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(-) Description

Title :  PUF4 T650C/C724R MUTANT BOUND TO COX17 RNA 3' UTR RECOGNITION SEQUENCE
 
Authors :  M. T. Miller, J. J. Higgin, T. M. T. Hall
Date :  11 Jan 08  (Deposition) - 11 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Puf4, Pumilio, Rna Binding, Ho Endonuclease, Puf4 T650C C724R Mutant, Transcription, Rna Binding Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. T. Miller, J. J. Higgin, T. M. T. Hall
Basis Of Altered Rna-Binding Specificity By Puf Proteins Revealed By Crystal Structures Of Yeast Puf4P
Nat. Struct. Mol. Biol. V. 15 397 2008
PubMed-ID: 18327269  |  Reference-DOI: 10.1038/NSMB.1390
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COX17 RNA TARGET SEQUENCE
    ChainsC, D
    EngineeredYES
    SyntheticYES
 
Molecule 2 - PROTEIN PUF4
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSINGLE STRANDED RNA BINDING DOMIN
    GenePUF4
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1SO49Ligand/IonSULFATE ION
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:682 , HIS A:721BINDING SITE FOR RESIDUE SO4 A 902
2AC2SOFTWAREHIS A:719 , HIS B:795BINDING SITE FOR RESIDUE SO4 B 903
3AC3SOFTWARETHR A:625 , THR A:626 , LYS A:661BINDING SITE FOR RESIDUE SO4 A 904
4AC4SOFTWARETHR A:735 , LYS A:774 , THR B:735 , LYS B:774BINDING SITE FOR RESIDUE SO4 A 905
5AC5SOFTWARECYS A:738 , CYS A:742 , GLU A:769 , LYS A:772BINDING SITE FOR RESIDUE SO4 A 906
6AC6SOFTWAREPRO A:638 , PRO B:675 , TYR B:676 , GLN B:679BINDING SITE FOR RESIDUE SO4 B 907
7AC7SOFTWAREARG B:728 , HIS B:732BINDING SITE FOR RESIDUE SO4 B 908
8AC8SOFTWAREGLN A:851 , HIS B:783BINDING SITE FOR RESIDUE SO4 B 909

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BX3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:588 -Gly A:589

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BX3)

(-) PROSITE Motifs  (1, 15)

Asymmetric Unit (1, 15)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUMPS50302 Pumilio RNA-binding repeat profile.PUF4_YEAST563-598
599-634
 
635-671
 
672-707
 
708-743
 
744-783
 
784-821
 
823-861
 
  15A:563-598
A:599-634
B:599-634
A:635-671
B:635-671
A:672-707
B:672-707
A:708-743
B:708-743
A:744-783
B:744-783
A:784-821
B:784-821
A:823-861
B:823-861
Biological Unit 1 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUMPS50302 Pumilio RNA-binding repeat profile.PUF4_YEAST563-598
599-634
 
635-671
 
672-707
 
708-743
 
744-783
 
784-821
 
823-861
 
  8A:563-598
A:599-634
-
A:635-671
-
A:672-707
-
A:708-743
-
A:744-783
-
A:784-821
-
A:823-861
-
Biological Unit 2 (1, 7)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUMPS50302 Pumilio RNA-binding repeat profile.PUF4_YEAST563-598
599-634
 
635-671
 
672-707
 
708-743
 
744-783
 
784-821
 
823-861
 
  7-
-
B:599-634
-
B:635-671
-
B:672-707
-
B:708-743
-
B:744-783
-
B:784-821
-
B:823-861

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YGL014W1YGL014W.1VII:466146-4688122667PUF4_YEAST1-8888882A:562-886
B:586-885
325
300

(-) Sequences/Alignments

Asymmetric 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:325
 aligned with PUF4_YEAST | P25339 from UniProtKB/Swiss-Prot  Length:888

    Alignment length:325
                                   571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881     
           PUF4_YEAST   562 DQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQNDYLYKRLSEIVAPLLVGPIRNTPHGKRIIGMLHL 886
               SCOP domains d3bx3a_ A: automated matches                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh......hhhhhhhhh......hhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -PUM  PDB: A:563-598 UniProt: 563-598PUM  PDB: A:599-634 UniProt: 599-634PUM  PDB: A:635-671 UniProt: 635-671 PUM  PDB: A:672-707 UniProt: 672-707PUM  PDB: A:708-743 UniProt: 708-743PUM  PDB: A:744-783 UniProt: 744-783    PUM  PDB: A:784-821 UniProt: 784-821  -PUM  PDB: A:823-861 UniProt: 823-861   ------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:562-886 UniProt: 1-888 [INCOMPLETE]                                                                                                                                                                                                                                                                                  Transcript 1
                 3bx3 A 562 DQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGCRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQNDYLYKRLSEIVAPLLVGPIRNTPHGKRIIGMLHL 886
                                   571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881     

Chain B from PDB  Type:PROTEIN  Length:300
 aligned with PUF4_YEAST | P25339 from UniProtKB/Swiss-Prot  Length:888

    Alignment length:300
                                   595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885
           PUF4_YEAST   586 DILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQNDYLYKRLSEIVAPLLVGPIRNTPHGKRIIGMLH 885
               SCOP domains d3bx3b_ B: automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE PUM  PDB: -  PUM  PDB: B:599-634 UniProt: 599-634PUM  PDB: B:635-671 UniProt: 635-671 PUM  PDB: B:672-707 UniProt: 672-707PUM  PDB: B:708-743 UniProt: 708-743PUM  PDB: B:744-783 UniProt: 744-783    PUM  PDB: B:784-821 UniProt: 784-821  -PUM  PDB: B:823-861 UniProt: 823-861   ------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:586-885 UniProt: 1-888 [INCOMPLETE]                                                                                                                                                                                                                                                         Transcript 1
                 3bx3 B 586 DILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGCRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQNDYLYKRLSEIVAPLLVGPIRNTPHGKRIIGMLH 885
                                   595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885

Chain C from PDB  Type:RNA  Length:8
                                        
                 3bx3 C   1 UGUAUAUA   8

Chain D from PDB  Type:RNA  Length:8
                                        
                 3bx3 D   1 UGUAUAUA   8

   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 Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3BX3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BX3)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PUF4_YEAST | P25339)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
biological process
    GO:0001308    negative regulation of chromatin silencing involved in replicative cell aging    The process, which occurs as a dividing cell ages, leading to expression of genes that are typically not expressed due to silencing by regulatory proteins.
    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:0000288    nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay    A major pathway of degradation of nuclear-transcribed mRNAs that proceeds through a series of ordered steps that includes poly(A) tail shortening and that can regulate mRNA stability.
    GO:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PUF4_YEAST | P253393bwt 3bx2 4dzs

(-) Related Entries Specified in the PDB File

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1m8x CRYSTAL STRUCTURE OF THE PUMILIO-HOMOLOGY DOMAIN FROM HUMAN PUMILIO1 IN COMPLEX WITH NRE1-14 RNA
1m8y CRYSTAL STRUCTURE OF THE PUMILIO-HOMOLOGY DOMAIN FROM HUMAN PUMILIO1 IN COMPLEX WITH NRE2-10 RNA
1m8z CRYSTAL STRUCTURE OF A PUMILIO-HOMOLOGY DOMAIN
3bwt
3bx2