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(-) Description

Title :  THE CRYSTAL STRUCTURE OF AN ARCHAEAL CPSF SUBUNIT, PH1404 FROM PYROCOCCUS HORIKOSHII COMPLEXED WITH RNA-ANALOG
 
Authors :  Y. Nishida, H. Ishikawa, N. Nakagawa, R. Masui, S. Kuramitsu
Date :  24 Feb 10  (Deposition) - 21 Apr 10  (Release) - 30 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Archaeal Cpsf, Beta-Casp Family, Kh Domain, Ribonuclease, Metallo- Beta-Lactamase Superfamily, Pyrococcus Horikoshii, Archaea, Rna- Analog, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Nishida, H. Ishikawa, S. Baba, N. Nakagawa, S. Kuramitsu, R. Masui
Crystal Structure Of An Archaeal Cleavage And Polyadenylation Specificity Factor Subunit From Pyrococcus Horikoshii
Proteins V. 78 2395 2010
PubMed-ID: 20544974  |  Reference-DOI: 10.1002/PROT.22748

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN PH1404
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PH1404
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3
 
Molecule 2 - 5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3'
    Chains: B, C
    Engineered: YES
    Other Details: RNA-ANALOG
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
2SSU8Mod. NucleotideURIDINE-5'-PHOSPHOROTHIOATE
3ZN2Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:202 , TYR A:229 , HIS A:234 , ASN A:644 , ARG A:649BINDING SITE FOR RESIDUE SO4 A 652
2AC2SOFTWARETHR A:209 , PHE A:213 , ASP A:236 , PRO A:238 , TYR A:242BINDING SITE FOR RESIDUE SO4 A 653
3AC3SOFTWARETYR A:325 , ASN A:341 , GLU A:377 , GLU A:474 , TYR A:475 , LEU A:476 , GLU A:573BINDING SITE FOR RESIDUE SO4 A 654
4AC4SOFTWAREASP A:260 , ASP A:367 , TYR A:550 , HIS A:594 , HIS A:618 , ZN A:658BINDING SITE FOR RESIDUE SO4 A 655
5AC5SOFTWAREASP A:324 , TYR A:325 , GLU A:474 , GLU A:573 , GLY A:574 , ARG A:575BINDING SITE FOR RESIDUE SO4 A 656
6AC6SOFTWAREHIS A:256 , HIS A:258 , HIS A:344 , ASP A:367BINDING SITE FOR RESIDUE ZN A 657
7AC7SOFTWAREASP A:260 , HIS A:261 , ASP A:367 , HIS A:618 , SO4 A:655BINDING SITE FOR RESIDUE ZN A 658

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AF6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:521 -Ser A:522
2Arg A:608 -Pro A:609

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AF6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AF6)

(-) Exons   (0, 0)

(no "Exon" information available for 3AF6)

(-) 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:637
 aligned with O50112_PYRHO | O50112 from UniProtKB/TrEMBL  Length:651

    Alignment length:643
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648   
         O50112_PYRHO     9 TQVDQILRDIRAVVNQMVPKEAKITEIEFEGPELVIYVKNPEAIMKDGELIKDLAKVLKKRISVRPDPEVLLPPEEAEKLIFEIVPKEAEITNIAFDPSVGEVLIEAKKPGLVIGKNGETLRLITQKVKWAPKVVRTPPLQSQTIYSIRQILQTESKDRRKFLRQVGRNIYRKPEYKSRWIRITGLGGFREVGRSALLVQTDESFVLVDFGVNVAMLNDPYKAFPHFDAPEFQYVLREGLLDAIIITHAHLDHCGMLPYLFRYNLFDGPIYTTPPTRDLMVLLQKDFIEIQQSNGQDPLYRPRDIKEVIKHTITLDYGEVRDISPDIRLTLHNAGHILGSAIVHLHIGNGLHNIAITGDFKFIPTRLLEPANAKFPRLETLVMESTYGGANDIQMPREEAEKRLIEVIHNTIKRGGKVLIPAMAVGRAQEVMMVLEEYARIGGIEVPIYLDGMIWEATAIHTAYPEYLSRRLREQIFKEGYNPFLSEIFHPVANSRERQDIIDSNEPAIIIASSGMLVGGPSVEYFKQLAPDPKNSIIFVSYQAEGTLGRQVQSGIREIPMVGEEGRTEVIKVNMEVHTIDGFSGHADRRELMNYVAKVRPRPERIITVHGEPQKCLDLATSIHRKFGISTRAPNNLDTIRLR 651
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...hhhh.eeeeeee..eeeeee....------.hhhhhhhhhh..eeeee............................eee....eeeeee.hhhhh.......hhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeee........eeeeee...eeee....hhhhh.hhhhhh....hhhhhhhhhh....eee....hhhhhh..hhhhhh......eeehhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhheee......eeee..eeeeeee.......eeeeeee....eeeee.......................eeeee...........hhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhhhhhhhhhh.............eee..hhhhhhhhhhh...eeeee.......hhhhhhhhhhh.....eeee.......hhhhhhhh...eeeee.hhh.eeeee...eeee........hhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhh.eee......eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3af6 A   9 TQVDQILRDIRAVVNQMVPKEAKITEIEFEGPELVIYVKNPE------ELIKDLAKVLKKRISVRPDPEVLLPPEEAEKLIFEIVPKEAEITNIAFDPSVGEVLIEAKKPGLVIGKNGETLRLITQKVKWAPKVVRTPPLQSQTIYSIRQILQTESKDRRKFLRQVGRNIYRKPEYKSRWIRITGLGGFREVGRSALLVQTDESFVLVDFGVNVAMLNDPYKAFPHFDAPEFQYVLREGLLDAIIITHAHLDHCGMLPYLFRYNLFDGPIYTTPPTRDLMVLLQKDFIEIQQSNGQDPLYRPRDIKEVIKHTITLDYGEVRDISPDIRLTLHNAGHILGSAIVHLHIGNGLHNIAITGDFKFIPTRLLEPANAKFPRLETLVMESTYGGANDIQMPREEAEKRLIEVIHNTIKRGGKVLIPAMAVGRAQEVMMVLEEYARIGGIEVPIYLDGMIWEATAIHTAYPEYLSRRLREQIFKEGYNPFLSEIFHPVANSRERQDIIDSNEPAIIIASSGMLVGGPSVEYFKQLAPDPKNSIIFVSYQAEGTLGRQVQSGIREIPMVGEEGRTEVIKVNMEVHTIDGFSGHADRRELMNYVAKVRPRPERIITVHGEPQKCLDLATSIHRKFGISTRAPNNLDTIRLR 651
                                    18        28        38        48 |      58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648   
                                                                    50     57                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:DNA/RNA  Length:6
                                      
                 3af6 B   1 uuuuuu   6
                            ||||||
                            1-SSU|
                             2-SSU
                              3-SSU
                               4-SSU
                                5-SSU
                                 6-SSU


Chain C from PDB  Type:DNA/RNA  Length:2
                                  
                 3af6 C   1 uu   2
                            ||
                            ||
                            1-SSU
                             2-SSU
   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 3AF6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AF6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AF6)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O50112_PYRHO | O50112)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.

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  3af6
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  O50112_PYRHO | O50112
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 Related Entries

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

UniProtKB/TrEMBL
        O50112_PYRHO | O50112: 3af5

(-) Related Entries Specified in the PDB File

3af5 SAME PROTEIN, FREE STRUCTURE