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(-) Description

Title :  REFINED SOLUTION STRUCTURE OF DER F 2, THE MAJOR MITE ALLERGEN FROM DERMATOPHAGOIDES FARINAE
 
Authors :  S. Ichikawa, T. Takai, T. Inoue, T. Yuuki, Y. Okumura, K. Ogura, F. Inagaki, H. Hatanaka
Date :  15 Oct 04  (Deposition) - 19 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (11x)
Keywords :  Allergen, Immunoglobulin Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ichikawa, T. Takai, T. Inoue, T. Yuuki, Y. Okumura, K. Ogura, F. Inagaki, H. Hatanaka
Nmr Study On The Major Mite Allergen Der F 2: Its Refined Tertiary Structure, Epitopes For Monoclonal Antibodies And Characteristics Shared By Ml Protein Group Members
J. Biochem. (Tokyo) V. 137 255 2005
PubMed-ID: 15809326  |  Reference-DOI: 10.1093/JB/MVI039
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MITE GROUP 2 ALLERGEN DER F 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PFLT1
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Common: AMERICAN HOUSE DUST MITE
    Organism Scientific: DERMATOPHAGOIDES FARINAE
    Organism Taxid: 6954
    Synonym: DER F II

 Structural Features

(-) Chains, Units

  
NMR Structure (11x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1WRF)

(-) SS Bonds  (3, 3)

NMR Structure
No.Residues
1A:8 -A:119
2A:21 -A:27
3A:73 -A:78

(-) Cis Peptide Bonds  (1, 11)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11Cys A:78 -Pro A:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

NMR Structure (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_ALL2_DERFA_001 *M93VALL2_DERFA  ---  ---AV76V
2UniProtVAR_ALL2_DERFA_002 *I105AALL2_DERFA  ---  ---AI88A
3UniProtVAR_ALL2_DERFA_003 *I128VALL2_DERFA  ---  ---AI111V
4UniProtVAR_ALL2_DERFA_004 *G142AALL2_DERFA  ---  ---AG125A
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WRF)

(-) 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:129
 aligned with ALL2_DERFA | Q00855 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:129
                                    27        37        47        57        67        77        87        97       107       117       127       137         
           ALL2_DERFA    18 DQVDVKDCANNEIKKVMVDGCHGSDPCIIHRGKPFTLEALFDANQNTKTAKIEIKASLDGLEIDVPGIDTNACHFMKCPLVKGQQYDIKYTWNVPKIAPKSENVVVTVKLIGDNGVLACAIATHGKIRD 146
               SCOP domains d1wrfa_ A: Major mite allergen                                                                                                    SCOP domains
               CATH domains 1wrfA00 A:1-129  [code=2.60.40.770, no name defined]                                                                              CATH domains
               Pfam domains E1_DerP2_DerF2-1wrfA01 A:1-125                                                                                               ---- Pfam domains
         Sec.struct. author ....eee.....eeeee.........eeee...eeeeeeeee........eeeeeeee..eee.......hhhhh.........eeeeeeeee..........eeeeeeeee..eeeeeeee..eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------V-----------A----------------------V-------------A---- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wrf A   1 DQVDVKDCANNEIKKVMVDGCHGSDPCIIHRGKPFTLEALFDANQNTKTAKIEIKASLDGLEIDVPGIDTNACHFVKCPLVKGQQYDIKYTWNVPKIAPKSENVVVTVKLIGDNGVLACAIATHGKIRD 129
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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, 1)

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

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: E1_DerP2_DerF2] (8)

(-) Gene Ontology  (1, 1)

NMR Structure(hide GO term definitions)
Chain A   (ALL2_DERFA | Q00855)
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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  Cis Peptide Bonds
    Cys A:78 - Pro A:79   [ RasMol ]  
 

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  1wrf
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  ALL2_DERFA | Q00855
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 Related Entries

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

UniProtKB/Swiss-Prot
        ALL2_DERFA | Q00855: 1ahk 1ahm 1xwv 2f08

(-) Related Entries Specified in the PDB File

1ahk THE OLD MINIMIZED AVERAGED STRUCTURE
1ahm THE OLD ENSEMBLE OF TEN CONFORMERS