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(-) Description

Title :  CRYSTAL STRUCTURE OF A RNA BINDING DOMAIN OF POLYADENYLATE-BINDING PROTEIN (PABPN1) FROM HOMO SAPIENS AT 1.95 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg), Partnership For Biology (Tcell)
Date :  26 Oct 11  (Deposition) - 23 Nov 11  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Ferredoxin-Like, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Partnership For T-Cell Biology, Tcell, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Joint Center For Structural Genomics (Jcsg), Partnership For T-Cell Biology
Crystal Structure Of A Rna Binding Domain Of Hypothetical Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens At 1. 95 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - POLYADENYLATE-BINDING PROTEIN 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidSPEEDET
    Expression System StrainHK100
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRNA BINDING DOMAIN
    GeneBC010939, PAB2, PABP2, PABPN1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPABP-2, POLY(A)-BINDING PROTEIN 2, NUCLEAR POLY(A)-BINDING PROTEIN 1, POLY(A)-BINDING PROTEIN II, PABII, POLYADENYLATE-BINDING NUCLEAR PROTEIN 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric Unit (5, 6)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MSE1Mod. Amino AcidSELENOMETHIONINE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PGE1Ligand/IonTRIETHYLENE GLYCOL
5SO41Ligand/IonSULFATE ION
Biological Unit 1 (5, 12)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2MSE2Mod. Amino AcidSELENOMETHIONINE
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4PGE2Ligand/IonTRIETHYLENE GLYCOL
5SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:211 , PRO A:212 , ARG A:227 , ARG A:240 , EDO A:301 , HOH A:354BINDING SITE FOR RESIDUE SO4 A 300
2AC2SOFTWAREASN A:178 , ARG A:227 , ARG A:240 , GLN A:241 , SO4 A:300BINDING SITE FOR RESIDUE EDO A 301
3AC3SOFTWAREASN A:199 , ASP A:206 , GLU A:219BINDING SITE FOR RESIDUE EDO A 302
4AC4SOFTWAREGLY A:0 , MSE A:167BINDING SITE FOR RESIDUE PEG A 303
5AC5SOFTWARELYS A:207 , ALA A:231BINDING SITE FOR RESIDUE PGE A 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.PABP2_HUMAN172-249  1A:172-249
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.PABP2_HUMAN172-249  2A:172-249

(-) Exons   (4, 4)

Asymmetric Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002167271aENSE00001099642chr14:23790498-23791029532PABP2_HUMAN1-1171170--
1.2ENST000002167272ENSE00000653914chr14:23791390-23791504115PABP2_HUMAN118-156390--
1.3ENST000002167273ENSE00000889215chr14:23792208-2379227568PABP2_HUMAN156-178231A:0-178 (gaps)22
1.4ENST000002167274ENSE00000653916chr14:23792586-23792692107PABP2_HUMAN179-214361A:179-21436
1.5ENST000002167275ENSE00000653918chr14:23793174-2379326188PABP2_HUMAN214-243301A:214-24330
1.6aENST000002167276aENSE00000653919chr14:23793347-23793498152PABP2_HUMAN244-294511A:244-25310
1.6cENST000002167276cENSE00001099644chr14:23794456-23795394939PABP2_HUMAN294-306130--

(-) 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:88
 aligned with PABP2_HUMAN | Q86U42 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:97
                                   166       176       186       196       206       216       226       236       246       
          PABP2_HUMAN   157 GPVIMSIEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRTNRPG 253
               SCOP domains d         3ucga_ A: automated matches                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author h---------hhhhhheeeee......hhhhhhhhhhhhh.eeeeeeee........eeeeeee..hhhhhhhhhhh..ee..ee.eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------RRM  PDB: A:172-249 UniProt: 172-249                                          ---- PROSITE
           Transcript 1 (1) Exon 1.3 [INCOMPLETE] Exon 1.4  PDB: A:179-214            -----------------------------Exon 1.6a  Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------Exon 1.5  PDB: A:214-243      ---------- Transcript 1 (2)
                 3ucg A   0 G---------mEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRTNRPG 253
                            |        -|      176       186       196       206       216       226       236       246       
                            |       167-MSE                                                                                  
                            0                                                                                                

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  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 Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A   (PABP2_HUMAN | Q86U42)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0031124    mRNA 3'-end processing    Any process involved in forming the mature 3' end of an mRNA molecule.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
    GO:0046778    modification by virus of host mRNA processing    Any viral process that interferes with the processing of mRNA in the host cell.
    GO:0006936    muscle contraction    A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
    GO:0016973    poly(A)+ mRNA export from nucleus    The directed movement of poly(A)+ mRNA out of the nucleus into the cytoplasm.
    GO:0006369    termination of RNA polymerase II transcription    The process in which the synthesis of an RNA molecule by RNA polymerase II using a DNA template is completed.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0042405    nuclear inclusion body    An intranuclear focus at which aggregated proteins have been sequestered.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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        PABP2_HUMAN | Q86U423b4d 3b4m

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