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(-) Description

Title :  CRYSTAL STRUCTURE OF APO GRANCALCIN
 
Authors :  J. Jia, Q. Han, N. Borregaard, K. Lollike, M. Cygler
Date :  08 Jun 00  (Deposition) - 27 Sep 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Penta-Ef-Hand Protein, Calcium Binding Protein, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Jia, Q. Han, N. Borregaard, K. Lollike, M. Cygler
Crystal Structure Of Human Grancalcin, A Member Of The Penta-Ef-Hand Protein Family.
J. Mol. Biol. V. 300 1271 2000
PubMed-ID: 10903868  |  Reference-DOI: 10.1006/JMBI.2000.3925
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GRANCALCIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX2T
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1F4Q)

(-) Sites  (0, 0)

(no "Site" information available for 1F4Q)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F4Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F4Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048657S80AGRAN_HUMANPolymorphism17783344A/BS80A
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.GRAN_HUMAN64-83
 
119-154
 
89-117
 		  6A:64-83
B:64-83
A:119-154
B:119-154
A:89-117
B:89-117
2EF_HAND_1PS00018 EF-hand calcium-binding domain.GRAN_HUMAN132-144
 		  2A:132-144
B:132-144

(-) Exons   (0, 0)

(no "Exon" information available for 1F4Q)

(-) 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:161
 aligned with GRAN_HUMAN | P28676 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:165
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212     
           GRAN_HUMAN    53 SVYTYFSAVAGQDGEVDAEELQRCLTQSGINGTYSPFSLETCRIMIAMLDRDHTGKMGFNAFKELWAALNAWKENFMTVDQDGSGTVEHHELRQAIGLMGYRLSPQTLTTIVKRYSKNGRIFFDDYVACCVKLRALTDFFRKRDHLQQGSANFIYDDFLQGTMAI 217
               SCOP domains d1f4qa_ A: Grancalcin                                                                                                                                                 SCOP domains
               CATH domains 1f4qA00 A:53-217 EF-hand                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh......hhhhhhhhhhhhh........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.----.eeehhhhhhhhhhh....hhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------A----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------EF_HAND_2           -----EF_HAND_2  PDB: A:89-117     -EF_HAND_2  PDB: A:119-154           --------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------EF_HAND_1    ------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f4q A  53 SVYTYFSAVAGQDGEVDAEELQRCLTQSGINGTYSPFSLETCRIMIAMLDRDHTGKMGFNAFKELWAALNAWKENFMTVD----GTVEHHELRQAIGLMGYRLSPQTLTTIVKRYSKNGRIFFDDYVACCVKLRALTDFFKKRDHLQQGSADFIYDDFLQGTMAI 217
                                    62        72        82        92       102       112       122       132    |  142       152       162       172       182       192       202       212     
                                                                                                         132  137                                                                                


Chain B from PDB  Type:PROTEIN  Length:165
 aligned with GRAN_HUMAN | P28676 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:165
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212     
           GRAN_HUMAN    53 SVYTYFSAVAGQDGEVDAEELQRCLTQSGINGTYSPFSLETCRIMIAMLDRDHTGKMGFNAFKELWAALNAWKENFMTVDQDGSGTVEHHELRQAIGLMGYRLSPQTLTTIVKRYSKNGRIFFDDYVACCVKLRALTDFFRKRDHLQQGSANFIYDDFLQGTMAI 217
               SCOP domains d1f4qb_ B: Grancalcin                                                                                                                                                 SCOP domains
               CATH domains 1f4qB00 B:53-217 EF-hand                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh......hhhhhhhhhhhhh........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhh....hhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------A----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------EF_HAND_2           -----EF_HAND_2  PDB: B:89-117     -EF_HAND_2  PDB: B:119-154           --------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------EF_HAND_1    ------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f4q B  53 SVYTYFSAVAGQDGEVDAEELQRCLTQSGINGTYSPFSLETCRIMIAMLDRDHTGKMGFNAFKELWAALNAWKENFMTVDQDGSGTVEHHELRQAIGLMGYRLSPQTLTTIVKRYSKNGRIFFDDYVACCVKLRALTDFFKKRDHLQQGSADFIYDDFLQGTMAI 217
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F4Q)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GRAN_HUMAN | P28676)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0004198    calcium-dependent cysteine-type endopeptidase activity    Catalysis of the hydrolysis of nonterminal peptide bonds in a polypeptide chain by a mechanism using a cysteine residue at the enzyme active center, and requiring the presence of calcium.
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0061025    membrane fusion    The membrane organization process that joins two lipid bilayers to form a single membrane.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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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  1f4q
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GRAN_HUMAN | P28676: 1f4o 1k94 1k95

(-) Related Entries Specified in the PDB File

1f4o GRANCALCIN WITH CALCIUM BOUND