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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PUMILIO1 IN COMPLEX WITH CYCLINB REVERSE RNA
 
Authors :  Y. K. Gupta, D. T. Nair, R. P. Wharton, A. K. Aggarwal
Date :  23 Dec 07  (Deposition) - 08 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  B,C  (1x)
Biol. Unit 2:  A  (1x)
Keywords :  Protein-Rna Complex, Alternative Splicing, Cytoplasm, Phosphoprotein, Rna-Binding, Translation Regulation, Rna Binding Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. K. Gupta, D. T. Nair, R. P. Wharton, A. K. Aggarwal
Structures Of Human Pumilio With Noncognate Rnas Reveal Molecular Mechanisms For Binding Promiscuity.
Structure V. 16 549 2008
PubMed-ID: 18328718  |  Reference-DOI: 10.1016/J.STR.2008.01.006
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUMILIO HOMOLOG 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-19B
    Expression System StrainBL21-GOLD
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentPUMILIO-PUF DOMAIN
    GenePUM1, KIAA0099, PUMH1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPUMILIO-1, HSPUM
 
Molecule 2 - 5'-R(*UP*UP*UP*AP*AP*UP*GP*UP*U)-3'
    ChainsC
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x) BC
Biological Unit 2 (1x)A  

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3BSB)

(-) Sites  (0, 0)

(no "Site" information available for 3BSB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 17)

Asymmetric Unit (2, 17)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUM_HDPS50303 Pumilio homology domain (PUM-HD) profile.PUM1_HUMAN828-1168  1B:828-1168
2PUMPS50302 Pumilio RNA-binding repeat profile.PUM1_HUMAN848-883
 
884-919
 
920-955
 
956-991
 
992-1027
 
1028-1063
 
1064-1099
 
1103-1142
 
  16A:848-883
B:848-883
A:884-919
B:884-919
A:920-955
B:920-955
A:956-991
B:956-991
A:992-1027
B:992-1027
A:1028-1063
B:1028-1063
A:1064-1099
B:1064-1099
A:1103-1142
B:1103-1142
Biological Unit 1 (2, 9)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUM_HDPS50303 Pumilio homology domain (PUM-HD) profile.PUM1_HUMAN828-1168  1B:828-1168
2PUMPS50302 Pumilio RNA-binding repeat profile.PUM1_HUMAN848-883
 
884-919
 
920-955
 
956-991
 
992-1027
 
1028-1063
 
1064-1099
 
1103-1142
 
  8-
B:848-883
-
B:884-919
-
B:920-955
-
B:956-991
-
B:992-1027
-
B:1028-1063
-
B:1064-1099
-
B:1103-1142
Biological Unit 2 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUM_HDPS50303 Pumilio homology domain (PUM-HD) profile.PUM1_HUMAN828-1168  0-
2PUMPS50302 Pumilio RNA-binding repeat profile.PUM1_HUMAN848-883
 
884-919
 
920-955
 
956-991
 
992-1027
 
1028-1063
 
1064-1099
 
1103-1142
 
  8A:848-883
-
A:884-919
-
A:920-955
-
A:956-991
-
A:992-1027
-
A:1028-1063
-
A:1064-1099
-
A:1103-1142
-

(-) Exons   (8, 16)

Asymmetric Unit (8, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1fENST000002570751fENSE00001830352chr1:31538545-3153846383PUM1_HUMAN-00--
1.3cENST000002570753cENSE00002154901chr1:31532424-31532051374PUM1_HUMAN1-1211210--
1.5aENST000002570755aENSE00001171922chr1:31501711-3150164369PUM1_HUMAN122-144230--
1.6ENST000002570756ENSE00001171914chr1:31479949-31479841109PUM1_HUMAN145-181370--
1.7ENST000002570757ENSE00001171904chr1:31478878-31478700179PUM1_HUMAN181-240600--
1.8bENST000002570758bENSE00000916523chr1:31468067-31467901167PUM1_HUMAN241-296560--
1.9bENST000002570759bENSE00000916522chr1:31465507-31465237271PUM1_HUMAN296-386910--
1.11bENST0000025707511bENSE00000916520chr1:31454252-3145415994PUM1_HUMAN387-418320--
1.12cENST0000025707512cENSE00001171885chr1:31453010-31452909102PUM1_HUMAN418-452350--
1.13bENST0000025707513bENSE00000916518chr1:31447649-31447498152PUM1_HUMAN452-502510--
1.14aENST0000025707514aENSE00001171865chr1:31441339-31441201139PUM1_HUMAN503-549470--
1.15bENST0000025707515bENSE00000916516chr1:31440157-31440014144PUM1_HUMAN549-597490--
1.16dENST0000025707516dENSE00000916515chr1:31439125-31438829297PUM1_HUMAN597-6961000--
1.17bENST0000025707517bENSE00000916514chr1:31437757-31437521237PUM1_HUMAN696-775800--
1.18aENST0000025707518aENSE00000916513chr1:31426828-31426561268PUM1_HUMAN775-864902A:829-864
B:828-864
36
37
1.19ENST0000025707519ENSE00000916512chr1:31425210-31425081130PUM1_HUMAN864-907442A:864-907
B:864-907
44
44
1.20aENST0000025707520aENSE00001234157chr1:31423108-31422980129PUM1_HUMAN908-950432A:908-950
B:908-950
43
43
1.21bENST0000025707521bENSE00000916510chr1:31418330-31418193138PUM1_HUMAN951-996462A:951-996
B:951-996
46
46
1.22aENST0000025707522aENSE00000916508chr1:31414970-31414845126PUM1_HUMAN997-1038422A:997-1038
B:997-1038
42
42
1.23ENST0000025707523ENSE00000916506chr1:31414119-31413998122PUM1_HUMAN1039-1079412A:1039-1079
B:1039-1079
41
41
1.24cENST0000025707524cENSE00001620412chr1:31409682-31409490193PUM1_HUMAN1079-1143652A:1079-1143
B:1079-1143
65
65
1.25gENST0000025707525gENSE00001065956chr1:31406189-314043531837PUM1_HUMAN1144-1186432A:1144-1168
B:1144-1168
25
25

(-) 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:340
 aligned with PUM1_HUMAN | Q14671 from UniProtKB/Swiss-Prot  Length:1186

    Alignment length:340
                                   838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148      1158      1168
          PUM1_HUMAN    829 RSRLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLEKYY 1168
               SCOP domains d3bsba_ A: Pumilio 1                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3bsbA00 A:829-1168 Leucine-rich Repeat Variant                                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh........hhhhh.hhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhee..eehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PUM_HD  PDB: - UniProt: 828-1168                                                                                                                                                                                                                                                                                                                     PROSITE (1)
                PROSITE (2) -------------------PUM  PDB: A:848-883 UniProt: 848-883PUM  PDB: A:884-919 UniProt: 884-919PUM  PDB: A:920-955 UniProt: 920-955PUM  PDB: A:956-991 UniProt: 956-991PUM  PDB: A:992-1027                PUM  PDB: A:1028-1063               PUM  PDB: A:1064-1099               ---PUM  PDB: A:1103-1142 UniProt: 1103-1142-------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.18a  PDB: A:829-864          -------------------------------------------Exon 1.20a  PDB: A:908-950 UniProt: 908-950Exon 1.21b  PDB: A:951-996 UniProt: 951-996   Exon 1.22a  PDB: A:997-1038               Exon 1.23  PDB: A:1039-1079              ----------------------------------------------------------------Exon 1.25g [INCOMPLETE]   Transcript 1 (1)
           Transcript 1 (2) -----------------------------------Exon 1.19  PDB: A:864-907 UniProt: 864-907  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.24c  PDB: A:1079-1143 UniProt: 1079-1143                  ------------------------- Transcript 1 (2)
                3bsb A  829 RSRLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLEKYY 1168
                                   838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148      1158      1168

Chain B from PDB  Type:PROTEIN  Length:341
 aligned with PUM1_HUMAN | Q14671 from UniProtKB/Swiss-Prot  Length:1186

    Alignment length:341
                                   837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167 
          PUM1_HUMAN    828 GRSRLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLEKYY 1168
               SCOP domains d3bsbb_ B: Pumilio 1                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3bsbB00 B:828-1168 Leucine-rich Repeat Variant                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.......hhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh...hhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PUM_HD  PDB: B:828-1168 UniProt: 828-1168                                                                                                                                                                                                                                                                                                             PROSITE (1)
                PROSITE (2) --------------------PUM  PDB: B:848-883 UniProt: 848-883PUM  PDB: B:884-919 UniProt: 884-919PUM  PDB: B:920-955 UniProt: 920-955PUM  PDB: B:956-991 UniProt: 956-991PUM  PDB: B:992-1027                PUM  PDB: B:1028-1063               PUM  PDB: B:1064-1099               ---PUM  PDB: B:1103-1142 UniProt: 1103-1142-------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.18a  PDB: B:828-864           -------------------------------------------Exon 1.20a  PDB: B:908-950 UniProt: 908-950Exon 1.21b  PDB: B:951-996 UniProt: 951-996   Exon 1.22a  PDB: B:997-1038               Exon 1.23  PDB: B:1039-1079              ----------------------------------------------------------------Exon 1.25g [INCOMPLETE]   Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.19  PDB: B:864-907 UniProt: 864-907  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.24c  PDB: B:1079-1143 UniProt: 1079-1143                  ------------------------- Transcript 1 (2)
                3bsb B  828 GRSRLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLEKYY 1168
                                   837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167 

Chain C from PDB  Type:RNA  Length:9
                                          
                3bsb C    1 UUUAAUGUU    9

   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  (1, 2)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PUM1_HUMAN | Q14671)
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:0008344    adult locomotory behavior    Locomotory behavior in a fully developed and mature organism.
    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:0061157    mRNA destabilization    Any process that decreases the stability of an mRNA molecule, making it more vulnerable to degradative processes. Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
    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:0016441    posttranscriptional gene silencing    The inactivation of gene expression by a posttranscriptional mechanism.
    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:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
    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:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0048863    stem cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
cellular component
    GO:0000932    P-body    A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PUM1_HUMAN | Q146711ib2 1m8w 1m8x 1m8y 1m8z 2yjy 3bsx 3q0l 3q0m 3q0n 3q0o 3q0p

(-) Related Entries Specified in the PDB File

1m8w CRYSTAL STRUCTURE OF THE PUMILIO-HOMOLOGY DOMAIN FROM HUMAN PUMILIO1 IN COMPLEX WITH NRE1-19 RNA
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
3bsx