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(-) Description

Title :  CRYSTAL STRUCTURE OF A RNA-BINDING PROTEIN 39 (RBM39) IN COMPLEX WITH FRAGMENT OF SPLICING FACTOR (U2AF) FROM UNKNOWN AT 2.20 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg), Partnership For Biology (Tcell)
Date :  29 Jul 15  (Deposition) - 14 Oct 15  (Release) - 20 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Biol. Unit 5:  I,J  (1x)
Biol. Unit 6:  K,L  (1x)
Biol. Unit 7:  M,N  (1x)
Biol. Unit 8:  O,P  (1x)
Biol. Unit 9:  Q,R  (1x)
Keywords :  Rbm39Linker (Pf15519), Rna Recognition Motif (Pf13893), Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Rna Binding Protein, Partnership For T-Cell Biology, Tcell (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. A. Stepanyuk, P. Serrano, E. Peralta, C. L. Farr, H. L. Axelrod, M. Geralt, D. Das, H. J. Chiu, L. Jaroszewski, A. M. Deacon, S. A. Lesley M. A. Elsliger, A. Godzik, I. A. Wilson, K. Wuthrich, D. R. Salomon, J. R. Williamson
Uhm-Ulm Interactions In The Rbm39-U2Af65 Splicing-Factor Complex.
Acta Crystallogr D Struct V. 72 497 2016 Biol
PubMed-ID: 27050129  |  Reference-DOI: 10.1107/S2059798316001248

(-) Compounds

Molecule 1 - RNA-BINDING PROTEIN 39
    Chains: A, C, E, G, I, K, M, O, Q
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX4T
    Expression System Strain: PB1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 418-530
    Gene: RBM39, CAPER, RNPC2
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: COACTIVATOR OF ACTIVATING PROTEIN 1 AND ESTROGEN RECEPTORS, COACTIVATOR OF AP-1 AND ERS,RNA-BINDING MOTIF PROTEIN 39,RNA-BINDING REGION-CONTAINING PROTEIN 2,TRANSCRIPTION COACTIVATOR CAPER
 
Molecule 2 - SPLICING FACTOR U2AF 65 KDA SUBUNIT
    Chains: B, D, F, H, J, L, N, P, R
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: PB1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 85-112
    Gene: U2AF2, U2AF65
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: U2 AUXILIARY FACTOR 65 KDA SUBUNIT,U2 SNRNP AUXILIARY FACTOR LARGE SUBUNIT

 Structural Features

(-) Chains, Units

  123456789101112131415161718
Asymmetric Unit : ABCDEFGHIJKLMNOPQR
Biological Unit 1 (1x): AB                
Biological Unit 2 (1x):   CD              
Biological Unit 3 (1x):     EF            
Biological Unit 4 (1x):       GH          
Biological Unit 5 (1x):         IJ        
Biological Unit 6 (1x):           KL      
Biological Unit 7 (1x):             MN    
Biological Unit 8 (1x):               OP  
Biological Unit 9 (1x):                 QR

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5CXT)

(-) Sites  (0, 0)

(no "Site" information available for 5CXT)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CXT)

(-) 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:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...hhhhh...hhhhhhhhhhhhhhh......eeee........eeee..hhhhhhhhhhhhh..ee..ee.eeee.hhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 5cxt A 420 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKYSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTYHNLFPDSMTATQLLVPSRR 530
                                   429       439       449       459       469       479       489       499       509       519       529 


Chain B from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 5cxt B  89 RKYWDVPPP  97


Chain C from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhh...hhhhhhhhhhhhhhh......eeee........eeee..hhhhhhhhhhhhh..ee..ee.eeee.hhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 5cxt C 419 QPLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKYSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTYHNLFPDSMTATQLLVPSRR 530
                                   428       438       448       458       468       478       488       498       508       518       528  


Chain D from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 5cxt D  88 VRKYWDVPPPG  98
                                    97 


Chain E from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhh...hhhhhhhhhhhhhhh......eeee........eeee..hhhhhhhhhhhhh..ee..ee.eeeeehhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 5cxt E 418 VQPLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKYSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTYHNLFPDSMTATQLLVPSR 529
                                   427       437       447       457       467       477       487       497       507       517       527  


Chain F from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 5cxt F  89 RKYWDVPPPG  98
                                    98


Chain G from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhh...hhhhhhhhhhhhhhh......eeee........eeee..hhhhhhhhhhhhh..ee..ee.eeee.hhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 5cxt G 419 QPLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKYSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTYHNLFPDSMTATQLLVPSRR 530
                                   428       438       448       458       468       478       488       498       508       518       528  


Chain H from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 5cxt H  88 VRKYWDVPPPG  98
                                    97 


Chain I from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...hhhhh...hhhhhhhhhhhhhhh......eeee........eeee..hhhhhhhhhhhhh..ee..ee.eeee.hhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 5cxt I 420 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKYSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTYHNLFPDSMTATQLLVPSRR 530
                                   429       439       449       459       469       479       489       499       509       519       529 


Chain J from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 5cxt J  88 VRKYWDVPPPG  98
                                    97 


Chain K from PDB  Type:PROTEIN  Length:113
                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhh...hhhhhhhhhhhhhhh......eeee........eeee..hhhhhhhhhhhhh..ee..ee.eeee.hhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 5cxt K   0 GVQPLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKYSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTYHNLFPDSMTATQLLVPSR 529
                            ||     426       436       446       456       466       476       486       496       506       516       526   
                            0|                                                                                                               
                           418                                                                                                               


Chain L from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 5cxt L  88 VRKYWDVPPPG  98
                                    97 


Chain M from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...hhhhh...hhhhhhhhhhhhhhh......eeee........eeee..hhhhhhhhhhhhh..ee..ee.eeee.hhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 5cxt M 420 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKYSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTYHNLFPDSMTATQLLVPSRR 530
                                   429       439       449       459       469       479       489       499       509       519       529 


Chain N from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 5cxt N  88 VRKYWDVPPPG  98
                                    97 


Chain O from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...hhhhh...hhhhhhhhhhhhhhh......eeee........eeee..hhhhhhhhhhhhh..ee..ee.eeee.hhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 5cxt O 420 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKYSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTYHNLFPDSMTATQLLVPSR 529
                                   429       439       449       459       469       479       489       499       509       519       529


Chain P from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 5cxt P  88 VRKYWDVPPP  97
                                    97


Chain Q from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhh...hhhhhhhhhhhhhhh......eeee........eeee..hhhhhhhhhhhhh..ee..ee.eeeeehhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 5cxt Q 418 VQPLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKYSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTYHNLFPDSMTATQLLVPSR 529
                                   427       437       447       457       467       477       487       497       507       517       527  


Chain R from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 5cxt R  89 RKYWDVPPPG  98
                                    98
   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 5CXT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 36)

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  5cxt
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  RBM39_MOUSE | Q8VH51
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  U2AF2_MOUSE | P26369
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 Related Entries

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

UniProtKB/Swiss-Prot
        RBM39_MOUSE | Q8VH51: 2lq5 3s6e 4j5o 4ru2
        U2AF2_MOUSE | P26369: 2m52 3v4m 4ru2 4z2x

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5CXT)