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(-) Description

Title :  STRUCTURAL GENOMICS OF CAENORHABDITIS ELEGANS : CALMODULIN
 
Authors :  J. Symersky, G. Lin, S. Li, S. Qiu, C. -H. Luan, D. Luo, J. Tsao, M. Carson, L. Delucas, M. Luo, Southeast Collaboratory For Structural Genomics (Secsg)
Date :  03 Mar 03  (Deposition) - 25 Mar 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Calmodulin, Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Symersky, G. Lin, S. Li, S. Qiu, M. Carson, N. Schormann, M. Luo
Structural Genomics Of Caenorhabditis Elegans: Crystal Structure Of Calmodulin.
Proteins V. 53 947 2003
PubMed-ID: 14635136  |  Reference-DOI: 10.1002/PROT.10517
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CALMODULIN CMD-1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST 17.1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:21 , ASP A:23 , ASP A:25 , THR A:27 , GLU A:32 , ASP A:119BINDING SITE FOR RESIDUE CA A 1001
2AC2SOFTWAREASP A:57 , ASP A:59 , ASN A:61 , THR A:63 , GLU A:68 , HOH A:2001 , HOH A:2018BINDING SITE FOR RESIDUE CA A 1002
3AC3SOFTWAREASP A:94 , ASP A:96 , ASN A:98 , PHE A:100 , GLU A:105 , HOH A:2071BINDING SITE FOR RESIDUE CA A 1003
4AC4SOFTWAREASP A:130 , ASP A:132 , ASP A:134 , GLN A:136 , GLU A:141 , HOH A:2075BINDING SITE FOR RESIDUE CA A 1004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CALM_CAEEL8-43
44-79
81-116
117-149		  4A:8-43
A:44-79
A:81-116
A:117-146
2EF_HAND_1PS00018 EF-hand calcium-binding domain.CALM_CAEEL21-33
57-69
94-106
130-142		  4A:21-33
A:57-69
A:94-106
A:130-142

(-) Exons   (0, 0)

(no "Exon" information available for 1OOJ)

(-) 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:141
 aligned with CALM_CAEEL | O16305 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:141
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145 
           CALM_CAEEL     6 TEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGFISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVTMM 146
               SCOP domains d1ooja_ A: Calmodulin                                                                                                                         SCOP domains
               CATH domains 1oojA01 A:6-79 EF-hand                                                    1oojA02 A:80-146 EF-hand                                            CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------EF_hand_5-1oojA01 A:85-146                                     Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------EF_hand_5-1oojA02 A:85-146                                     Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhh.....eehhhhhhhhhhhh....hhhhhhhhhhh........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhh.....hhhhhhhhhhhhh......eehhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --EF_HAND_2  PDB: A:8-43 UniProt: 8-43EF_HAND_2  PDB: A:44-79             -EF_HAND_2  PDB: A:81-116            EF_HAND_2  PDB: A:117-146      PROSITE (1)
                PROSITE (2) ---------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ---- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ooj A   6 TEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGFISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVTMM 146
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145
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  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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: EF_hand (270)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CALM_CAEEL | O16305)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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).
biological process
    GO:0043277    apoptotic cell clearance    The recognition and removal of an apoptotic cell by a neighboring cell or by a phagocyte.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0009792    embryo development ending in birth or egg hatching    The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell.
    GO:0051296    establishment of meiotic spindle orientation    Any process that set the alignment of meiotic spindle relative to other cellular structures.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
    GO:0032880    regulation of protein localization    Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.
cellular component
    GO:0071944    cell periphery    The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0072686    mitotic spindle    A spindle that forms as part of mitosis. Mitotic and meiotic spindles contain distinctive complements of proteins associated with microtubules.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.

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  1ooj
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 Related Entries

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

UniProtKB/Swiss-Prot
        CALM_CAEEL | O16305: 5h7d

(-) Related Entries Specified in the PDB File

1cll
1clm
1exr RELATED ID: T21H3.3 RELATED DB: TARGETDB
4cln