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(-) Description

Title :  CRYSTAL STRUCTURE OF TRANSTHYRETIN FROM SPARUS AURATA
 
Authors :  N. Pasquato, I. Ramazzina, C. Folli, R. Battistutta, R. Berni, G. Zanotti
Date :  03 Mar 03  (Deposition) - 20 Jan 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.56
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transthyretin, Retinol-Binding Protein, Tetramer, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Folli, N. Pasquato, I. Ramazzina, R. Battistutta, G. Zanotti, R. Berni
Distinctive Binding And Structural Properties Of Piscine Transthyretin.
Febs Lett. V. 555 279 2003
PubMed-ID: 14644428  |  Reference-DOI: 10.1016/S0014-5793(03)01248-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSTHYRETIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11B
    Expression System Strain: BL21-CODONPLUS-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TTR
    Organism Common: GILTHEAD SEABREAM
    Organism Scientific: SPARUS AURATA
    Organism Taxid: 8175

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CD2Ligand/IonCADMIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:38 , HOH A:134 , GLU C:72 , HOH C:425 , HOH C:467BINDING SITE FOR RESIDUE CD C 401
2AC2SOFTWAREGLU C:61 , HIS C:104 , HOH C:470 , HOH C:479BINDING SITE FOR RESIDUE CD C 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OO2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly C:101 -His C:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OO2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OO2)

(-) Exons   (0, 0)

(no "Exon" information available for 1OO2)

(-) 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:116
 aligned with O93330_SPAAU | O93330 from UniProtKB/TrEMBL  Length:149

    Alignment length:116
                                      42                                                                                                        
                                    41 |                                                                                                        
                                    41 |      50        60        70        80        90       100       110       120       130       140      
         O93330_SPAAU    32 RCPLMVKILD-VKGTPAGSVALKVSQKTADGGWTQIATGVTDATGEIHNLITEQQFPAGVYRVEFDTKAYWTNQGSTPFHEVAEVVFDAHPEGHRHYTLALLLSPFSYTTTAVVSS 146
               SCOP domains d1oo2a_ A: Transthyretin (synonym: prealbumin)                                                                       SCOP domains
               CATH domains 1oo2A00 A:9-124  [code=2.60.40.180, no name defined]                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....ee....eeeeeee.....eeeeeeee...........hhhhh..eeeeeeehhhhhhhhh.....eeeeeeeeee.......eeeeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1oo2 A   9 RCPLMVKILDAVKGTPAGSVALKVSQKTADGGWTQIATGVTDATGEIHNLITEQQFPAGVYRVEFDTKAYWTNQGSTPFHEVAEVVFDAHPEGHGHYTLALLLSPFSYTTTAVVSS 124
                                    18        28        38        48        58        68        78        88        98       108       118      


Chain A from PDB  Type:PROTEIN  Length:116
 aligned with Q9PTT3_SPAAU | Q9PTT3 from UniProtKB/TrEMBL  Length:151

    Alignment length:116
                                    42        52        62        72        82        92       102       112       122       132       142      
         Q9PTT3_SPAAU    33 RCPLMVKILDAVKGTPAGSVALKVSQKTADGGWTQIATGVTDATGEIHNLITEQQFPAGVYRVEFDTKAYWTNQGSTPFHEVAEVVFDAHPEGHRHYTLALLLSPFSYTTTAVVSS 148
               SCOP domains d1oo2a_ A: Transthyretin (synonym: prealbumin)                                                                       SCOP domains
               CATH domains 1oo2A00 A:9-124  [code=2.60.40.180, no name defined]                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....ee....eeeeeee.....eeeeeeee...........hhhhh..eeeeeeehhhhhhhhh.....eeeeeeeeee.......eeeeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1oo2 A   9 RCPLMVKILDAVKGTPAGSVALKVSQKTADGGWTQIATGVTDATGEIHNLITEQQFPAGVYRVEFDTKAYWTNQGSTPFHEVAEVVFDAHPEGHGHYTLALLLSPFSYTTTAVVSS 124
                                    18        28        38        48        58        68        78        88        98       108       118      


Chain B from PDB  Type:PROTEIN  Length:116
 aligned with O93330_SPAAU | O93330 from UniProtKB/TrEMBL  Length:149

    Alignment length:116
                                      42                                                                                                        
                                    41 |                                                                                                        
                                    41 |      50        60        70        80        90       100       110       120       130       140      
         O93330_SPAAU    32 RCPLMVKILD-VKGTPAGSVALKVSQKTADGGWTQIATGVTDATGEIHNLITEQQFPAGVYRVEFDTKAYWTNQGSTPFHEVAEVVFDAHPEGHRHYTLALLLSPFSYTTTAVVSS 146
               SCOP domains d1oo2b_ B: Transthyretin (synonym: prealbumin)                                                                       SCOP domains
               CATH domains 1oo2B00 B:9-124  [code=2.60.40.180, no name defined]                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....ee....eeeeeee.....eeeeeeee...........hhhhh..eeeeeeehhhhhhhhhh....eeeeeeeeee......eeeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1oo2 B   9 RCPLMVKILDAVKGTPAGSVALKVSQKTADGGWTQIATGVTDATGEIHNLITEQQFPAGVYRVEFDTKAYWTNQGSTPFHEVAEVVFDAHPEGHGHYTLALLLSPFSYTTTAVVSS 124
                                    18        28        38        48        58        68        78        88        98       108       118      


Chain B from PDB  Type:PROTEIN  Length:116
 aligned with Q9PTT3_SPAAU | Q9PTT3 from UniProtKB/TrEMBL  Length:151

    Alignment length:116
                                    42        52        62        72        82        92       102       112       122       132       142      
         Q9PTT3_SPAAU    33 RCPLMVKILDAVKGTPAGSVALKVSQKTADGGWTQIATGVTDATGEIHNLITEQQFPAGVYRVEFDTKAYWTNQGSTPFHEVAEVVFDAHPEGHRHYTLALLLSPFSYTTTAVVSS 148
               SCOP domains d1oo2b_ B: Transthyretin (synonym: prealbumin)                                                                       SCOP domains
               CATH domains 1oo2B00 B:9-124  [code=2.60.40.180, no name defined]                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....ee....eeeeeee.....eeeeeeee...........hhhhh..eeeeeeehhhhhhhhhh....eeeeeeeeee......eeeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1oo2 B   9 RCPLMVKILDAVKGTPAGSVALKVSQKTADGGWTQIATGVTDATGEIHNLITEQQFPAGVYRVEFDTKAYWTNQGSTPFHEVAEVVFDAHPEGHGHYTLALLLSPFSYTTTAVVSS 124
                                    18        28        38        48        58        68        78        88        98       108       118      


Chain C from PDB  Type:PROTEIN  Length:116
 aligned with O93330_SPAAU | O93330 from UniProtKB/TrEMBL  Length:149

    Alignment length:116
                                      42                                                                                                        
                                    41 |                                                                                                        
                                    41 |      50        60        70        80        90       100       110       120       130       140      
         O93330_SPAAU    32 RCPLMVKILD-VKGTPAGSVALKVSQKTADGGWTQIATGVTDATGEIHNLITEQQFPAGVYRVEFDTKAYWTNQGSTPFHEVAEVVFDAHPEGHRHYTLALLLSPFSYTTTAVVSS 146
               SCOP domains d1oo2c_ C: Transthyretin (synonym: prealbumin)                                                                       SCOP domains
               CATH domains 1oo2C00 C:9-124  [code=2.60.40.180, no name defined]                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....ee....eeeeeee.....eeeeeeee...........hhhhh..eeeeeeehhhhhhhhhh....eeeeeeeeee......eeeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1oo2 C   9 RCPLMVKILDAVKGTPAGSVALKVSQKTADGGWTQIATGVTDATGEIHNLITEQQFPAGVYRVEFDTKAYWTNQGSTPFHEVAEVVFDAHPEGHGHYTLALLLSPFSYTTTAVVSS 124
                                    18        28        38        48        58        68        78        88        98       108       118      


Chain C from PDB  Type:PROTEIN  Length:116
 aligned with Q9PTT3_SPAAU | Q9PTT3 from UniProtKB/TrEMBL  Length:151

    Alignment length:116
                                    42        52        62        72        82        92       102       112       122       132       142      
         Q9PTT3_SPAAU    33 RCPLMVKILDAVKGTPAGSVALKVSQKTADGGWTQIATGVTDATGEIHNLITEQQFPAGVYRVEFDTKAYWTNQGSTPFHEVAEVVFDAHPEGHRHYTLALLLSPFSYTTTAVVSS 148
               SCOP domains d1oo2c_ C: Transthyretin (synonym: prealbumin)                                                                       SCOP domains
               CATH domains 1oo2C00 C:9-124  [code=2.60.40.180, no name defined]                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....ee....eeeeeee.....eeeeeeee...........hhhhh..eeeeeeehhhhhhhhhh....eeeeeeeeee......eeeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1oo2 C   9 RCPLMVKILDAVKGTPAGSVALKVSQKTADGGWTQIATGVTDATGEIHNLITEQQFPAGVYRVEFDTKAYWTNQGSTPFHEVAEVVFDAHPEGHGHYTLALLLSPFSYTTTAVVSS 124
                                    18        28        38        48        58        68        78        88        98       108       118      


Chain D from PDB  Type:PROTEIN  Length:116
 aligned with O93330_SPAAU | O93330 from UniProtKB/TrEMBL  Length:149

    Alignment length:116
                                      42                                                                                                        
                                    41 |                                                                                                        
                                    41 |      50        60        70        80        90       100       110       120       130       140      
         O93330_SPAAU    32 RCPLMVKILD-VKGTPAGSVALKVSQKTADGGWTQIATGVTDATGEIHNLITEQQFPAGVYRVEFDTKAYWTNQGSTPFHEVAEVVFDAHPEGHRHYTLALLLSPFSYTTTAVVSS 146
               SCOP domains d1oo2d_ D: Transthyretin (synonym: prealbumin)                                                                       SCOP domains
               CATH domains 1oo2D00 D:9-124  [code=2.60.40.180, no name defined]                                                                 CATH domains
           Pfam domains (1) -Transthyretin-1oo2D01 D:10-121                                                                                  --- Pfam domains (1)
           Pfam domains (2) -Transthyretin-1oo2D02 D:10-121                                                                                  --- Pfam domains (2)
           Pfam domains (3) -Transthyretin-1oo2D03 D:10-121                                                                                  --- Pfam domains (3)
           Pfam domains (4) -Transthyretin-1oo2D04 D:10-121                                                                                  --- Pfam domains (4)
         Sec.struct. author ...eeeeeee....ee....eeeeeee.....eeeeeeee...........hhhhh..eeeeeeehhhhhhhhhh....eeeeeeeeee.......eeeeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1oo2 D   9 RCPLMVKILDAVKGTPAGSVALKVSQKTADGGWTQIATGVTDATGEIHNLITEQQFPAGVYRVEFDTKAYWTNQGSTPFHEVAEVVFDAHPEGHGHYTLALLLSPFSYTTTAVVSS 124
                                    18        28        38        48        58        68        78        88        98       108       118      


Chain D from PDB  Type:PROTEIN  Length:116
 aligned with Q9PTT3_SPAAU | Q9PTT3 from UniProtKB/TrEMBL  Length:151

    Alignment length:116
                                    42        52        62        72        82        92       102       112       122       132       142      
         Q9PTT3_SPAAU    33 RCPLMVKILDAVKGTPAGSVALKVSQKTADGGWTQIATGVTDATGEIHNLITEQQFPAGVYRVEFDTKAYWTNQGSTPFHEVAEVVFDAHPEGHRHYTLALLLSPFSYTTTAVVSS 148
               SCOP domains d1oo2d_ D: Transthyretin (synonym: prealbumin)                                                                       SCOP domains
               CATH domains 1oo2D00 D:9-124  [code=2.60.40.180, no name defined]                                                                 CATH domains
           Pfam domains (1) -Transthyretin-1oo2D01 D:10-121                                                                                  --- Pfam domains (1)
           Pfam domains (2) -Transthyretin-1oo2D02 D:10-121                                                                                  --- Pfam domains (2)
           Pfam domains (3) -Transthyretin-1oo2D03 D:10-121                                                                                  --- Pfam domains (3)
           Pfam domains (4) -Transthyretin-1oo2D04 D:10-121                                                                                  --- Pfam domains (4)
         Sec.struct. author ...eeeeeee....ee....eeeeeee.....eeeeeeee...........hhhhh..eeeeeeehhhhhhhhhh....eeeeeeeeee.......eeeeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1oo2 D   9 RCPLMVKILDAVKGTPAGSVALKVSQKTADGGWTQIATGVTDATGEIHNLITEQQFPAGVYRVEFDTKAYWTNQGSTPFHEVAEVVFDAHPEGHGHYTLALLLSPFSYTTTAVVSS 124
                                    18        28        38        48        58        68        78        88        98       108       118
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: Transthyretin (88)

(-) Gene Ontology  (5, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q9PTT3_SPAAU | Q9PTT3)
molecular function
    GO:0070324    thyroid hormone binding    Interacting selectively and non-covalently with thyroxine (T4) or triiodothyronine (T3), tyrosine-based hormones produced by the thyroid gland.
biological process
    GO:0042572    retinol metabolic process    The chemical reactions and pathways involving retinol, one of the three compounds that makes up vitamin A.
    GO:0070327    thyroid hormone transport    The directed movement of thyroid hormone into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
    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.

Chain A,B,C,D   (O93330_SPAAU | O93330)
molecular function
    GO:0070324    thyroid hormone binding    Interacting selectively and non-covalently with thyroxine (T4) or triiodothyronine (T3), tyrosine-based hormones produced by the thyroid gland.
biological process
    GO:0043627    response to estrogen    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics.
    GO:0042572    retinol metabolic process    The chemical reactions and pathways involving retinol, one of the three compounds that makes up vitamin A.
    GO:0070327    thyroid hormone transport    The directed movement of thyroid hormone into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
    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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q9PTT3_SPAAU | Q9PTT3: 1sn0 1sn2 1sn5

(-) Related Entries Specified in the PDB File

1f41 HUMAN TRANSTHYRETIN
1fhn HUMAN TRANSTHYRETIN (MUTANT)
1ie4 RAT TRANSTHYRETIN COMPLEX WITH THYROXINE (T4)
1qab TRANSTHYRETIN-RBP COMPLEX
1rlb TRANSTHYRETIN-RBP COMPLEX