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(-) Description

Title :  STRUCTURE OF U2AF65 VARIANT WITH BRU5A6 DNA
 
Authors :  K. J. Mclaughlin, J. L. Jenkins, A. A. Agrawal, C. L. Kielkopf
Date :  24 Jun 14  (Deposition) - 26 Nov 14  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
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*DA*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  (7, 32)

Asymmetric/Biological Unit (7, 32)
No.NameCountTypeFull Name
1BRU2Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2CPQ1Ligand/IonN,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE
3DIO7Ligand/Ion1,4-DIETHYLENE DIOXIDE
4DU9Mod. Residue
5EDO9Ligand/Ion1,2-ETHANEDIOL
6GOL1Ligand/IonGLYCEROL
7SO43Ligand/IonSULFATE ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:268 , TYR A:269 , LEU A:270 , 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
03AC3SOFTWAREGLY A:146 , SER A:147 , ALA A:148 , ARG A:150 , SER A:281 , HOH A:515binding site for residue GOL A 403
04AC4SOFTWARELEU A:285binding site for residue EDO A 404
05AC5SOFTWAREVAL A:205 , ASP A:206 , GLY A:319 , LEU A:320 , ASN A:321 , MET A:323 , LYS A:329 , HOH A:501binding site for residue EDO A 405
06AC6SOFTWAREARG A:150 , GLN A:190 , GLU A:201binding site for residue EDO A 406
07AC7SOFTWAREPRO A:144 , GLN A:274binding site for residue EDO A 408
08AC8SOFTWARELYS A:225 , ARG A:227binding site for residue SO4 A 409
09AC9SOFTWAREARG A:228 , ILE A:310 , HOH A:639binding site for residue SO4 A 410
10AD1SOFTWARELYS B:276 , LEU B:285 , LYS B:286binding site for residue DIO B 401
11AD2SOFTWAREPRO B:182 , GLY B:183 , HIS B:259 , HOH B:507binding site for residue DIO B 402
12AD3SOFTWAREASN B:268 , TYR B:269 , LEU B:270 , ASN B:271 , GLY B:297 , LEU B:298 , SER B:299 , HOH B:522binding site for residue DIO B 403
13AD4SOFTWARESER B:204 , VAL B:205 , HOH B:549binding site for residue DIO B 404
14AD5SOFTWAREARG B:228 , HOH B:598 , HOH B:622binding site for residue DIO B 405
15AD6SOFTWARETYR B:269 , GLN B:274 , GLY B:326 , EDO B:408 , EDO B:409 , HOH B:596 , HOH B:615binding site for residue CPQ B 406
16AD7SOFTWARELYS B:292 , ASP B:293 , SER B:294 , LYS B:300 , BRU P:5 , DA P:6binding site for residue EDO B 407
17AD8SOFTWAREASP B:327 , CPQ B:406binding site for residue EDO B 408
18AD9SOFTWARECPQ B:406binding site for residue EDO B 409
19AE1SOFTWAREALA B:318 , GLY B:319 , ASN B:321 , MET B:323binding site for residue EDO B 410
20AE2SOFTWAREARG A:174 , LYS B:225 , ARG B:227 , HOH E:109binding site for residue SO4 B 411

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4TU8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4TU8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4TU8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4TU8)

(-) Exons   (0, 0)

(no "Exon" information available for 4TU8)

(-) 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
                 4tu8 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 .hhhhh.eeeee......hhhhhhhhhhhhhhhh.........eeeeeee....eeeeee.hhhhhhhhhhhh..ee..ee.eee.............eeee......hhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhhhhh..ee..ee.eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4tu8 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:6
                                      
                 4tu8 E   1 xxxxuA   6
                            ||||| 
                            1-DU| 
                             2-DU 
                              3-DU
                               4-DU
                                5-BRU


Chain P from PDB  Type:DNA  Length:7
                                       
                 4tu8 P   1 xxxxuAx   7
                            ||||| |
                            ||||| |
                            1-DU| |
                             2-DU |
                              3-DU|
                               4-DU
                                5-BRU
                                  7-DU
   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  (0, 0)

(no "SCOP Domain" information available for 4TU8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4TU8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4TU8)

(-) 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 4tu9 5ev1 5ev2 5ev3 5ev4

(-) Related Entries Specified in the PDB File

4tu7 4tu9