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(-) Description

Title :  STRUCTURE I OF INTACT U2AF65 RECOGNIZING A 3' SPLICE SITE SIGNAL
 
Authors :  A. A. Agrawal, J. L. Jenkins, C. L. Kielkopf
Date :  19 Nov 15  (Deposition) - 24 Feb 16  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Rna Complex, Rna Splicing Factor, Rna Recognition Motif, Polypyrimidine Tract, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Agrawal, E. Salsi, R. Chatrikhi, S. Henderson, J. L. Jenkins, M. R. Green, D. N. Ermolenko, C. L. Kielkopf
An Extended U2Af(65)-Rna-Binding Domain Recognizes The 3' Splice Site Signal.
Nat Commun V. 7 10950 2016
PubMed-ID: 26952537  |  Reference-DOI: 10.1038/NCOMMS10950

(-) Compounds

Molecule 1 - SPLICING FACTOR U2AF 65 KDA SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 141-341
    Gene: U2AF2, U2AF65
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: U2 AUXILIARY FACTOR 65 KDA SUBUNIT,HU2AF65,U2 SNRNP AUXILIARY FACTOR LARGE SUBUNIT
 
Molecule 2 - DNA/RNA (5'-R(*UP*UP*U)-D(P*UP*UP*(BRU)P*U)-R(P*UP*U)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: THE 3' U IS DISORDERED IN THIS 9MER
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
1BRU1Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2DU3Mod. Residue
3NA2Ligand/IonSODIUM ION
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:206binding site for residue NA A 401
2AC2SOFTWAREGLN A:172 , VAL A:246 , HOH A:569binding site for residue PGE A 402
3AC3SOFTWARETYR A:245binding site for residue PEG A 403
4AC4SOFTWAREU B:2 , U B:3binding site for residue NA B 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EV1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5EV1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EV1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EV1)

(-) Exons   (0, 0)

(no "Exon" information available for 5EV1)

(-) 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:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhh.eeeee......hhhhhhhhhhhhhhhh.........eeeeeee....eeeeee.hhhhhhhhhhhh..ee..ee.eee.................................eeee......hhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhhhhh.........eeee.hhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ev1 A 143 QMTRQARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK 340
                                   152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332        


Chain B from PDB  Type:DNA/RNA  Length:8
                                        
                 5ev1 B   2 UUUxxuxU   9
                               |||| 
                               5-DU 
                                6-DU
                                 7-BRU
                                  8-DU
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 5EV1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EV1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EV1)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)

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  U2AF2_HUMAN | P26368
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 Related Entries

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

UniProtKB/Swiss-Prot
        U2AF2_HUMAN | P26368: 1jmt 1o0p 1opi 1u2f 2g4b 2hzc 2m0g 2u2f 2yh0 2yh1 3vaf 3vag 3vah 3vai 3vaj 3vak 3val 3vam 4fxw 4tu7 4tu8 4tu9 5ev2 5ev3 5ev4

(-) Related Entries Specified in the PDB File

5ev2 5ev3 5ev4