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(-) Description

Title :  STRUCTURE AND CONFORMATIONAL PLASTICITY OF THE U6 SMALL NUCLEAR RIBONUCLEOPROTEIN CORE
 
Authors :  E. J. Montemayor, D. A. Brow, S. E. Butcher
Date :  24 Sep 16  (Deposition) - 11 Jan 17  (Release) - 18 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Ribonucleoprotein, Spliceosome, Snrnp, U6, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. J. Montemayor, A. L. Didychuk, H. Liao, P. Hu, D. A. Brow, S. E. Butche
Structure And Conformational Plasticity Of The U6 Small Nuclear Ribonucleoprotein Core.
Acta Crystallogr D Struct V. 73 1 2017 Biol
PubMed-ID: 28045380  |  Reference-DOI: 10.1107/S2059798316018222

(-) Compounds

Molecule 1 - U4/U6 SNRNA-ASSOCIATED-SPLICING FACTOR PRP24
    ChainsA, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET3A
    Expression System StrainBL21(DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 34-400
    GenePRP24, YMR268C, YM8156.10C
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainATCC 204508 / S288C
    SynonymU4/U6 SNRNP PROTEIN
 
Molecule 2 - U6 SNRNA
    ChainsB, D
    EngineeredYES
    MutationYES
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2GOL5Ligand/IonGLYCEROL
3K5Ligand/IonPOTASSIUM ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3K-1Ligand/IonPOTASSIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3K-1Ligand/IonPOTASSIUM ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:37 , HOH A:836 , HOH A:857 , HOH A:898 , HOH B:325 , HOH B:370binding site for residue K A 501
02AC2SOFTWAREARG A:36 , THR A:41 , HOH A:707 , HOH C:700binding site for residue CL A 502
03AC3SOFTWARESER A:193 , PRO A:195 , HOH A:857 , HOH A:898 , G B:50binding site for residue CL A 503
04AC4SOFTWAREASN A:179 , VAL A:189 , LYS A:191 , THR A:386 , ASN A:388 , ASP A:389 , ARG A:392 , HOH A:624 , HOH A:662binding site for residue GOL A 504
05AC5SOFTWARESER A:127 , THR A:129 , ASN A:132 , GLU A:184 , GLN A:330 , HOH A:771 , HOH A:788binding site for residue GOL A 505
06AC6SOFTWAREA B:59 , G B:60 , G B:86 , U B:87 , HOH B:354binding site for residue K B 201
07AC7SOFTWAREA B:53 , U B:54 , HOH B:311 , HOH B:350binding site for residue GOL B 202
08AC8SOFTWAREASN A:279 , HOH A:826 , MET C:370 , ILE C:371 , ASN C:373binding site for residue K C 501
09AC9SOFTWAREASN C:37 , HOH C:727 , HOH C:792 , HOH C:817 , HOH C:833 , HOH D:309 , HOH D:363binding site for residue K C 502
10AD1SOFTWARESER C:193 , PRO C:195 , HOH C:833 , G D:50binding site for residue CL C 503
11AD2SOFTWAREARG C:36 , THR C:41 , HOH C:680binding site for residue CL C 504
12AD3SOFTWAREARG A:89 , TYR A:90 , HOH A:707 , THR C:41 , ALA C:88 , ARG C:89 , TYR C:90 , HOH C:680 , HOH C:700 , HOH C:722binding site for residue GOL C 505
13AD4SOFTWAREGLN C:54 , ILE C:68 , HIS C:69 , VAL C:70 , HOH C:603 , HOH C:613 , HOH C:648binding site for residue GOL C 506
14AD5SOFTWAREA D:59 , G D:60 , G D:86binding site for residue K D 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5TF6)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Phe A:317 -Pro A:318
2Cys C:64 -Gly C:65
3Phe C:317 -Pro C:318

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5TF6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5TF6)

(-) Exons   (0, 0)

(no "Exon" information available for 5TF6)

(-) 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:367
                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhheeeeeee....hhhhhhhhhhhhh.eeeeeeee......eeeeeee.hhhhhhhhhh....ee..ee.eeee....eeeee......hhhhhhhhhhh....eeeee...........eeeeee.hhhhhhhhhhhhh..ee..ee.eeee.hhhhh....hhhhhh..eeeeeee.....hhhhhhhhhhhhh.eeeee............eeeeeee.hhhhhhhhhhhh.eee..eeeeeee..hhhhhhhhhhhhhh...hhhhhhheeeee......hhhhhhhhhhhh...hhh.eeeeeeehhhheeeeee.hhhhhhhhhhhhh..ee..ee.eeehhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tf6 A  33 MLTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLADKKPFLERNEVKRLLASRNSKELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGTINDMKRYYNNQQN 399
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       

Chain B from PDB  Type:RNA  Length:71
                                                                                                       
                 5tf6 B  30 GGUCAAUUUGAAACAAUACAGAGAUGAUCAGCAGUUCCCCUGCAUAAGGAUGAACCGUUUUACAAAGAGAC 100
                                    39        49        59        69        79        89        99 

Chain C from PDB  Type:PROTEIN  Length:366
                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhh.eeeeeee....hhhhhhhhhhhhh.eeeeeeee......eeeeeee.hhhhhhhhhh....ee..ee.eeee....eeeee......hhhhhhhhhhh....eeeee...........eeeeee.hhhhhhhhhhhhh..ee..ee.eeee.hhhhh......hhhhh.eeeeeee.....hhhhhhhhhhhhh.eeeee............eeeeeee.hhhhhhhhhhhh..ee..ee.eeee..hhhhhhhhhhhhhh...hhhhhh.eeeee......hhhhhhhhhhhhh..hhh.eeeeeeehhhheeeeee.hhhhhhhhhhhhh..ee..ee.eeehhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5tf6 C  33 MLTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLADKKPFLERNEVKRLLASRNSKELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGTINDMKRYYNNQQ 398
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392      

Chain D from PDB  Type:RNA  Length:52
                                                                                    
                 5tf6 D  30 GGUCAAUUUGAAACAAUACAGAGAUGAUCAGCAGCCGUUUUACAAAGAGACC 101
                                    39        49        59   ||   89        99  
                                                            63|                 
                                                             84                 

   Legend:   → Mismatch (orange background)
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    → 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 5TF6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5TF6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5TF6)

(-) Gene Ontology  (12, 12)

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        PRP24_YEAST | P499602ghp 2go9 2kh9 2l9w 4n0t

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