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(-) Description

Title :  STRUCTURE IV OF INTACT U2AF65 RECOGNIZING THE 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 :  1.57
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: 562
    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(P*UP*UP*UP*(UD)P*UP*U)-D(P*(BRU)P*(UD))- R(P*C)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: 5' PHOSPHORYLATION
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1BRU1Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2DU2Mod. Residue
3GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:227 , VAL A:253 , ASN A:311 , ASP A:314 , HOH A:508 , HOH A:534 , HOH A:551 , HOH A:565binding site for residue GOL A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EV4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5EV4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EV4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EV4)

(-) Exons   (0, 0)

(no "Exon" information available for 5EV4)

(-) 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:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh.eeeee......hhhhhhhhhhhhhhhh.........eeeeeee....eeeeee.hhhhhhhhhhhh..ee..ee.eee.................................eeee......hhhhhhhhhhh...eeeeeeee......eeeeeeeee...hhhhhhhhhhh..ee..ee.eeeehhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ev4 A 144 MTRQARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK 340
                                   153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       


Chain B from PDB  Type:DNA/RNA  Length:9
                                         
                 5ev4 B   1 UUUxUUuxC   9
                               |  || 
                               4-DU| 
                                  7-BRU
                                   8-DU
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 5EV4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EV4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EV4)

(-) 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 5ev1 5ev2 5ev3

(-) Related Entries Specified in the PDB File

5ev1 5ev2 5ev3