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(-) Description

Title :  STRUCTURE OF S. POMBE PCT1 RNA TRIPHOSPHATASE IN COMPLEX WITH THE SPT5 CTD
 
Authors :  C. D. Lima, S. K. Doamekpor
Date :  22 May 14  (Deposition) - 12 Nov 14  (Release) - 31 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,E,F  (1x)
Biol. Unit 2:  C,D,G,H  (1x)
Biol. Unit 3:  A,B,C,D,E,F,G,H  (1x)
Keywords :  Mrna Triphosphatase, Hydrolase, Polynucleotide 5' Triphosphatase, Mrna Processing, Mrna Capping, Dimer, Transcription Elongation Factor, Hydrolase-Transcription Regulator Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. K. Doamekpor, B. Schwer, A. M. Sanchez, S. Shuman, C. D. Lima
Fission Yeast Rna Triphosphatase Reads An Spt5 Ctd Code.
Rna V. 21 113 2015
PubMed-ID: 25414009  |  Reference-DOI: 10.1261/RNA.048181.114

(-) Compounds

Molecule 1 - MRNA-CAPPING ENZYME SUBUNIT BETA
    Chains: A, B, C, D
    EC Number: 3.1.3.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSMT3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: CODON PLUS RIL
    Gene: PCT1
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 4896
    Synonym: POLYNUCLEOTIDE 5'-TRIPHOSPHATASE,MRNA 5'-TRIPHOSPHATASE, TPASE
 
Molecule 2 - SYNTHETIC PEPTIDE
    Chains: E, F, G, H
    Engineered: YES
    Other Details: SYNTHETIC PEPTIDE DERIVED FROM THE REPEATING SEQUENCE FOUND AT THE C-TERMINAL DOMAIN OF SPT5
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB  EF  
Biological Unit 2 (1x):   CD  GH
Biological Unit 3 (1x): ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2FMT6Ligand/IonFORMIC ACID
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2FMT3Ligand/IonFORMIC ACID
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2FMT3Ligand/IonFORMIC ACID
Biological Unit 3 (2, 8)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2FMT6Ligand/IonFORMIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:263 , GLY A:264 , ASN A:265 , LEU A:269 , ARG A:287binding site for residue FMT A 401
2AC2SOFTWAREPRO A:55 , ASP A:56 , GLU B:102 , ARG B:296 , ARG B:299 , ARG B:300binding site for residue FMT A 402
3AC3SOFTWAREASP A:118 , GLU A:255binding site for residue EDO A 403
4AC4SOFTWAREPHE B:263 , GLY B:264 , ASN B:265 , LEU B:269 , ARG B:287binding site for residue FMT B 401
5AC5SOFTWAREPRO B:107 , LEU B:111 , THR B:113 , PHE B:192binding site for residue EDO B 402
6AC6SOFTWAREGLU C:236 , PHE C:263 , GLY C:264 , ASN C:265 , LEU C:269 , ARG C:287binding site for residue FMT C 401
7AC7SOFTWAREPRO C:55 , ASP C:56 , GLU D:102 , ARG D:296 , ARG D:299 , ARG D:300binding site for residue FMT C 402
8AC8SOFTWAREPHE D:263 , GLY D:264 , ASN D:265 , LEU D:269 , ARG D:287binding site for residue FMT D 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PN1)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser B:216 -Gly B:217

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PN1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PN1)

(-) Exons   (0, 0)

(no "Exon" information available for 4PN1)

(-) 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:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhh......eeeeeeeeeeee..............ee........eeee...hhhhhhhhhhhhhhhhhhh........eeeeeeeeeeee.......eeeeee.....eeeeeeeeeeeeeeee......eeeeeeeeeee...........eeeeeeeeeeee..eeeeeeeeee.......eeeeeeeeee.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pn1 A  43 KIEMNFLNKPIVPDTTKVISNFLTHYLITEPVEHVEIEAKLGTLIDLETQNRFEFPVMNETILNPEFNLRTRFESDMTASEHKYLNEFLNQAFRDSQKPGRLPFAYKHTKQVDLFYETEDNDKIRVSKNQSDNQVLACVKKRRVADLFLYCPNDAFDIRISISDELPVSMPSGNQQPSLTRLKDRVGYVHQEIKIDLTKTTQNDPVYDTTERHELEVEFGNIADLRDRAQKAKDGMEAPLFRRVQLFMDNVRILRREHS 303
                                    52        62        72        82        92       102       112       122       132       142       152       162||     174       184       194       204       214       224       234       244       254       264       274       284       294         
                                                                                                                                                  163|                                                                                                                                         
                                                                                                                                                   166                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhh......eeeeeeeeeeee..............ee........eeee...hhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeeeee...eeeeeee.....eeeeeeeeeeeeeeee......eeeeeeeeeee...........eeeeeeeeeeee..eeeeeeeeee.......eeeeeeeeee.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pn1 B  39 VAVPKIEMNFLNKPIVPDTTKVISNFLTHYLITEPVEHVEIEAKLGTLIDLETQNRFEFPVMNETILNPEFNLRTRFESDMTASEHKYLNEFLNQAFRDSQKPGRLPFAYKHTKQVDLFYETEDKIRVSKNQSDNQVLACVKKRRVADLFLYCPNDAFDIRISISDELPVSMPSGNQQPSLTRLKDRVGYVHQEIKIDLTKTTQNDPVYDTTERHELEVEFGNIADLRDRAQKAKDGMEAPLFRRVQLFMDNVRILRREHS 303
                                    48        58        68        78        88        98       108       118       128       138       148       158  ||   172       182       192       202       212       222       232       242       252       262       272       282       292       302 
                                                                                                                                                    161|                                                                                                                                         
                                                                                                                                                     166                                                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhh......eeeeeeeeeeee..............ee........eeee...hhhhhhhhhhhhhhhhhhh........eeeeeeeeeeeee.......eeeeeee.....eeeeeeeeeeeeeeee......eeeeeeeeeee...........eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeee.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pn1 C  43 KIEMNFLNKPIVPDTTKVISNFLTHYLITEPVEHVEIEAKLGTLIDLETQNRFEFPVMNETILNPEFNLRTRFESDMTASEHKYLNEFLNQAFRDSQKPGRLPFAYKHTKQVDLFYETEDNSRDKIRVSKNQSDNQVLACVKKRRVADLFLYCPNDAFDIRISISDELPVSMPSGNQQPSLTRLKDRVGYVHQEIKIDLTKTTQNTTERHELEVEFGNIADLRDRAQKAKDGMEAPLFRRVQLFMDNVRILRREHS 303
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242    || 257       267       277       287       297      
                                                                                                                                                                                                                                      247|                                                  
                                                                                                                                                                                                                                       253                                                  


Chain D from PDB  Type:PROTEIN  Length:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhh........eeeeeeeeeeee..............ee........eeee...hhhhhhhhhhhhhhhhhhh........eeeeeeeeeeeee.....eeeeeee.....eeeeeeeeeeeeeeee......eeeeeeeeeee...........eeeeeeeeeeee..eeeeeeeee...eeeeeeee.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pn1 D  40 AVPKIEMNFLNKPIVPDTTKVISNFLTHYLITEPVEHVEIEAKLGTLIDLETQNRFEFPVMNETILNPEFNLRTRFESDMTASEHKYLNEFLNQAFRDSQKPGRLPFAYKHTKQVDLFYETESRDKIRVSKNQSDNQVLACVKKRRVADLFLYCPNDAFDIRISISDELPVSMPSGNQQPSLTRLKDRVGYVHQEIKIDLTKTTQTERHELEVEFGNIADLRDRAQKAKDGMEAPLFRRVQLFMDNVRILRREHS 303
                                    49        59        69        79        89        99       109       119       129       139       149       159 ||    171       181       191       201       211       221       231       241    || 258       268       278       288       298     
                                                                                                                                                   161|                                                                               246|                                                 
                                                                                                                                                    164                                                                                254                                                 


Chain E from PDB  Type:PROTEIN  Length:6
                                      
               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
                 4pn1 E   9 RTPAWN  14


Chain F from PDB  Type:PROTEIN  Length:6
                                      
               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
                 4pn1 F   9 RTPAWN  14


Chain G from PDB  Type:PROTEIN  Length:6
                                      
               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
                 4pn1 G   9 RTPAWN  14


Chain H from PDB  Type:PROTEIN  Length:6
                                      
               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
                 4pn1 H   9 RTPAWN  14
   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 4PN1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PN1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PN1)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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        CET1_SCHPO | Q9P6Q6: 4pn0

(-) Related Entries Specified in the PDB File

4pn0