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(-) Description

Title :  NMR STRUCTURE OF INTRAMOLECULAR DIMER ANTIFREEZE PROTEIN RD3, 40 SA STRUCTURES
 
Authors :  K. Miura, S. Tsuda
Date :  04 May 00  (Deposition) - 28 Feb 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (40x)
Keywords :  Antifreeze, Thermal Hysteresis Protein, Ice Binding Protein, Antifreeze Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Miura, S. Ohgiya, T. Hoshino, N. Nemoto, T. Suetake, A. Miura, L. Spyracopoulos, H. Kondo, S. Tsuda
Nmr Analysis Of Type Iii Antifreeze Protein Intramolecular Dimer. Structural Basis For Enhanced Activity.
J. Biol. Chem. V. 276 1304 2001
PubMed-ID: 11010977  |  Reference-DOI: 10.1074/JBC.M007902200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTIFREEZE PROTEIN TYPE III
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK223-3UC
    Expression System Strain: JM105
    Expression System Taxid: 562
    Expression System Vector: PLASMID
    Expression System Vector Type: PLASMID
    Organism Scientific: PACHYCARA BRACHYCEPHALUM
    Organism Taxid: 36221
    Other Details: SYNTHETIC GENE
    Synonym: RD3
    Tissue: BLOOD PLASMA
    Variant: RD3

 Structural Features

(-) Chains, Units

  
NMR Structure (40x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1C89)

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1IC1AUTHORGLN A:9 , ASN A:14 , THR A:15 , ALA A:16 , THR A:18 , GLN A:44ICE BINDING SITE
2IC2AUTHORGLN A:79 , ASN A:84 , THR A:85 , ALA A:86 , THR A:88 , GLN A:114ICE BINDING SITE

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1C89)

(-) Cis Peptide Bonds  (2, 80)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40Thr A:28 -Pro A:29
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40Ser A:98 -Pro A:99

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1C89)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AFP_LIKEPS50844 Antifreeze protein-like domain profile.ANP3_LYCDA4-63
74-133		  2A:4-63
A:74-133

(-) Exons   (0, 0)

(no "Exon" information available for 1C89)

(-) Sequences/Alignments

NMR Structure
   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:134
 aligned with ANP3_LYCDA | P35753 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    
           ANP3_LYCDA     1 NKASVVANQLIPINTALTLIMMKAEVVTPMGIPAEEIPNLVGMQVNRAVPLGTTLMPDMVKNYEDGTTSPGLKSVVANQLIPINTALTLVMMKAEEVSPKGIPSEEISKLVGMQVNRAVYLDQTLMPDMVKNYE 134
               SCOP domains d1c89a1 A:1-68 Type III antifreeze protein, AFP III                 d1c89a2 A:69-134 Type III antifreeze protein, AFP III              SCOP domains
               CATH domains 1c89A01 A:1-66 Type Iii Antifreeze Protein Isoform Hplc 12        ----1c89A02 A:71-134 Type Iii Antifreeze Protein Isoform Hplc 12     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..............eeee..........hhhhhh...........ee..................eeeee...............eeee.........hhhhhh...........ee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---AFP_LIKE  PDB: A:4-63 UniProt: 4-63                         ----------AFP_LIKE  PDB: A:74-133 UniProt: 74-133                     - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c89 A   1 NKASVVANQLIPINTALTLIMMKAEVVTPMGIPAEEIPNLVGMQVNRAVPLGTTLMPDMVKNYEDGTTSPGLKSVVANQLIPINTALTLVMMKAEEVSPKGIPSEEISKLVGMQVNRAVYLDQTLMPDMVKNYE 134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1C89)

(-) Gene Ontology  (2, 2)

NMR Structure(hide GO term definitions)
Chain A   (ANP3_LYCDA | P35753)
biological process
    GO:0050826    response to freezing    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 a freezing stimulus, temperatures below 0 degrees Celsius.
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/Swiss-Prot
        ANP3_LYCDA | P35753: 1c8a 3nla 3rdn

(-) Related Entries Specified in the PDB File

1c8a MINIMIZED AVERAGE STRUCTURE