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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PUMILIO-HOMOLOGY DOMAIN FROM HUMAN PUMILIO2 IN COMPLEX WITH P38ALPHA NREA
 
Authors :  G. Lu, T. M. T. Hall
Date :  15 Dec 10  (Deposition) - 16 Mar 11  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Puf, Pumilio-Homolgy Domain, Gene Regulation, Rna Binding, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Lu, T. M. Hall
Alternate Modes Of Cognate Rna Recognition By Human Pumilio Proteins.
Structure V. 19 361 2011
PubMed-ID: 21397187  |  Reference-DOI: 10.1016/J.STR.2010.12.019

(-) Compounds

Molecule 1 - PUMILIO HOMOLOG 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDEST527
    Expression System StrainROSETTA2(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 706-1056
    GenePUM2, KIAA0235, PUMH2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPUMILIO-2
 
Molecule 2 - 5'-R(UP*GP*UP*AP*AP*AP*UP*A)-3'
    ChainsB
    EngineeredYES
    Other DetailsTHIS RNA SEQUENCE OCCURS NATURALLY IN HUMANS.
    SyntheticYES

 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 3Q0Q)

(-) Sites  (0, 0)

(no "Site" information available for 3Q0Q)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:982 -A:983

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q0Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q0Q)

(-) PROSITE Motifs  (2, 9)

Asymmetric/Biological Unit (2, 9)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUM_HDPS50303 Pumilio homology domain (PUM-HD) profile.PUM2_HUMAN706-1048  1A:706-1048
2PUMPS50302 Pumilio RNA-binding repeat profile.PUM2_HUMAN726-761
762-797
798-835
836-871
872-907
908-943
944-979
980-1022
  8A:726-761
A:762-797
A:798-835
A:836-871
A:872-907
A:908-943
A:944-979
A:980-1022

(-) Exons   (0, 0)

(no "Exon" information available for 3Q0Q)

(-) 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:343
 aligned with PUM2_HUMAN | Q8TB72 from UniProtKB/Swiss-Prot  Length:1066

    Alignment length:343
                                   715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045   
          PUM2_HUMAN    706 GRSRLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQVISEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKLEKYY 1048
               SCOP domains d3q0qa_ A: automated matches                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3q0qA01 A:990-1021          --------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3q0qA02 A:990-1021          --------------------------- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3q0qA03 A:990-1021          --------------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3q0qA04 A:990-1021          --------------------------- Pfam domains (4)
           Pfam domains (5) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3q0qA05 A:990-1021          --------------------------- Pfam domains (5)
           Pfam domains (6) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3q0qA06 A:990-1021          --------------------------- Pfam domains (6)
           Pfam domains (7) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3q0qA07 A:990-1021          --------------------------- Pfam domains (7)
           Pfam domains (8) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3q0qA08 A:990-1021          --------------------------- Pfam domains (8)
         Sec.struct. author ..hhhhhhhhh......hhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PUM_HD  PDB: A:706-1048 UniProt: 706-1048                                                                                                                                                                                                                                                                                                               PROSITE (1)
                PROSITE (2) --------------------PUM  PDB: A:726-761 UniProt: 726-761PUM  PDB: A:762-797 UniProt: 762-797PUM  PDB: A:798-835 UniProt: 798-835  PUM  PDB: A:836-871 UniProt: 836-871PUM  PDB: A:872-907 UniProt: 872-907PUM  PDB: A:908-943 UniProt: 908-943PUM  PDB: A:944-979 UniProt: 944-979PUM  PDB: A:980-1022 UniProt: 980-1022     -------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3q0q A  706 GRSRLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQVISEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKLEKYY 1048
                                   715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045   

Chain B from PDB  Type:RNA  Length:8
                                         
                3q0q B    1 UGUAAAUA    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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q0Q)

(-) Pfam Domains  (1, 8)

Asymmetric/Biological Unit
(-)
Clan: TPR (230)
(-)
Family: PUF (24)
1aPUF-3q0qA01A:990-1021
1bPUF-3q0qA02A:990-1021
1cPUF-3q0qA03A:990-1021
1dPUF-3q0qA04A:990-1021
1ePUF-3q0qA05A:990-1021
1fPUF-3q0qA06A:990-1021
1gPUF-3q0qA07A:990-1021
1hPUF-3q0qA08A:990-1021

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PUM2_HUMAN | Q8TB72)
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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:1900246    positive regulation of RIG-I signaling pathway    Any process that activates or increases the frequency, rate or extent of RIG-I signaling pathway.
    GO:2000637    positive regulation of gene silencing by miRNA    Any process that activates or increases the frequency, rate or extent of gene silencing by miRNA.
    GO:0010608    posttranscriptional regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript.
    GO:0051983    regulation of chromosome segregation    Any process that modulates the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets.
    GO:0060964    regulation of gene silencing by miRNA    Any process that modulates the rate, frequency, or extent of the downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: mRNA cleavage or translational repression.
    GO:0043488    regulation of mRNA stability    Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
    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.
    GO:0034063    stress granule assembly    The aggregation, arrangement and bonding together of proteins and RNA molecules to form a stress granule.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0010494    cytoplasmic stress granule    A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PUM2_HUMAN | Q8TB723q0r 3q0s

(-) Related Entries Specified in the PDB File

3q0l 3q0m 3q0n 3q0o 3q0p 3q0r 3q0s