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(-) Description

Title :  STRUCTURE OF U2AF65 VARIANT WITH BRU5G6 DNA
 
Authors :  J. L. Jenkins, K. J. Mclaughlin, A. A. Agrawal, C. L. Kielkopf
Date :  24 Jun 14  (Deposition) - 26 Nov 14  (Release) - 02 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A,B,E,P
Keywords :  Rna Splicing Factor, Rna Recognition Motif, Rna Binding Protein, Rna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Agrawal, K. J. Mclaughlin, J. L. Jenkins, C. L. Kielkopf
Structure-Guided U2Af65 Variant Improves Recognition And Splicing Of A Defective Pre-Mrna.
Proc. Natl. Acad. Sci. Usa V. 111 17420 2014
PubMed-ID: 25422459  |  Reference-DOI: 10.1073/PNAS.1412743111

(-) Compounds

Molecule 1 - SPLICING FACTOR U2AF 65 KDA SUBUNIT
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21
    Expression System Plasmid: PGEX-6P
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 148-336
    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 (5'-D(*UP*UP*UP*UP*(BRU)P*DG*U)-3')
    Chains: P, E
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABEP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 25)

Asymmetric/Biological Unit (6, 25)
No.NameCountTypeFull Name
1BRU2Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2CPQ1Ligand/IonN,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE
3DIO5Ligand/Ion1,4-DIETHYLENE DIOXIDE
4DU9Mod. Residue
5GOL2Ligand/IonGLYCEROL
6SO46Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:268 , ASN A:271 , GLY A:297 , LEU A:298 , SER A:299binding site for residue DIO A 401
02AC2SOFTWAREPRO A:144 , ALA A:148 , TYR A:232 , GLN A:233 , LEU A:325binding site for residue DIO A 402
03AC3SOFTWARELEU A:285 , LYS A:286binding site for residue DIO A 403
04AC4SOFTWARELYS A:225 , ARG A:227 , HOH A:608 , HOH A:610binding site for residue SO4 A 404
05AC5SOFTWAREGLY A:146 , SER A:147 , ARG A:150 , SER A:281 , HOH A:502 , HOH A:513 , HOH A:515binding site for residue SO4 A 405
06AC6SOFTWAREMET A:212 , ARG A:228 , HOH A:596binding site for residue SO4 A 406
07AC7SOFTWAREILE A:191 , ASN A:192 , GLN A:193 , ASP A:194binding site for residue GOL A 407
08AC8SOFTWARELYS B:276 , LEU B:285 , LYS B:286 , PHE B:288binding site for residue DIO B 401
09AC9SOFTWAREASN B:268 , TYR B:269 , LEU B:270 , ASN B:271 , GLY B:297 , LEU B:298 , SER B:299binding site for residue DIO B 402
10AD1SOFTWARETYR B:269 , GLN B:274 , GLY B:326binding site for residue CPQ B 403
11AD2SOFTWAREARG B:149 , SER B:204 , VAL B:205 , HOH B:538binding site for residue SO4 B 404
12AD3SOFTWAREARG A:174 , LYS B:225 , ARG B:227 , HOH B:514binding site for residue SO4 B 405
13AD4SOFTWAREARG B:228 , HOH B:606binding site for residue SO4 B 406
14AD5SOFTWAREGLN B:190 , PHE B:199binding site for residue GOL B 407

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4TU9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4TU9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4TU9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4TU9)

(-) Exons   (0, 0)

(no "Exon" information available for 4TU9)

(-) 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:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeee......hhhhhhhhhhhhhhhh.........eeeeeee....eeeeee.hhhhhhhhhhhh..ee..ee.eee.............eeee......hhhhhhhhhhh...eeeeeeee......eeeeeeeee...hhhhhhhhhhh..ee..ee.eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4tu9 A 143 GPLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 336
                                   152       162       172       182       192       202       212       222       232    || 262       272       282       292       302       312       322       332    
                                                                                                                        237|                                                                              
                                                                                                                         258                                                                              


Chain B from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               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.hhhhhhhhhhhhh..ee..ee.eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4tu9 B 143 GPLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 336
                                   152       162       172       182       192       202       212       222       232    || 262       272       282       292       302       312       322       332    
                                                                                                                        237|                                                                              
                                                                                                                         258                                                                              


Chain E from PDB  Type:DNA  Length:7
                                       
                 4tu9 E   1 xxxxuGx   7
                            ||||| |
                            1-DU| |
                             2-DU |
                              3-DU|
                               4-DU
                                5-BRU
                                  7-DU


Chain P from PDB  Type:DNA  Length:6
                                      
                 4tu9 P   1 xxxxuG   6
                            ||||| 
                            ||||| 
                            1-DU| 
                             2-DU 
                              3-DU
                               4-DU
                                5-BRU
   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 4TU9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4TU9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4TU9)

(-) 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 5ev1 5ev2 5ev3 5ev4

(-) Related Entries Specified in the PDB File

4tu7 4tu8