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(-) Description

Title :  CRYSTAL STRUCTURE OF PUF-6 IN COMPLEX WITH 5BE13 RNA
 
Authors :  C. Qiu, A. Kershner, Y. Wang, C. H. Holley, D. Wilinski, S. Keles, J. Kimb M. Wickens, T. M. T. Hall
Date :  20 Dec 11  (Deposition) - 04 Jan 12  (Release) - 04 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Puf Repeats, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Qiu, A. Kershner, Y. Wang, C. H. Holley, D. Wilinski, S. Keles, J. Kimble, M. Wickens, T. M. T. Hall
Divergence Of Puf Protein Specificity Through Variations In An Rna-Binding Pocket
J. Biol. Chem. 2012
PubMed: search

(-) Compounds

Molecule 1 - PUF (PUMILIO/FBF) DOMAIN-CONTAINING PROTEIN 7, CONFIRMED BY TRANSCRIPT EVIDENCE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST15
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 164-575
    Gene: PUF-7, B0273.2
    Organism Common: NEMATODE
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
 
Molecule 2 - RNA (5'-R(*CP*UP*CP*UP*GP*UP*AP*UP*CP*UP*UP*GP*U)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:342 , G B:4 , U B:5BINDING SITE FOR RESIDUE EPE B 13

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V71)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3V71)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V71)

(-) PROSITE Motifs  (1, 8)

Asymmetric/Biological Unit (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUMPS50302 Pumilio RNA-binding repeat profile.PUF7_CAEEL86-124
128-163
164-200
237-279
201-225
287-324
326-361
370-411		  8A:86-124
A:128-163
A:164-200
A:237-279
A:201-225
A:287-324
A:326-361
A:370-411

(-) Exons   (0, 0)

(no "Exon" information available for 3V71)

(-) 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:364
 aligned with PUF7_CAEEL | O44169 from UniProtKB/Swiss-Prot  Length:485

    Alignment length:371
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451 
           PUF7_CAEEL    82 ISLEDVLLNGQLIDFAIDPSGVKFLEANYPLDSEDQIRKAVFEKFTESTTLFVGLCHSRNGNFIVQKLVELATPAEQRELLRQMIDGGLLAMCKDKFACRVVQLALQKFDHSNVFQLIQELSTFDLAAMCTDQISIHVIQRVVKQLPVDMWTFFVHFLSSGDSLMAVCQDKYGCRLVQQVIDRLAENPKLPCFKFRIQLLHSLMTCIVRNCYRLSSNEFANYVIQYVIKSSGIMEMYRDTIIDKCLLRNLLSMSQDKYASHVIEGAFLFAPPALLHEMMEEIFSGYVKDVESNRDALDILLFHQYGNYVVQQMISICTAALIGKEERELPPAILLLYSGWYEKMKQRVLQHASRLERFSSGKKIIDSVMRH 452
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh......hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.--........hhhhhhhh..hhhhhhhhhhhhhhhhh.-----.....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PUM  PDB: A:86-124 UniProt: 86-124     ---PUM  PDB: A:128-163 UniProt: 128-163PUM  PDB: A:164-200 UniProt: 164-200 PUM  PDB: A:201-225      -----------PUM  PDB: A:237-279 UniProt: 237-279       -------PUM  PDB: A:287-324 UniProt: 287-324  -PUM  PDB: A:326-361 UniProt: 326-361--------PUM  PDB: A:370-411 UniProt: 370-411      ----------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v71 A  82 ISLEDVLLNGQLIDFAIDPSGVKFLEANYPLDSEDQIRKAVFEKFTESTTLFVGLCHSRNGNFIVQKLVELATPAEQRELLRQMIDGGLLAMCKDKFACRVVQLALQKFDHSNVFQLIQELSTFDLAAMCTDQISIHVIQRVVKQLPVDMWTFFVHFLSSGDSLMAVCQDKYGCRLVQQVIDRLAENPKLPCFKFRIQLLHSLMTCIVRNCYRLSSNEFANYVIQYVIKSSGIMEMYRDTIIDKCLLRNLLSMSQDKYASHVIEGAFLFAPPALLHEMMEEIFS--VKDVESNRDALDILLFHQYGNYVVQQMISICTAALI-----ELPPAILLLYSGWYEKMKQRVLQHASRLERFSSGKKIIDSVMRH 452
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361   |  |371       381       391       401 |     411       421       431       441       451 
                                                                                                                                                                                                                                                                                                                     365  |                                403   409                                           
                                                                                                                                                                                                                                                                                                                        368                                                                                    


Chain B from PDB  Type:RNA  Length:7
                                       
                 3v71 B   1 CUGUAUC   8
                            ||     
                            1|     
                             3
   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  (0, 0)

(no "SCOP Domain" information available for 3V71)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V71)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V71)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PUF7_CAEEL | O44169)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    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:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0007281    germ cell development    The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism.
    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:0048477    oogenesis    The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.

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  3v71
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 Related Entries

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(-) Related Entries Specified in the PDB File

3v6y 3v74