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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ARCHAEAL BOX H/ACA SRNP NOP10-CBF5 COMPLEX
 
Authors :  C. Charron, X. Manival, B. Charpentier, J. -B. Fourmann, F. Godard, C. B
Date :  29 Aug 05  (Deposition) - 11 Jul 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C,D  (2x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Biol. Unit 4:  A,B  (1x)
Biol. Unit 5:  A,B  (2x)
Keywords :  Isomerase, Structural Protein, Isomerase-Structural Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Manival, C. Charron, J. B. Fourmann, F. Godard, B. Charpentier, C. Branlant
Crystal Structure Determination And Site-Directed Mutagenesis Of The Pyrococcus Abyssi Acbf5-Anop10 Complex Reveal Crucial Roles Of The C-Terminal Domains Of Both Proteins In H/Aca Srnp Activity
Nucleic Acids Res. V. 34 826 2006
PubMed-ID: 16456033  |  Reference-DOI: 10.1093/NAR/GKJ482

(-) Compounds

Molecule 1 - PSEUDOURIDINE SYNTHASE
    ChainsC, A
    EC Number5.4.99.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P1
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificPYROCOCCUS ABYSSI
    Organism Taxid29292
    SynonymPROBABLE TRNA PSEUDOURIDINE SYNTHASE B, CBF5, TRNA PSEUDOURIDINE 55 SYNTHASE, PSI55 SYNTHASE, TRNA-URIDINE ISOMERASE, TRNA PSEUDOURIDYLATE SYNTHASE
 
Molecule 2 - RIBOSOME BIOGENESIS PROTEIN NOP10
    ChainsD, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P1
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificPYROCOCCUS ABYSSI
    Organism Taxid29292
    SynonymNOP10

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (2x)  CD
Biological Unit 2 (1x)AB  
Biological Unit 3 (1x)  CD
Biological Unit 4 (1x)AB  
Biological Unit 5 (2x)AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1PO45Ligand/IonPHOSPHATE ION
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1PO44Ligand/IonPHOSPHATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 3)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 5 (1, 6)
No.NameCountTypeFull Name
1PO46Ligand/IonPHOSPHATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:8 , CYS B:11 , CYS B:20 , CYS B:23BINDING SITE FOR RESIDUE ZN B 1070
2AC2SOFTWARECYS D:8 , CYS D:11 , CYS D:20 , CYS D:23BINDING SITE FOR RESIDUE ZN D 1071
3AC3SOFTWAREGLU C:229 , GLU D:43 , ARG D:46 , ARG D:50 , HOH D:140BINDING SITE FOR RESIDUE PO4 D 1001
4AC4SOFTWAREHIS A:225 , GLU A:229 , GLU B:43 , ARG B:46 , ARG B:50 , HOH B:1083BINDING SITE FOR RESIDUE PO4 B 1002
5AC5SOFTWAREGLY A:79 , THR A:80 , LYS A:108 , ALA A:176 , GLY A:177 , ARG A:202 , HOH A:1022 , HOH A:1073BINDING SITE FOR RESIDUE PO4 A 1003
6AC6SOFTWARELYS C:108 , TYR C:110 , GLY C:177 , ARG C:202BINDING SITE FOR RESIDUE PO4 C 1004
7AC7SOFTWAREHIS A:218 , ARG B:34 , SER B:36 , ASP B:39 , PRO B:40 , HOH B:1072 , HOH B:1076BINDING SITE FOR RESIDUE PO4 B 1006

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2AUS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2AUS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2AUS)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUAPS50890 PUA domain profile.TRUB_PYRAB250-325
 
  2A:250-325
C:250-325
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUAPS50890 PUA domain profile.TRUB_PYRAB250-325
 
  2-
C:250-325
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUAPS50890 PUA domain profile.TRUB_PYRAB250-325
 
  1A:250-325
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUAPS50890 PUA domain profile.TRUB_PYRAB250-325
 
  1-
C:250-325
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUAPS50890 PUA domain profile.TRUB_PYRAB250-325
 
  1A:250-325
-
Biological Unit 5 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUAPS50890 PUA domain profile.TRUB_PYRAB250-325
 
  2A:250-325
-

(-) Exons   (0, 0)

(no "Exon" information available for 2AUS)

(-) 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:309
 aligned with TRUB_PYRAB | Q9V1A5 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:323
                                    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       301       311       321       331   
           TRUB_PYRAB    12 ADIKREVIVKDDKAETNPKWGFPPDKRPIELHIQYGVINLDKPPGPTSHEVVAWIKRILNLEKAGHGGTLDPKVSGVLPVALERATRVVQALLPAGKEYVALMHLHGDVPEDKIRAVMKEFEGEIIQRPPLRSAVKRRLRTRKVYYIEILEIDGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMAELRRTRSGPFKEDETLVTLHDLVDYYHFWKEDGIEEYIRKAIQPMEKAVEHLPKIWIKDSAVAAVAHGANLTVPGIVKLNAGIKKGDLVAIMTLKDELVALGKAMMSTQEMIERSKGIAVDVEKVFMPRDWYPKLW 334
               SCOP domains d2ausa1 A:12-248 automated matches                                                                                                                                                                                                           d2ausa2 A:249-334 automated matches                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.............hhhhhhhhhhhhheeeeeee....hhhhhhhhhhhhh....eee........eeeeeeee.hhhhhhhhhh..eeeeeeeeee....hhhhhhhhhhhh.ee...--------------.eeeeeeeeeee..eeeeeeeee...hhhhhhhhhhhhh...eeeeeeeeeee..ee....eehhhhhhhhhhhhhh...hhhhhhhhee.hhhhh...eeeehhhhhhhhhh...ee...eeeee.......eeeee.....eeeeeee..hhhhhhhh...eeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUA  PDB: A:250-325 UniProt: 250-325                                        --------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aus A  12 ADIKREVIVKDDKAETNPKWGFPPDKRPIELHIQYGVINLDKPPGPTSHEVVAWIKRILNLEKAGHGGTLDPKVSGVLPVALERATRVVQALLPAGKEYVALMHLHGDVPEDKIRAVMKEFEGEIIQ--------------RKVYYIEILEIDGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMAELRRTRSGPFKEDETLVTLHDLVDYYHFWKEDGIEEYIRKAIQPMEKAVEHLPKIWIKDSAVAAVAHGANLTVPGIVKLNAGIKKGDLVAIMTLKDELVALGKAMMSTQEMIERSKGIAVDVEKVFMPRDWYPKLW 334
                                    21        31        41        51        61        71        81        91       101       111       121       131      |  -         - |     161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331   
                                                                                                                                                        138            153                                                                                                                                                                                     

Chain B from PDB  Type:PROTEIN  Length:53
 aligned with NOP10_PYRAB | Q9V0E3 from UniProtKB/Swiss-Prot  Length:60

    Alignment length:53
                                    13        23        33        43        53   
          NOP10_PYRAB     4 RIRKCPKCGRYTLKETCPVCGEKTKVAHPPRFSPEDPYGEYRRRLKRELLGIG  56
               SCOP domains d2ausb_ B: automated matches                          SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......ee............ee...........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 2aus B   4 RIRKCPKCGRYTLKETCPVCGEKTKVAHPPRFSPEDPYGEYRRRLKRELLGIG  56
                                    13        23        33        43        53   

Chain C from PDB  Type:PROTEIN  Length:311
 aligned with TRUB_PYRAB | Q9V1A5 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:323
                                    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       301       311       321       331   
           TRUB_PYRAB    12 ADIKREVIVKDDKAETNPKWGFPPDKRPIELHIQYGVINLDKPPGPTSHEVVAWIKRILNLEKAGHGGTLDPKVSGVLPVALERATRVVQALLPAGKEYVALMHLHGDVPEDKIRAVMKEFEGEIIQRPPLRSAVKRRLRTRKVYYIEILEIDGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMAELRRTRSGPFKEDETLVTLHDLVDYYHFWKEDGIEEYIRKAIQPMEKAVEHLPKIWIKDSAVAAVAHGANLTVPGIVKLNAGIKKGDLVAIMTLKDELVALGKAMMSTQEMIERSKGIAVDVEKVFMPRDWYPKLW 334
               SCOP domains d2ausc1 C:12-248 automated matches                                                                                                                                                                                                           d2ausc2 C:249-334 automated matches                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.............hhhhhhhhhhhhheeeeeee....hhhhhhhhhhhhh....eee........eeeeeeee.hhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhh.eeee.------------.eeeeeeeeeeeee..eeeeeeee....hhhhhhhhhhhhhh..eeeeeeeeeee..ee....eehhhhhhhhhhhhhh...hhhhhhhhee.hhhhh...eeeehhhhhhhhhh...ee...eeeee.......eeeeee....eeeeeee..hhhhhhhh...eeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUA  PDB: C:250-325 UniProt: 250-325                                        --------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aus C  12 ADIKREVIVKDDKAETNPKWGFPPDKRPIELHIQYGVINLDKPPGPTSHEVVAWIKRILNLEKAGHGGTLDPKVSGVLPVALERATRVVQALLPAGKEYVALMHLHGDVPEDKIRAVMKEFEGEIIQ------------RTRKVYYIEILEIDGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMAELRRTRSGPFKEDETLVTLHDLVDYYHFWKEDGIEEYIRKAIQPMEKAVEHLPKIWIKDSAVAAVAHGANLTVPGIVKLNAGIKKGDLVAIMTLKDELVALGKAMMSTQEMIERSKGIAVDVEKVFMPRDWYPKLW 334
                                    21        31        41        51        61        71        81        91       101       111       121       131      |  -       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331   
                                                                                                                                                        138          151                                                                                                                                                                                       

Chain D from PDB  Type:PROTEIN  Length:53
 aligned with NOP10_PYRAB | Q9V0E3 from UniProtKB/Swiss-Prot  Length:60

    Alignment length:53
                                    13        23        33        43        53   
          NOP10_PYRAB     4 RIRKCPKCGRYTLKETCPVCGEKTKVAHPPRFSPEDPYGEYRRRLKRELLGIG  56
               SCOP domains d2ausd_ D: automated matches                          SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......ee............ee...........hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 2aus D   4 RIRKCPKCGRYTLKETCPVCGEKTKVAHPPRFSPEDPYGEYRRRLKRELLGIG  56
                                    13        23        33        43        53   

   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  (3, 6)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2AUS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AUS)

(-) Gene Ontology  (12, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (TRUB_PYRAB | Q9V1A5)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0009982    pseudouridine synthase activity    Catalysis of the reaction: RNA uridine = RNA pseudouridine. Conversion of uridine in an RNA molecule to pseudouridine by rotation of the C1'-N-1 glycosidic bond of uridine in RNA to a C1'-C5.
biological process
    GO:0009451    RNA modification    The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
    GO:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0001522    pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine within an RNA molecule. This posttranscriptional base modification occurs in tRNA, rRNA, and snRNAs.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
    GO:0031119    tRNA pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine in a tRNA molecule.

Chain B,D   (NOP10_PYRAB | Q9V0E3)
molecular function
    GO:0030515    snoRNA binding    Interacting selectively and non-covalently with small nucleolar RNA.
biological process
    GO:0001522    pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine within an RNA molecule. This posttranscriptional base modification occurs in tRNA, rRNA, and snRNAs.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    GO:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
cellular component
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.

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