SOFTWAREASP B:109 , ASP B:111 , ASN B:113 , TYR B:115 , GLU B:120 , HOH B:616BINDING SITE FOR RESIDUE CA B 407
6AC6SOFTWAREASP B:157 , ASN B:159 , ASP B:161 , LYS B:163 , GLU B:168 , HOH B:507BINDING SITE FOR RESIDUE CA B 408

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BJF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BJF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 14)

Asymmetric/Biological Unit (2, 14)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.NCALD_BOVIN40-58
 
60-95
 
96-131
 
144-179
 		  8A:40-58
B:40-58
A:60-95
B:60-95
A:96-131
B:96-131
A:144-179
B:144-179
2EF_HAND_1PS00018 EF-hand calcium-binding domain.NCALD_BOVIN73-85
 
109-121
 
157-169
 		  6A:73-85
B:73-85
A:109-121
B:109-121
A:157-169
B:157-169

(-) Exons   (0, 0)

(no "Exon" information available for 1BJF)

(-) 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:181
 aligned with NCALD_BOVIN | P61602 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:181
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184 
          NCALD_BOVIN     5 NSKLRPEVMQDLLESTDFTEHEIQEWYKGFLRDCPSGHLSMEEFKKIYGNFFPYGDASKFAEHVFRTFDANGDGTIDFREFIIALSVTSRGKLEQKLKWAFSMYDLDGNGYISKAEMLEIVQAIYKMVSSVMKMPEDESTPEKRTEKIFRQMDTNRDGKLSLEEFIRGAKSDPSIVRLLQC 185
               SCOP domains d1bjfa_ A: Neurocalcin                                                                                                                                                                SCOP domains
               CATH domains ----1bjfA01 A:9-96 EF-hand                                                                  1bjfA02 A:97-185 EF-hand                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh....hhhhhhhhhhhhhh....eeehhhhhhhhhh.......hhhhhhhhhhh......eeehhhhhhhhhhh....hhhhhhhhhhhh.........hhhhhhhhhhhh..........hhh..hhhhhhhhhhh..........hhhhhhhhhh..hhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------EF_HAND_2          -EF_HAND_2  PDB: A:60-95             EF_HAND_2  PDB: A:96-131            ------------EF_HAND_2  PDB: A:144-179           ------ PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------EF_HAND_1    -----------------------EF_HAND_1    -----------------------------------EF_HAND_1    ---------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bjf A   5 NSKLRPEVMQDLLESTDFTEHEIQEWYKGFLRDCPSGHLSMEEFKKIYGNFFPYGDASKFAEHVFRTFDANGDGTIDFREFIIALSVTSRGKLEQKLKWAFSMYDLDGNGYISKAEMLEIVQAIYKMVSSVMKMPEDESTPEKRTEKIFRQMDTNRDGKLSLEEFIRGAKSDPSIVRLLQC 185
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184 


Chain B from PDB  Type:PROTEIN  Length:181
 aligned with NCALD_BOVIN | P61602 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:181
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184 
          NCALD_BOVIN     5 NSKLRPEVMQDLLESTDFTEHEIQEWYKGFLRDCPSGHLSMEEFKKIYGNFFPYGDASKFAEHVFRTFDANGDGTIDFREFIIALSVTSRGKLEQKLKWAFSMYDLDGNGYISKAEMLEIVQAIYKMVSSVMKMPEDESTPEKRTEKIFRQMDTNRDGKLSLEEFIRGAKSDPSIVRLLQC 185
               SCOP domains d1bjfb_ B: Neurocalcin                                                                                                                                                                SCOP domains
               CATH domains ----1bjfB01 B:9-96 EF-hand                                                                  1bjfB02 B:97-185 EF-hand                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh....hhhhhhhhhhhhhh....eeehhhhhhhhhh.......hhhhhhhhhhh......eeehhhhhhhhhhh....hhhhhhhhhhhh.........hhhhhhhhhhhhhh.............hhhhhhhhhhh..........hhhhhhhhhh.hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------EF_HAND_2          -EF_HAND_2  PDB: B:60-95             EF_HAND_2  PDB: B:96-131            ------------EF_HAND_2  PDB: B:144-179           ------ PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------EF_HAND_1    -----------------------EF_HAND_1    -----------------------------------EF_HAND_1    ---------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bjf B   5 NSKLRPEVMQDLLESTDFTEHEIQEWYKGFLRDCPSGHLSMEEFKKIYGNFFPYGDASKFAEHVFRTFDANGDGTIDFREFIIALSVTSRGKLEQKLKWAFSMYDLDGNGYISKAEMLEIVQAIYKMVSSVMKMPEDESTPEKRTEKIFRQMDTNRDGKLSLEEFIRGAKSDPSIVRLLQC 185
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184
   Legend:   → Mismatch (orange background)
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  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, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NCALD_BOVIN | P61602)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0030276    clathrin binding    Interacting selectively and non-covalently with a clathrin heavy or light chain, the main components of the coat of coated vesicles and coated pits, and which also occurs in synaptic vesicles.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0015631    tubulin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of tubulin, including microtubules.
biological process
    GO:0019722    calcium-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via calcium ions.
    GO:0003073    regulation of systemic arterial blood pressure    The process that modulates the force with which blood travels through the systemic arterial circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
cellular component
    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: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.

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