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(-) Description

Title :  CRYSTAL STRUCTURE OF FBF-2/GLD-1 FBEA G4A MUTANT COMPLEX
 
Authors :  Y. Wang, L. Opperman, M. Wickens, T. M. T. Hall
Date :  08 Oct 09  (Deposition) - 03 Nov 09  (Release) - 22 Dec 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fbf, Fem-3 Binding Factor, Puf, Rna-Binding Specificity, Base Flipping, Base Stacking (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Wang, L. Opperman, M. Wickens, T. M. Hall
Structural Basis For Specific Recognition Of Multiple Mrna Targets By A Puf Regulatory Protein.
Proc. Natl. Acad. Sci. Usa V. 106 20186 2009
PubMed-ID: 19901328  |  Reference-DOI: 10.1073/PNAS.0812076106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FEM-3 MRNA-BINDING FACTOR 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P1
    Expression System Strain: BL21 STAR (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 164-575, RNA-BINDING DOMAIN
    Gene: F21H12.5, FBF-2
    Organism Common: NEMATODE
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
 
Molecule 2 - 5'-R(*UP*GP*UP*AP*CP*CP*AP*UP*A)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES

 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 3K5Z)

(-) Sites  (0, 0)

(no "Site" information available for 3K5Z)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K5Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3K5Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K5Z)

(-) PROSITE Motifs  (1, 8)

Asymmetric/Biological Unit (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUMPS50302 Pumilio RNA-binding repeat profile.FBF2_CAEEL187-225
226-264
271-307
345-384
308-332
400-436
438-473
484-521		  8A:187-225
A:226-264
A:271-307
A:345-384
A:308-332
A:400-436
A:438-473
A:484-521

(-) Exons   (0, 0)

(no "Exon" information available for 3K5Z)

(-) 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:394
 aligned with FBF2_CAEEL | Q09312 from UniProtKB/Swiss-Prot  Length:632

    Alignment length:400
                                   177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567
           FBF2_CAEEL   168 LPTWSLDSNGEMRSRLSLSEVLDSGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNIFGNYLVQSVIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACRVIQSSLQNMDLSLACKLVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHIVSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIPHPDTGKDALDIMMFHQFGNYVVQCMLTICCDAVSGRRQTKEGGYDHAISFQDWLKKLHSRVTKERHRLSRFSSGKKMIETLANLRS 567
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3k5zA01 A:351-376     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh------....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..hhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhh..hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------PUM  PDB: A:187-225 UniProt: 187-225   PUM  PDB: A:226-264 UniProt: 226-264   ------PUM  PDB: A:271-307 UniProt: 271-307 PUM  PDB: A:308-332      ------------PUM  PDB: A:345-384 UniProt: 345-384    ---------------PUM  PDB: A:400-436 UniProt: 400-436 -PUM  PDB: A:438-473 UniProt: 438-473----------PUM  PDB: A:484-521 UniProt: 484-521  ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k5z A 168 LPTWSL------RSRLSLSEVLDSGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNIFGNYLVQSVIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACRVIQSSLQNMDLSLACKLVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHIVSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIPHPDTGKDALDIMMFHQFGNYVVQCMLTICCDAVSGRRQTKEGGYDHAISFQDWLKKLHSRVTKERHRLSRFSSGKKMIETLANLRS 567
                                 |   -  |    187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567
                               173    180                                                                                                                                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:RNA  Length:9
                                         
                 3k5z B   1 UGUACCAUA   9
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3K5Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K5Z)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: TPR (230)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FBF2_CAEEL | Q09312)
molecular function
    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.
biological process
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0007548    sex differentiation    The establishment of the sex of an organism by physical differentiation.
cellular component
    GO:0043186    P granule    A small cytoplasmic, non-membranous RNA/protein complex aggregates in the primordial germ cells of many higher eukaryotes.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FBF2_CAEEL | Q09312: 3k5q 3k5y 3k61 3k62 3k64 3qg9 3qgb 3qgc 3v6y 3v74

(-) Related Entries Specified in the PDB File

3k5q 3k5y 3k61 3k62 3k64