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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
Keywords :  Antifreeze, Antifreeze Protein, Thermal Hysteresis Protein, Ice Binding 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 - PROTEIN (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 : 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1C8A)

(-) 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 1C8A)

(-) Cis Peptide Bonds  (2, 2)

NMR Structure
No.Residues
1Thr A:28 -Pro A:29
2Ser A:98 -Pro A:99

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1C8A)

(-) 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 1C8A)

(-) 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 d1c8aa1 A:1-68 Type III antifreeze protein, AFP III                 d1c8aa2 A:69-134 Type III antifreeze protein, AFP III              SCOP domains
               CATH domains 1c8aA01 A:1-66 Type Iii Antifreeze Protein Isoform Hplc 12        ----1c8aA02 A:71-134 Type Iii Antifreeze Protein Isoform Hplc 12     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..............eeee..........hhhhhh...........ee..................eeeee........ee....eeeee.........hhhhhh.ee........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
                 1c8a A   1 NKASVVANQLIPINTALTLIMMKAEVVTPMGIPAEEIPNLVGMQVNRAVPLGTTLMPDMVKNYEDGTTSPGLKSVVANQLIPINTALTLVMMKAEEVSPKGIPSEEISKLVGMQVNRAVYLDQTLMPDMVKNYE 134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
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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 1C8A)

(-) 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: 1c89 3nla 3rdn

(-) Related Entries Specified in the PDB File

1c89 40 STRUCTURES