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(-) Description

Title :  CRYSTAL STRUCTURE OF HUD AND AU-RICH ELEMENT OF THE TUMOR NECROSIS FACTOR ALPHA RNA
 
Authors :  X. Wang, T. M. T. Hall
Date :  18 Oct 00  (Deposition) - 05 Feb 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Rna Complex, Hud, Au-Rich Element, Tumor Necrosis Factor, Transcription/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Wang, T. M. Tanaka Hall
Structural Basis For Recognition Of Au-Rich Element Rna By The Hud Protein.
Nat. Struct. Biol. V. 8 141 2001
PubMed-ID: 11175903  |  Reference-DOI: 10.1038/84131
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-R(P*UP*AP*UP*UP*UP*AP*UP*UP*UP*A)-3'
    Chains: B
    Engineered: YES
    Fragment: FRAGMENT OF AU-RICH ELEMENT OF THE TUMOR NECROSIS FACTOR ALPHA RNA
    Synthetic: YES
 
Molecule 2 - PARANEOPLASTIC ENCEPHALOMYELITIS ANTIGEN HUD
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PPROEXHTC
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL TWO RRM-DOMAINS
    Organ: BRAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1G2E)

(-) Sites  (0, 0)

(no "Site" information available for 1G2E)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G2E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1G2E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_058091D166GELAV4_HUMANPolymorphism17853533AD159G
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.ELAV4_HUMAN46-124
132-212
297-375		  2A:39-117
A:125-203
-

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.4bENST000003718234bENSE00001456196chr1:50574638-50574870233ELAV4_HUMAN1-330--
1.10dENST0000037182310dENSE00001064508chr1:50610629-50610869241ELAV4_HUMAN4-84811A:37-7741
1.11aENST0000037182311aENSE00001722912chr1:50642761-50642864104ELAV4_HUMAN84-118351A:77-11135
1.13ENST0000037182313ENSE00001803839chr1:50659437-50659590154ELAV4_HUMAN119-170521A:112-16352
1.14ENST0000037182314ENSE00001064512chr1:50661233-50661458226ELAV4_HUMAN170-245761A:163-20341
1.15aENST0000037182315aENSE00001800957chr1:50663101-5066313939ELAV4_HUMAN245-258140--
1.16aENST0000037182316aENSE00001456193chr1:50666481-50667074594ELAV4_HUMAN258-3801230--

(-) 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:167
 aligned with ELAV4_HUMAN | P26378 from UniProtKB/Swiss-Prot  Length:380

    Alignment length:167
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       
          ELAV4_HUMAN    44 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 210
               SCOP domains d1g2ea1 A:37-118 Hu antigen D (Hud)                                               d1g2ea2 A:119-203 Hu antigen D (Hud)                                                  SCOP domains
               CATH domains ----1g2eA01 A:41-111  [code=3.30.70.330, no name defined]                  ---------------1g2eA02 A:127-203  [code=3.30.70.330, no name defined]                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......hhhhhhhhhhh...eeeeeeee......eeeeeeeee.hhhhhhhhhhhhh..ee..ee.eeee....hhhhh..eeeee......hhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhhhhh...........eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------G-------------------------------------------- SAPs(SNPs)
                    PROSITE --RRM  PDB: A:39-117 UniProt: 46-124                                             -------RRM  PDB: A:125-203 UniProt: 132-212                                            PROSITE
           Transcript 1 (1) Exon 1.10d  PDB: A:37-77 UniProt: 4-84   ----------------------------------Exon 1.13  PDB: A:112-163 UniProt: 119-170          ---------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.11a  PDB: A:77-111          ---------------------------------------------------Exon 1.14  PDB: A:163-203 [INCOMPLETE]    Transcript 1 (2)
                 1g2e A  37 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 203
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       


Chain B from PDB  Type:RNA  Length:10
                                          
                 1g2e B   2 UAUUUAUUUA  11
                                    11
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G2E)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ELAV4_HUMAN | P26378)
molecular function
    GO:0017091    AU-rich element binding    Interacting selectively and non-covalently with a region of RNA containing frequent adenine and uridine bases.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003730    mRNA 3'-UTR binding    Interacting selectively and non-covalently with the 3' untranslated region of an mRNA molecule.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ELAV4_HUMAN | P26378: 1fxl

(-) Related Entries Specified in the PDB File

1fxl 1FXL CONTAINS THE SAME PROTEIN FRAGMENT.