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(-) Description

Title :  DROSOPHILA PUMILIO RNA BINDING DOMAIN (PUF DOMAIN)
 
Authors :  T. A. Edwards, A. K. Aggarwal, R. P. Wharton
Date :  16 Apr 09  (Deposition) - 28 Apr 09  (Release) - 28 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  X,Y
Biol. Unit 1:  X  (1x)
Biol. Unit 2:  Y  (1x)
Keywords :  Pumilio, Puf, Rna Binding Domain, Alternative Splicing, Cytoplasm, Developmental Protein, Phosphoprotein, Repressor, Rna-Binding, Translation Regulation, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. A. Edwards, S. E. Pyle, R. P. Wharton, A. K. Aggarwal
Structure Of Pumilio Reveals Similarity Between Rna And Peptide Binding Motifs
Cell(Cambridge, Mass. ) V. 105 281 2001
PubMed-ID: 11336677
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MATERNAL PROTEIN PUMILIO
    ChainsX, Y
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET19B
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentPUF DOMAIN
    GenePUMILIO
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit XY
Biological Unit 1 (1x)X 
Biological Unit 2 (1x) Y

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3H3D)

(-) Sites  (0, 0)

(no "Site" information available for 3H3D)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H3D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3H3D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H3D)

(-) PROSITE Motifs  (2, 17)

Asymmetric Unit (2, 17)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUM_HDPS50303 Pumilio homology domain (PUM-HD) profile.PUM_DROME1091-1428  1Y:316-627
2PUMPS50302 Pumilio RNA-binding repeat profile.PUM_DROME1111-1146
 
1147-1182
 
1183-1218
 
1219-1254
 
1255-1290
 
1291-1326
 
1327-1362
 
1366-1402
 
  16X:20-55
Y:334-369
X:56-91
Y:370-405
X:92-127
Y:406-441
X:128-163
Y:442-477
X:164-199
Y:478-513
X:200-235
Y:514-549
X:236-271
Y:550-585
X:275-311
Y:589-625
Biological Unit 1 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUM_HDPS50303 Pumilio homology domain (PUM-HD) profile.PUM_DROME1091-1428  0-
2PUMPS50302 Pumilio RNA-binding repeat profile.PUM_DROME1111-1146
 
1147-1182
 
1183-1218
 
1219-1254
 
1255-1290
 
1291-1326
 
1327-1362
 
1366-1402
 
  8X:20-55
-
X:56-91
-
X:92-127
-
X:128-163
-
X:164-199
-
X:200-235
-
X:236-271
-
X:275-311
-
Biological Unit 2 (2, 9)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUM_HDPS50303 Pumilio homology domain (PUM-HD) profile.PUM_DROME1091-1428  1Y:316-627
2PUMPS50302 Pumilio RNA-binding repeat profile.PUM_DROME1111-1146
 
1147-1182
 
1183-1218
 
1219-1254
 
1255-1290
 
1291-1326
 
1327-1362
 
1366-1402
 
  8-
Y:334-369
-
Y:370-405
-
Y:406-441
-
Y:442-477
-
Y:478-513
-
Y:514-549
-
Y:550-585
-
Y:589-625

(-) Exons   (0, 0)

(no "Exon" information available for 3H3D)

(-) 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 X from PDB  Type:PROTEIN  Length:313
 aligned with PUM_DROME | P25822 from UniProtKB/Swiss-Prot  Length:1533

    Alignment length:313
                                  1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271      1281      1291      1301      1311      1321      1331      1341      1351      1361      1371      1381      1391      1401   
           PUM_DROME   1092 RSRLLEDFRNQRYPNLQLRDLANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEFGTPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNVVEKCVTHATRGERTGLIDEVCTFNDNALHVMMKDQYANYVVQKMIDVSEPTQLKKLMTKI 1404
               SCOP domains d3h3dx_ X: automated matches                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 3h3dX00 X:1-313 Leucine-rich Repeat Variant                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh......hhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh.hhhhhhhhhhhh.hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PUM_HD  PDB: - UniProt: 1091-1428                                                                                                                                                                                                                                                                                         PROSITE (1)
                PROSITE (2) -------------------PUM  PDB: X:20-55 UniProt: 1111-1146PUM  PDB: X:56-91 UniProt: 1147-1182PUM  PDB: X:92-127                  PUM  PDB: X:128-163                 PUM  PDB: X:164-199                 PUM  PDB: X:200-235                 PUM  PDB: X:236-271                 ---PUM  PDB: X:275-311                  -- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3h3d X    1 MSRLLEDFRNQRYPNLQLRDLANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEFGTPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNVVEKCVTHATRGERTGLIDEVCTFNDNALHVMMKDQYANYVVQKMIDVSEPTQLKKLMTKI  313
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310   

Chain Y from PDB  Type:PROTEIN  Length:314
 aligned with PUM_DROME | P25822 from UniProtKB/Swiss-Prot  Length:1533

    Alignment length:314
                                  1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320      1330      1340      1350      1360      1370      1380      1390      1400    
           PUM_DROME   1091 GRSRLLEDFRNQRYPNLQLRDLANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEFGTPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNVVEKCVTHATRGERTGLIDEVCTFNDNALHVMMKDQYANYVVQKMIDVSEPTQLKKLMTKI 1404
               SCOP domains d3h3dy_ Y: automated matches                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 3h3dY00 Y:314-627 Leucine-rich Repeat Variant                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh......hhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PUM_HD  PDB: Y:316-627 UniProt: 1091-1428                                                                                                                                                                                                                                                                                  PROSITE (1)
                PROSITE (2) --------------------PUM  PDB: Y:334-369                 PUM  PDB: Y:370-405                 PUM  PDB: Y:406-441                 PUM  PDB: Y:442-477                 PUM  PDB: Y:478-513                 PUM  PDB: Y:514-549                 PUM  PDB: Y:550-585                 ---PUM  PDB: Y:589-625                  -- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3h3d Y  314 HMSRLLEDFRNQRYPNLQLRDLANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEFGTPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNVVEKCVTHATRGERTGLIDEVCTFNDNALHVMMKDQYANYVVQKMIDVSEPTQLKKLMTKI  627
                                   323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623    

   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 3H3D)

(-) Gene Ontology  (33, 33)

Asymmetric Unit(hide GO term definitions)
Chain X,Y   (PUM_DROME | P25822)
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:0000900    translation repressor activity, nucleic acid binding    Antagonizes the ribosome-mediated translation of mRNA into a polypeptide via direct binding (through a selective and non-covalent interaction) to nucleic acid.
biological process
    GO:0008595    anterior/posterior axis specification, embryo    The specification of the anterior/posterior axis of the embryo by the products of genes expressed maternally and genes expressed in the zygote.
    GO:0048149    behavioral response to ethanol    Any process that results in a change in the behavior of an organism as a result of an ethanol stimulus.
    GO:0001709    cell fate determination    A process involved in cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:0048813    dendrite morphogenesis    The process in which the anatomical structures of a dendrite are generated and organized. A dendrite is a freely branching protoplasmic process of a nerve cell.
    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:0042078    germ-line stem cell division    The self-renewing division of a germline stem cell to produce a daughter stem cell and a daughter germ cell, which will divide to form the gametes.
    GO:0008258    head involution    Movement of the anterior ectoderm to the interior of the embryo.
    GO:0007616    long-term memory    The memory process that deals with the storage, retrieval and modification of information a long time (typically weeks, months or years) after receiving that information. This type of memory is typically dependent on gene transcription regulated by second messenger activation.
    GO:0050804    modulation of chemical synaptic transmission    Any process that modulates the frequency or amplitude of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. Amplitude, in this case, refers to the change in postsynaptic membrane potential due to a single instance of synaptic transmission.
    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:0045786    negative regulation of cell cycle    Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
    GO:0042059    negative regulation of epidermal growth factor receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    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: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:0007280    pole cell migration    The directed movement of a pole cell (germline progenitors in insects) from its site of production at the posterior pole of the embryo through to the site where the gonads will form.
    GO:0060213    positive regulation of nuclear-transcribed mRNA poly(A) tail shortening    Any process that increases the frequency, rate or extent of poly(A) tail shortening of a nuclear-transcribed mRNA. Poly(A) tail shortening is the decrease in length of the poly(A) tail of an mRNA from full length to an oligo(A) length.
    GO:0045727    positive regulation of translation    Any process that activates or increases 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:0016441    posttranscriptional gene silencing    The inactivation of gene expression by a posttranscriptional mechanism.
    GO:0008582    regulation of synaptic growth at neuromuscular junction    Any process that modulates the frequency, rate or extent of synaptic growth at neuromuscular junctions.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0097482    muscle cell postsynaptic density    A postsynaptic specialization that is part of a neuromuscular junction.
    GO:0031594    neuromuscular junction    The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential.
    GO:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    GO:0061176    type Ib terminal bouton    Terminal inflated portion of the axon of a glutamatergic neuron, containing the specialized apparatus necessary for the tonic release neurotransmitters that will induce the contraction of muscle. Type Ib terminal boutons are larger than type Is terminal boutons.
    GO:0061177    type Is terminal bouton    Terminal inflated portion of the axon of a glutamatergic neuron, containing the specialized apparatus necessary for the phasic release neurotransmitters that will induce the contraction of muscle. Type Is terminal boutons are smaller than type Ib terminal boutons.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PUM_DROME | P258225kl1 5kl8 5kla

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3H3D)