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(-) Description

Title :  CRYSTAL STRUCTURE OF S. POMBE DCP1/DCP2 IN COMPLEX WITH H. SAPIENS PNRC2 AND SYNTHETIC CAP ANALOG
 
Authors :  J. S. Mugridge, M. Ziemniak, J. Jemielity, J. D. Gross
Date :  05 Jul 16  (Deposition) - 05 Oct 16  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.56
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Decapping Mrna Decay Nudix Cap Analog, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. S. Mugridge, M. Ziemniak, J. Jemielity, J. D. Gross
Structural Basis Of Mrna-Cap Recognition By Dcp1-Dcp2.
Nat. Struct. Mol. Biol. V. 23 987 2016
PubMed-ID: 27694842  |  Reference-DOI: 10.1038/NSMB.3301

(-) Compounds

Molecule 1 - MRNA-DECAPPING ENZYME SUBUNIT 1
    Chains: D, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21*DE3
    Expression System Taxid: 469008
    Gene: DCP1, SPBC3B9.21
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE (STRAIN 972 / ATCC 24843)
    Organism Taxid: 284812
    Strain: 972 / ATCC 24843
 
Molecule 2 - PROLINE-RICH NUCLEAR RECEPTOR COACTIVATOR 2
    Chains: F, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21*DE3
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 72-102
    Gene: PNRC2, HSPC208
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - MRNA DECAPPING COMPLEX SUBUNIT 2
    Chains: E, B
    EC Number: 3.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21*DE3
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 1-244
    Gene: DCP2, SPAC19A8.12
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE (STRAIN 972 / ATCC 24843)
    Organism Taxid: 284812
    Strain: 972 / ATCC 24843

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
16VQ2Ligand/Ion[[(2~{R},3~{S},4~{R},5~{R})-5-(2-AZANYL-7-METHYL-6-OXIDANYLIDENE-3~{H}-PURIN-7-IUM-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-SULFANYL-PHOSPHORYL][[[(2~{R},3~{S},4~{R},5~{R})-5-(2-AZANYL-7-METHYL-6-OXIDANYLIDENE-3~{H}-PURIN-7-IUM-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-SULFANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL] HYDROGEN PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP E:117 , LYS E:118 , SER E:120 , SER E:121 , GLY E:122 , LYS E:129 , ARG E:167 , GLN E:169 , TYR E:220binding site for residue 6VQ E 301
2AC2SOFTWAREGLU B:39 , TRP B:43 , ASP B:47 , ASP B:88 , PHE B:89 , TYR B:92 , LYS B:93 , ARG B:95 , LYS B:127 , ARG B:167 , TYR B:220binding site for residue 6VQ B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KQ4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5KQ4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KQ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KQ4)

(-) Exons   (0, 0)

(no "Exon" information available for 5KQ4)

(-) 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 .hhhhhhhhhhhhhhhhhh...eeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeee....eeeeeee......eeee......eeee..eeeee.....eeeeee..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kq4 A   1 MEDENILRNAVNLQVLKFHYPEIESIIDIASHVAVYQFDVGSQKWLKTSIEGTFFLVKDQRARVGYVILNRNSPENLYLFINHPSNVHLVDRYLIHRTENQHVVGLWMFDPNDMSRIFNIVKES 124
                                    10        20        30        40        50        60        70        80        90       100       110       120    


Chain B from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhh.......hhh.hhhhhhhhhhhhhhhhh.............hhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhh..eeeeee......eeeeee...........eee......hhhhhhhhhhhhh............eeeeee..eeeeeeee..................eeeeeehhh............hhh.hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kq4 B  -2 GGSMSFTNATFSQVLDDLSARFILNLPAEEQSSVERLCFQIEQAHWFYEDFIRAQNDQLPSLGLRVFSAKLFAHCPLLWKWSKVHEEAFDDFLRYKTRIPVRGAIMLDMSMQQCVLVKGWKASSGWGFPKGKIDKDESDVDCAIREVYEETGFDCSSRINPNEFIDMTIRGQNVRLYIIPGISLDTRFESRTRKEISKIEWHNLMDLPTFKKNKPQTMKNKFYMVIPFLAPLKKWIKKRNIA 239
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237  


Chain C from PDB  Type:PROTEIN  Length:23
                                                       
               SCOP domains ----------------------- SCOP domains
               CATH domains ----------------------- CATH domains
               Pfam domains ----------------------- Pfam domains
         Sec.struct. author .............hhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------- SAPs(SNPs)
                    PROSITE ----------------------- PROSITE
                 Transcript ----------------------- Transcript
                 5kq4 C  99 SEPPSPSVLPKPPSHWVPVSFNP 121
                                   108       118   


Chain D from PDB  Type:PROTEIN  Length:126
                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh...eeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeee....eeeeeee......eeeee.....eeee..eeeee.....eeeeee..hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5kq4 D   1 MEDENILRNAVNLQVLKFHYPEIESIIDIASHVAVYQFDVGSQKWLKTSIEGTFFLVKDQRARVGYVILNRNSPENLYLFINHPSNVHLVDRYLIHRTENQHVVGLWMFDPNDMSRIFNIVKESLL 126
                                    10        20        30        40        50        60        70        80        90       100       110       120      


Chain E from PDB  Type:PROTEIN  Length:235
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhh.....hhhh..hhhhhhhhhhhhhhhhh.hhhh........hhhhhhhhhhh.hhh.........hhhhhhhh...eeeeeeee......eeeeee...........eee......hhhhhhhhhhhhh............eeeeee..eeeeeeee................eeeeeehhh...............hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kq4 E   0 SMSFTNATFSQVLDDLSARFILNLPAEEQSSVERLCFQIEQAHWFYEDFIRAQNDQLPSLGLRVFSAKLFAHCPLLWKWSKVHEEAFDDFLRYKTRIPVRGAIMLDMSMQQCVLVKGWKASSGWGFPKGKIDKDESDVDCAIREVYEETGFDCSSRINPNEFIDMTIRGQNVRLYIIPGISLDTRFESRTEISKIEWHNLMDLPTFKKNKPNKFYMVIPFLAPLKKWIKKRNIAN 240
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189|      201       211||     225       235     
                                                                                                                                                                                                                       189|                 212|                       
                                                                                                                                                                                                                        192                  217                       


Chain F from PDB  Type:PROTEIN  Length:22
                                                      
               SCOP domains ---------------------- SCOP domains
               CATH domains ---------------------- CATH domains
               Pfam domains ---------------------- Pfam domains
         Sec.struct. author ....hhh.....hhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------- SAPs(SNPs)
                    PROSITE ---------------------- PROSITE
                 Transcript ---------------------- Transcript
                 5kq4 F 100 EPPSPSVLPKPPSHWVPVSFNP 121
                                   109       119
   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 5KQ4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KQ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KQ4)

(-) Gene Ontology  (29, 47)

Asymmetric/Biological Unit(hide GO term definitions)

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  5kq4
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  DCP1_SCHPO | Q9P805
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  DCP2_SCHPO | O13828
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 Related Entries

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

UniProtKB/Swiss-Prot
        DCP1_SCHPO | Q9P805: 2qkl 2qkm 5j3q 5j3t 5j3y 5jp4 5kq1 5n2v
        DCP2_SCHPO | O13828: 2a6t 2qkl 2qkm 4a54 5j3t 5j3y 5kq1 5n2v
        PNRC2_HUMAN | Q9NPJ4: 4b6h 5kq1

(-) Related Entries Specified in the PDB File

5kq1