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(-) Description

Title :  CRYSTAL STRUCTURE OF ASHBYA GOSSYPII RAI1 IN COMPLEX WITH PU(S)6-MN2+
 
Authors :  V. Y. Wang, L. Tong
Date :  03 Jun 15  (Deposition) - 22 Jul 15  (Release) - 05 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  B,D  (1x)
Biol. Unit 2:  A,C  (1x)
Keywords :  Rai1, Rna, Decapping, Mrna 5'-Processing, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Y. Wang, X. Jiao, M. Kiledjian, L. Tong
Structural And Biochemical Studies Of The Distinct Activity Profiles Of Rai1 Enzymes.
Nucleic Acids Res. V. 43 6596 2015
PubMed-ID: 26101253  |  Reference-DOI: 10.1093/NAR/GKV620

(-) Compounds

Molecule 1 - AFR263CP
    Chains: B, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: AGOS_AFR263C
    Organism Common: YEAST
    Organism Scientific: ASHBYA GOSSYPII (STRAIN ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
    Organism Taxid: 284811
    Strain: ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056
 
Molecule 2 - RNA (5'-R(P*UP*(U37)P*(U37)P*UP*UP*U)-3')
    Chains: D, C
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):  B D
Biological Unit 2 (1x): A C 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1MN6Ligand/IonMANGANESE (II) ION
2SO42Ligand/IonSULFATE ION
3U374Mod. NucleotideURIDINE 5'-MONOTHIOPHOSPHATE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2SO41Ligand/IonSULFATE ION
3U372Mod. NucleotideURIDINE 5'-MONOTHIOPHOSPHATE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2SO41Ligand/IonSULFATE ION
3U372Mod. NucleotideURIDINE 5'-MONOTHIOPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:217 , GLU B:235 , LEU B:236 , HOH B:535 , U D:2binding site for residue MN B 401
2AC2SOFTWAREGLU B:215 , ASP B:217 , HOH B:530 , HOH B:552 , HOH B:572 , U D:2binding site for residue MN B 402
3AC3SOFTWAREHOH B:515 , HOH B:531 , HOH B:538 , HOH B:541 , HOH B:543 , HOH B:623binding site for residue MN B 403
4AC4SOFTWAREARG B:106 , GLY B:107 , LYS B:198 , GLY B:213 , ALA B:214 , GLU B:215 , HOH B:532 , HOH B:593binding site for residue SO4 B 404
5AC5SOFTWAREASP A:217 , GLU A:235 , LEU A:236 , HOH A:540 , U C:2binding site for residue MN C 401
6AC6SOFTWAREGLU A:215 , ASP A:217 , HOH A:527 , HOH A:536 , HOH A:598 , U C:2binding site for residue MN C 402
7AC7SOFTWAREHOH A:504 , HOH A:522 , HOH A:539 , HOH A:545 , HOH A:565 , HOH A:604binding site for residue MN A 401
8AC8SOFTWAREARG A:106 , GLY A:107 , LYS A:198 , GLY A:213 , ALA A:214 , GLU A:215 , HOH A:524 , HOH A:607binding site for residue SO4 A 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BTE)

(-) 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:365
                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.............eeeeeeeee...eeee.......ee..hhhhhh.............hhhhhh......hhhhhhhhhhhhhhhh......eeeehhhhhhhhhh....hhhh.eeeeeee..eeeeee.............hhhhhhhhhhhhhhhhhee..hhhhhhhhhhh...........eeeeeeeeee..eeeeeeee..ee.........hhh.eeeeeeee...hhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeeee..hhhhhhhh..hhhhhhhhhhhhhhhhhhh..........eeeeeee..eeeeeee.hhhhhhh....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bte A   5 SELLLQRRLATTALKQPKELGYYSTNVGGELKVMDESNLSYYYLPDADIEKHIDLSAGARKFQDEQAEAEDDTGSLHGLLQTLMEYERRKSKKVNADIIAFRGQVKRLIHCAFGGHATDVDMYVMSFDGQLFIRAARKKLEFPTSPRESWAYLAYYSGYKFERMALLDRPVAETPREVLESRGKQVVRNGPQYKTVVRTGVGEHKLVLGAEVDGIFDFREPTGDNLKHYVELKVAKKVQTLKDATNFEQKLFSVWLQCFLVGINRVIIGFRDEKFVLKSVEEFSTSEIPLLLKSTRNACVDAIKWYGALTKWLCELPRGPEDDFKLYRLSCSRGALHLRQLHDEDLANGDDIIPGWFREWRRSLS 371
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294    || 306       316       326       336       346       356       366     
                                                                                                                                                                                                                                                                                                                                299|                                                                     
                                                                                                                                                                                                                                                                                                                                 302                                                                     


Chain B from PDB  Type:PROTEIN  Length:368
                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.............eeeeeeeee...eeee.......ee..hhhhhh.............hhhhhh......hhhhhhhhhhhhhhhh......eeeehhhhhhhhhh....hhhh.eeeeeee..eeeeee.............hhhhhhhhhhhhhhhhhee..hhhhhhhhhhh...........eeeeeeeeee..eeeeeeee..ee.........hhh.eeeeeeee...hhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeeee..hhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhh..eeeeeee..eeeeeee.hhhhhhh....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bte B   2 VFESELLLQRRLATTALKQPKELGYYSTNVGGELKVMDESNLSYYYLPDADIEKHIDLSAGARKFQDEQAEAEDDTGSLHGLLQTLMEYERRKSKKVNADIIAFRGQVKRLIHCAFGGHATDVDMYVMSFDGQLFIRAARKKLEFPTSPRESWAYLAYYSGYKFERMALLDRPVAETPREVLESRGKQVVRNGPQYKTVVRTGVGEHKLVLGAEVDGIFDFREPTGDNLKHYVELKVAKKVQTLKDATNFEQKLFSVWLQCFLVGINRVIIGFRDEKFVLKSVEEFSTSEIPLLLKSTRNACVDAIKWYGALTKWLCELPRGPEDDFKLYRLSCSRGALHLRQLHDEDLANGDDIIPGWFREWRRSLS 371
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       303       313       323       333       343       353       363        
                                                                                                                                                                                                                                                                                                                                   299|                                                                     
                                                                                                                                                                                                                                                                                                                                    302                                                                     


Chain C from PDB  Type:RNA  Length:6
                                      
                 5bte C   2 UxxUUU   7
                             ||   
                             3-U37
                              4-U37


Chain D from PDB  Type:RNA  Length:6
                                      
                 5bte D   2 UxxUUU   7
                             ||   
                             ||   
                             3-U37
                              4-U37
   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 5BTE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5BTE)

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