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(-) Description

Title :  CRYSTAL STRUCTURE AND TRIMER-MONOMER TRANSITION OF N-TERMINAL DOMAIN OF EHCABP1 FROM ENTAMOEBA HISTOLYTICA
 
Authors :  S. Kumar, E. Ahmad, S. Kumar, M. S. Mansuri, R. H. Khan, G. Samudrala
Date :  24 Jan 10  (Deposition) - 02 Feb 10  (Release) - 30 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,D,G,J
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  D  (3x)
Biol. Unit 3:  G  (3x)
Biol. Unit 4:  J  (3x)
Keywords :  Calcium Binding Protein, Calcium Signaling Protein, Assembled-Domain, Free Energy, Dynamic Behaviour, Cytoskeleton, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kumar, E. Ahmad, M. S. Mansuri, S. Kumar, R. Jain, R. H. Khan, S. Gourinath
Crystal Structure And Trimer-Monomer Transition Of N-Terminal Domain Of Ehcabp1 From Entamoeba Histolytica
Biophys. J. V. 98 2933 2010
PubMed-ID: 20550906  |  Reference-DOI: 10.1016/J.BPJ.2010.03.048

(-) Compounds

Molecule 1 - CALCIUM-BINDING PROTEIN
    Chains: A, D, G, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN, RESIDUES 1-66
    Gene: EHCABP1
    Organism Scientific: ENTAMOEBA HISTOLYTICA
    Organism Taxid: 294381
    Synonym: CALCIUM BINDING PROTEIN-1, CABP

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ADGJ
Biological Unit 1 (3x): A   
Biological Unit 2 (3x):  D  
Biological Unit 3 (3x):   G 
Biological Unit 4 (3x):    J

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1CA8Ligand/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
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:10 , ASN A:12 , ASP A:14 , ALA A:16 , GLU A:21 , HOH A:71BINDING SITE FOR RESIDUE CA A 149
2AC2SOFTWAREASP A:46 , ASP A:48 , ASN A:50 , GLU A:52 , ASP A:54 , GLU A:57 , HOH A:75BINDING SITE FOR RESIDUE CA A 150
3AC3SOFTWAREASP D:10 , ASN D:12 , ASP D:14 , ALA D:16 , GLU D:21 , HOH D:82BINDING SITE FOR RESIDUE CA D 149
4AC4SOFTWAREASP D:46 , ASP D:48 , ASN D:50 , GLU D:52 , GLU D:57 , HOH D:70BINDING SITE FOR RESIDUE CA D 150
5AC5SOFTWAREASP G:10 , ASN G:12 , ASP G:14 , ALA G:16 , GLU G:21 , HOH G:81BINDING SITE FOR RESIDUE CA G 149
6AC6SOFTWAREASP G:46 , ASP G:48 , ASN G:50 , GLU G:52 , GLU G:57 , HOH G:67BINDING SITE FOR RESIDUE CA G 150
7AC7SOFTWAREASP J:10 , ASN J:12 , ASP J:14 , ALA J:16 , GLU J:21 , HOH J:81BINDING SITE FOR RESIDUE CA J 149
8AC8SOFTWAREASP J:46 , ASP J:48 , ASN J:50 , GLU J:52 , GLU J:57 , HOH J:82BINDING SITE FOR RESIDUE CA J 150

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LI6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly J:63 -Ser J:64
2Ser J:64 -Ile J:65

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LI6)

(-) PROSITE Motifs  (2, 12)

Asymmetric Unit (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CALBP_ENTHI1-32
33-68
 
 
 
72-107
108-134		  4-
A:33-65
D:33-66
G:33-65
J:33-65
-
-
2EF_HAND_1PS00018 EF-hand calcium-binding domain.CALBP_ENTHI10-22
 
 
 
46-58
 
 
 
85-97
117-129		  8A:10-22
D:10-22
G:10-22
J:10-22
A:46-58
D:46-58
G:46-58
J:46-58
-
-
Biological Unit 1 (2, 9)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CALBP_ENTHI1-32
33-68
 
 
 
72-107
108-134		  3-
A:33-65
-
-
-
-
-
2EF_HAND_1PS00018 EF-hand calcium-binding domain.CALBP_ENTHI10-22
 
 
 
46-58
 
 
 
85-97
117-129		  6A:10-22
-
-
-
A:46-58
-
-
-
-
-
Biological Unit 2 (2, 9)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CALBP_ENTHI1-32
33-68
 
 
 
72-107
108-134		  3-
-
D:33-66
-
-
-
-
2EF_HAND_1PS00018 EF-hand calcium-binding domain.CALBP_ENTHI10-22
 
 
 
46-58
 
 
 
85-97
117-129		  6-
D:10-22
-
-
-
D:46-58
-
-
-
-
Biological Unit 3 (2, 9)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CALBP_ENTHI1-32
33-68
 
 
 
72-107
108-134		  3-
-
-
G:33-65
-
-
-
2EF_HAND_1PS00018 EF-hand calcium-binding domain.CALBP_ENTHI10-22
 
 
 
46-58
 
 
 
85-97
117-129		  6-
-
G:10-22
-
-
-
G:46-58
-
-
-
Biological Unit 4 (2, 9)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CALBP_ENTHI1-32
33-68
 
 
 
72-107
108-134		  3-
-
-
-
J:33-65
-
-
2EF_HAND_1PS00018 EF-hand calcium-binding domain.CALBP_ENTHI10-22
 
 
 
46-58
 
 
 
85-97
117-129		  6-
-
-
J:10-22
-
-
-
J:46-58
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 3LI6)

(-) 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:64
 aligned with CALBP_ENTHI | P38505 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:64
                                    11        21        31        41        51        61    
           CALBP_ENTHI    2 AEALFKEIDVNGDGAVSYEEVKAFVSKKRAIKNEQLLQLIFKSIDADGNGEIDQNEFAKFYGSI 65
               SCOP domains d3li6a_ A: automated matches                                     SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) EF_HAND_2  PDB: - UniProt: 1-32EF_HAND_2  PDB: A:33-65           PROSITE (1)
                PROSITE (2) --------EF_HAND_1    -----------------------EF_HAND_1    ------- PROSITE (2)
                 Transcript ---------------------------------------------------------------- Transcript
                  3li6 A  2 AEALFKEIDVNGDGAVSYEEVKAFVSKKRAIKNEQLLQLIFKSIDADGNGEIDQNEFAKFYGSI 65
                                    11        21        31        41        51        61    


Chain D from PDB  Type:PROTEIN  Length:65
 aligned with CALBP_ENTHI | P38505 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:65
                                    11        21        31        41        51        61     
           CALBP_ENTHI    2 AEALFKEIDVNGDGAVSYEEVKAFVSKKRAIKNEQLLQLIFKSIDADGNGEIDQNEFAKFYGSIQ 66
               SCOP domains d3li6d_ D: automated matches                                      SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) EF_HAND_2  PDB: - UniProt: 1-32EF_HAND_2  PDB: D:33-66            PROSITE (1)
                PROSITE (2) --------EF_HAND_1    -----------------------EF_HAND_1    -------- PROSITE (2)
                 Transcript ----------------------------------------------------------------- Transcript
                  3li6 D  2 AEALFKEIDVNGDGAVSYEEVKAFVSKKRAIKNEQLLQLIFKSIDADGNGEIDQNEFAKFYGSIQ 66
                                    11        21        31        41        51        61     


Chain G from PDB  Type:PROTEIN  Length:64
 aligned with CALBP_ENTHI | P38505 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:64
                                    11        21        31        41        51        61    
           CALBP_ENTHI    2 AEALFKEIDVNGDGAVSYEEVKAFVSKKRAIKNEQLLQLIFKSIDADGNGEIDQNEFAKFYGSI 65
               SCOP domains d3li6g_ G: automated matches                                     SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) EF_HAND_2  PDB: - UniProt: 1-32EF_HAND_2  PDB: G:33-65           PROSITE (1)
                PROSITE (2) --------EF_HAND_1    -----------------------EF_HAND_1    ------- PROSITE (2)
                 Transcript ---------------------------------------------------------------- Transcript
                  3li6 G  2 AEALFKEIDVNGDGAVSYEEVKAFVSKKRAIKNEQLLQLIFKSIDADGNGEIDQNEFAKFYGSI 65
                                    11        21        31        41        51        61    


Chain J from PDB  Type:PROTEIN  Length:64
 aligned with CALBP_ENTHI | P38505 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:64
                                    11        21        31        41        51        61    
           CALBP_ENTHI    2 AEALFKEIDVNGDGAVSYEEVKAFVSKKRAIKNEQLLQLIFKSIDADGNGEIDQNEFAKFYGSI 65
               SCOP domains d3li6j_ J: automated matches                                     SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
           Pfam domains (1) efhand-3li6J01 J:2-29       ------------------------------------ Pfam domains (1)
           Pfam domains (2) efhand-3li6J02 J:2-29       ------------------------------------ Pfam domains (2)
           Pfam domains (3) efhand-3li6J03 J:2-29       ------------------------------------ Pfam domains (3)
           Pfam domains (4) efhand-3li6J04 J:2-29       ------------------------------------ Pfam domains (4)
         Sec.struct. author .hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) EF_HAND_2  PDB: - UniProt: 1-32EF_HAND_2  PDB: J:33-65           PROSITE (1)
                PROSITE (2) --------EF_HAND_1    -----------------------EF_HAND_1    ------- PROSITE (2)
                 Transcript ---------------------------------------------------------------- Transcript
                  3li6 J  2 AEALFKEIDVNGDGAVSYEEVKAFVSKKRAIKNEQLLQLIFKSIDADGNGEIDQNEFAKFYGSI 65
                                    11        21        31        41        51        61
   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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LI6)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: EF_hand (270)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,D,G,J   (CALBP_ENTHI | P38505)
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.

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  3li6
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  CALBP_ENTHI | P38505
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 Related Entries

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

UniProtKB/Swiss-Prot
        CALBP_ENTHI | P38505: 1jfj 1jfk 2i18 2m7k 2m7m 2m7n 2nxq 3px1 3qjk 3ulg

(-) Related Entries Specified in the PDB File

2nxq FULL-LENGTH PROTEIN WITH C-TERMINAL HALF MISSING