Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A PUMILIO-HOMOLOGY DOMAIN
 
Authors :  X. Wang, P. D. Zamore, T. M. T. Hall
Date :  26 Mar 01  (Deposition) - 09 May 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Pumilio-Homology Domain, Puf Motif, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Wang, P. D. Zamore, T. M. Hall
Crystal Structure Of A Pumilio Homology Domain.
Mol. Cell V. 7 855 2001
PubMed-ID: 11336708  |  Reference-DOI: 10.1016/S1097-2765(01)00229-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUMILIO 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PTYB3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PUMILIO-HOMOLOGY DOMAIN (RESIDUES 828-1176)
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:900 , GLU A:943 , GLU A:979 , CYS A:980BINDING SITE FOR RESIDUE BME A 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IB2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IB2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IB2)

(-) PROSITE Motifs  (2, 9)

Asymmetric/Biological Unit (2, 9)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUM_HDPS50303 Pumilio homology domain (PUM-HD) profile.PUM1_HUMAN828-1168  1A:828-1149
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, 8)

Asymmetric/Biological Unit (8, 8)
 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_HUMAN775-864901A:828-86437
1.19ENST0000025707519ENSE00000916512chr1:31425210-31425081130PUM1_HUMAN864-907441A:864-90744
1.20aENST0000025707520aENSE00001234157chr1:31423108-31422980129PUM1_HUMAN908-950431A:908-95043
1.21bENST0000025707521bENSE00000916510chr1:31418330-31418193138PUM1_HUMAN951-996461A:951-99646
1.22aENST0000025707522aENSE00000916508chr1:31414970-31414845126PUM1_HUMAN997-1038421A:997-103842
1.23ENST0000025707523ENSE00000916506chr1:31414119-31413998122PUM1_HUMAN1039-1079411A:1039-107941
1.24cENST0000025707524cENSE00001620412chr1:31409682-31409490193PUM1_HUMAN1079-1143651A:1079-114365
1.25gENST0000025707525gENSE00001065956chr1:31406189-314043531837PUM1_HUMAN1144-1186431A:1144-11496

(-) 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:322
 aligned with PUM1_HUMAN | Q14671 from UniProtKB/Swiss-Prot  Length:1186

    Alignment length:322
                                   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  
          PUM1_HUMAN    828 GRSRLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIA 1149
               SCOP domains d1ib2a_ A: Pumilio 1                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1ib2A00 A:828-1149 Leucine-rich Repeat Variant                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhee..eehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PUM_HD  PDB: A:828-1149 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:828-864           -------------------------------------------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              ----------------------------------------------------------------1.25g  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)
                1ib2 A  828 GRSRLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIA 1149
                                   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
   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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IB2)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BME  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ib2)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1ib2
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PUM1_HUMAN | Q14671
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PUM1_HUMAN | Q14671
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PUM1_HUMAN | Q14671: 1m8w 1m8x 1m8y 1m8z 2yjy 3bsb 3bsx 3q0l 3q0m 3q0n 3q0o 3q0p

(-) Related Entries Specified in the PDB File

1ib3 1IB3 CONTAINS THE SAME PROTEIN