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(-) Description

Title :  CRYSTAL STRUCTURE OF MSL5 PROTEIN IN COMPLEX WITH RNA AT 1.8 A
 
Authors :  A. Jacewicz, P. Smith, L. Chico, B. Schwer, S. Shuman
Date :  29 Aug 14  (Deposition) - 17 Dec 14  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Msl5, Bbp, Rna Binding, Yeast Pre-Mrna Splicing, Protein Binding-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Jacewicz, L. Chico, P. Smith, B. Schwer, S. Shuman
Structural Basis For Recognition Of Intron Branchpoint Rna By Yeast Msl5 And Selective Effects Of Interfacial Mutation On Splicing Of Yeast Pre-Mrnas.
Rna V. 21 401 2015
PubMed-ID: 25587180  |  Reference-DOI: 10.1261/RNA.048942.114

(-) Compounds

Molecule 1 - BRANCHPOINT-BRIDGING PROTEIN
    Chains: A, C, E, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Gene: MSL5, BBP, SF1, YLR116W, L2949
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: MUD SYNTHETIC-LETHAL 5 PROTEIN,SPLICING FACTOR 1,ZINC FINGER PROTEIN BBP
 
Molecule 2 - RNA (5'-R(P*UP*AP*CP*UP*AP*AP*CP*A)-3')
    Chains: B, D, F, H
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL5Ligand/IonGLYCEROL
3SO44Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:192 , HOH A:467 , HOH A:492binding site for residue SO4 A 301
02AC2SOFTWARECYS A:185 , HOH A:466 , HOH A:487 , HOH A:488 , HOH A:489binding site for residue GOL A 302
03AC3SOFTWAREARG A:174 , ARG G:177binding site for residue ACT A 303
04AC4SOFTWAREARG A:177 , A B:10 , HOH B:223 , HOH B:226binding site for residue SO4 B 101
05AC5SOFTWAREGLN C:149 , LYS C:151binding site for residue GOL C 301
06AC6SOFTWAREARG C:174 , LYS C:178 , GLU C:258 , ARG E:172 , ARG E:174 , ARG E:177binding site for residue GOL C 302
07AC7SOFTWAREARG C:192 , PRO C:214 , HOH C:475 , HOH C:477 , HOH C:480binding site for residue ACT C 303
08AC8SOFTWARESER E:223 , GLU E:224 , ASP E:225 , HOH E:491binding site for residue GOL E 301
09AC9SOFTWARELYS E:178 , ASP E:182 , LEU E:251 , HOH E:419binding site for residue GOL E 302
10AD1SOFTWAREARG G:172 , ARG G:174 , ARG G:177binding site for residue SO4 G 301
11AD2SOFTWARETYR A:152 , GLN A:235 , TYR G:152 , GLN G:235binding site for residue SO4 G 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Glu A:197 -Gly A:198
2Glu E:197 -Gly E:198
3Pro G:206 -Gly G:207

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WAN)

(-) 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:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.........hhhhhhhh..hhhhhhhhhhhh.eeeee.........hhhhh...........eeeeee.hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wan A 145 PTKFQDKYYIPVDQYPDVNFVGLLLGPRGRTLRKLQEDSNCKIAIRGRGSVKEGKNASDLPPGAMNFEDPLHCLIIADSEDKIQKGIKVCQNIVIKAVTSPEGQNDLKRGQLRELAELNGTLRE 268
                                   154       164       174       184       194       204       214       224       234       244       254       264    


Chain B from PDB  Type:DNA/RNA  Length:9
                                         
                 4wan B   2 AUACUAACA  10


Chain C from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.........hhhhhhhh..hhhhhhhhhhhh.eeeee.........hhhhh...........eeeeee.hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wan C 145 PTKFQDKYYIPVDQYPDVNFVGLLLGPRGRTLRKLQEDSNCKIAIRGRGSVKEGKNASDLPPGAMNFEDPLHCLIIADSEDKIQKGIKVCQNIVIKAVTSPEGQNDLKRGQLRELAELNGTLRED 269
                                   154       164       174       184       194       204       214       224       234       244       254       264     


Chain D from PDB  Type:DNA/RNA  Length:10
                                          
                 4wan D   1 UAUACUAACA  10
                                    10


Chain E from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........hhhhhhhh..hhhhhhhhhhhh.eeeee.........................eeeeee.hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wan E 146 TKFQDKYYIPVDQYPDVNFVGLLLGPRGRTLRKLQEDSNCKIAIRGRGSVKEGKNASDLPPGAMNFEDPLHCLIIADSEDKIQKGIKVCQNIVIKAVTSPEGQNDLKRGQLRELAELNGTLR 267
                                   155       165       175       185       195       205       215       225       235       245       255       265  


Chain F from PDB  Type:DNA/RNA  Length:10
                                          
                 4wan F   1 UAUACUAACA  10
                                    10


Chain G from PDB  Type:PROTEIN  Length:116
                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........hhhhhhhh..hhhhhhhhhhhh.eeeee...................eeeeee.hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 4wan G 147 KFQDKYYIPVDQYPDVNFVGLLLGPRGRTLRKLQEDSNCKIAIRGRGSVKELPPGAMNFEDPLHCLIIADSEDKIQKGIKVCQNIVIKAVTSPEGQNDLKRGQLRELAELNGTLRE 268
                                   156       166       176       186       196||     212       222       232       242       252       262      
                                                                            197|                                                                
                                                                             204                                                                


Chain H from PDB  Type:DNA/RNA  Length:9
                                         
                 4wan H   2 AUACUAACA  10
   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 4WAN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu A:197 - Gly A:198   [ RasMol ]  
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    Pro G:206 - Gly G:207   [ RasMol ]  
 

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  BBP_YEAST | Q12186
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 Related Entries

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

UniProtKB/Swiss-Prot
        BBP_YEAST | Q12186: 3fma 4wal

(-) Related Entries Specified in the PDB File

4wal