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(-) Description

Title :  CRYSTAL STRUCTURE OF CANDIDA ALBICANS RAI1 IN COMPLEX WITH PU5-MN2+
 
Authors :  V. Y. Wang, L. Tong
Date :  03 Jun 15  (Deposition) - 08 Jul 15  (Release) - 05 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (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 - DECAPPING NUCLEASE RAI1
    Chains: A, B
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RAI1, CAO19.13610, CAO19.6230
    Organism Common: YEAST
    Organism Scientific: CANDIDA ALBICANS (STRAIN SC5314 / ATCC MYA- 2876)
    Organism Taxid: 237561
    Strain: SC5314 / ATCC MYA-2876
 
Molecule 2 - RNA (5'-R(P*UP*UP*UP*U)-3')
    Chains: D, E
    Engineered: YES
    Organism Scientific: CANDIDA ALBICANS
    Organism Taxid: 5476
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABDE
Biological Unit 1 (1x): A D 
Biological Unit 2 (1x):  B E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1MN6Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:225 , GLU A:244 , LEU A:245 , MN A:402 , HOH A:581 , U D:2binding site for residue MN A 401
2AC2SOFTWAREGLU A:223 , ASP A:225 , MN A:401 , HOH A:599 , HOH A:628 , U D:2binding site for residue MN A 402
3AC3SOFTWAREGLU A:174 , GLU A:223 , HOH A:524 , HOH A:563 , HOH A:628 , HOH A:737 , HOH A:898binding site for residue MN A 403
4AC4SOFTWAREASP B:225 , GLU B:244 , LEU B:245 , MN B:402 , HOH B:582 , U E:2binding site for residue MN B 401
5AC5SOFTWAREGLU B:223 , ASP B:225 , MN B:401 , HOH B:556 , HOH B:610 , HOH B:860 , U E:2binding site for residue MN B 402
6AC6SOFTWAREGLU B:174 , GLU B:223 , HOH B:546 , HOH B:610 , HOH B:625 , HOH B:863 , HOH B:946binding site for residue MN B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BUD)

(-) 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:391
                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...............eeeeeeee.....ee..hhhhhh.ee..hhhhhhh......hhhhh...hhhhh..hhhhhhhhhhhhhhhhh......eeeehhhhhhhhhhhhh....eeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhhhhhh......eeeeeeeeee..eeeeeeeee.ee......hhhhhhh.eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..hhhhhhhh............hhhhhhhhhhhhhhhhhhhh........eeeeee....eeeeee.hhhhhhhhhh....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bud A   0 HMAKSLPLNSRSKTTALKQPRELFSYARDIDGKYVYDDPENSLSYYYLPDSTIDTGIDLQGGYSKFKKIPDEQNLADFNSLLKAIIKYETSEGKKISSDIITFREIMTKILSLPYNLTDPIDLYVVPFDGQLFIKSDDELDMKRRKEQEVRMKQTNTVERYDYMKRCEYVGYKFETIATIPKPWSQVSRSQIENRNKKVVNNYEQYLSVIRTGIGNVKLVLAGEIDCCWDYLPDEQNKKLNHYVELKTSRIIENNSQVVSFEQKLFKAWCQCFLMGVTKIIYGFRDNNLILKNVELFNTEEIPILIKNNPLTNAATEKKINCTNALKWYGAVVDWLNTTVDKKDEIKSYRLKYDPVRKSFTLSETDSETNEKLRNGQLLTPEFTEWRQSLK 390
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389 


Chain B from PDB  Type:PROTEIN  Length:387
                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.............eeeeeeee.....ee..hhhhhh.ee..hhhhhh.......hhhhh...hhhhh..hhhhhhhhhhhhhhhhh......eeeehhhhhhhhhhhhh....eeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhhhhhh......eeeeeeeeee..eeeeeeee..ee......hhhhhhh.eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh........eeeeee....eeeeee.hhhhhhhhhh....hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bud B   1 MAKSLPLNSRSKTTKQPRELFSYARDIDGKYVYDDPENSLSYYYLPDSTIDTGIDLQGGYSKFKKIPDEQNLADFNSLLKAIIKYETSEGKKISSDIITFREIMTKILSLPYNLTDPIDLYVVPFDGQLFIKSDDELDMKRRKEQEVRMKQTNTVERYDYMKRCEYVGYKFETIATIPKPWSQVSRSQIENRNKKVVNNYEQYLSVIRTGIGNVKLVLAGEIDCCWDYLPDEQNKKLNHYVELKTSRIIENNSQVVSFEQKLFKAWCQCFLMGVTKIIYGFRDNNLILKNVELFNTEEIPILIKNNPLTNAATEKKINCTNALKWYGAVVDWLNTTVDKKDEIKSYRLKYDPVRKSFTLSETDSETNEKLRNGQLLTPEFTEWRQSL 389
                                    10   ||   22        32        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       
                                        14|                                                                                                                                                                                                                                                                                                                                                                                    
                                         17                                                                                                                                                                                                                                                                                                                                                                                    


Chain D from PDB  Type:RNA  Length:4
                                    
                 5bud D   2 UUUU   5


Chain E from PDB  Type:DNA/RNA  Length:5
                                     
                 5bud E   2 UUUUU   6
   Legend:   → Mismatch (orange background)
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  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 5BUD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

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