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(-) Description

Title :  CRYSTAL STRUCTURE OF THE METHANOCOCCUS JANNASCHII CBF5 NOP10 COMPLEX
 
Authors :  T. Hamma, S. L. Reichow, G. Varani, A. R. Ferre-D'Amare
Date :  16 Aug 05  (Deposition) - 15 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Protein Complex, Box H/Aca, Snornp, Pseudouridine Synthase, Rna Modification, Zinc Ribbon, Pua Domain, Isomerase/Rna Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Hamma, S. L. Reichow, G. Varani, A. R. Ferre-D'Amare
The Cbf5-Nop10 Complex Is A Molecular Bracket That Organizes Box H/Aca Rnps.
Nat. Struct. Mol. Biol. V. 12 1101 2005
PubMed-ID: 16286935  |  Reference-DOI: 10.1038/NSMB1036
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE TRNA PSEUDOURIDINE SYNTHASE B
    Chains: A
    EC Number: 5.4.99.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET16B
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TRUB
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: TRNA PSEUDOURIDINE 55 SYNTHASE, PSI55 SYNTHASE, TRNA-URIDINE ISOMERASE, TRNA PSEUDOURIDYLATE SYNTHASE
 
Molecule 2 - RIBOSOME BIOGENESIS PROTEIN NOP10
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET16B
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NOP10
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1K2Ligand/IonPOTASSIUM ION
2MSE3Mod. Amino AcidSELENOMETHIONINE
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:409 , CYS B:412 , CYS B:421 , CYS B:424BINDING SITE FOR RESIDUE ZN B 501
2AC2SOFTWAREGLY A:164 , LYS A:165BINDING SITE FOR RESIDUE K A 502
3AC3SOFTWAREGLY A:77 , GLY A:78 , SER A:204 , HOH A:614BINDING SITE FOR RESIDUE K A 503

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1B:409 -B:424

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUAPS50890 PUA domain profile.TRUB_METJA248-323  1A:248-323

(-) Exons   (0, 0)

(no "Exon" information available for 2APO)

(-) 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:304
 aligned with TRUB_METJA | Q57612 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:315
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326     
           TRUB_METJA    17 ELIVKEEVETNWDYGCNPYERKIEDLIKYGVVVVDKPRGPTSHEVSTWVKKILNLDKAGHGGTLDPKVTGVLPVALERATKTIPMWHIPPKEYVCLMHLHRDASEEDILRVFKEFTGRIYQRPPLKAAVKRRLRIRKIHELELLDKDGKDVLFRVKCQSGTYIRKLCEDIGEALGTSAHMQELRRTKSGCFEEKDAVYLQDLLDAYVFWKEDGDEEELRRVIKPMEYGLRHLKKVVVKDSAVDAICHGADVYVRGIAKLSKGIGKGETVLVETLKGEAVAVGKALMNTKEILNADKGVAVDVERVYMDRGTYPRM 331
               SCOP domains d2apoa2 A:17-246 Pseudouridine synthase II TruB                                                                                                                                                                                       d2apoa1 A:247-331 Pseudouridine synthase II TruB, C-terminal domain                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee............hhhhhhhhhhhhheeeeeee....hhhhhhhhhhhhh....eee........eeeeeeee.hhhhhhhhh....eeeeeeeee....hhhhhhhhhhhhheeee..-----------.eeeeeeeeeeeee..eeeeeeee....hhhhhhhhhhhhh...eeeeeeeeeee..ee.hhh.hhhhhhhhhhhhhh...hhhhhhheee.hhhhh..eeeee...hhhhhhh...ee...eeeee.......eeeee.....eeeeeee..hhhhhhhh...eeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUA  PDB: A:248-323 UniProt: 248-323                                        -------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2apo A  17 ELIVKEEVETNWDYGCNPYERKIEDLIKYGVVVVDKPRGPTSHEVSTWVKKILNLDKAGHGGTLDPKVTGVLPVALERATKTIPMWHIPPKEYVCLMHLHRDASEEDILRVFKEFTGRIYQR-----------RIRKIHELELLDKDGKDVLFRVKCQSGTYIRKLCEDIGEALGTSAHMQELRRTKSGCFEEKDAVYLQDLLDAYVFWKEDGDEEELRRVIKPMEYGLRHLKKVVVKDSAVDAICHGADVYVRGIAKLSKGIGKGETVLVETLKGEAVAVGKALMNTKEILNADKGVAVDVERVYMDRGTYPRM 331
                                    26        36        46        56        66        76        86        96       106       116       126       136 |       -   |   156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326     
                                                                                                                                                   138         150                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:55
 aligned with NOP10_METJA | P81303 from UniProtKB/Swiss-Prot  Length:60

    Alignment length:55
                                    12        22        32        42        52     
          NOP10_METJA     3 EMRMKKCPKCGLYTLKEICPKCGEKTVIPKPPKFSLEDRWGKYRRMLKRALKNKN  57
               SCOP domains d2apob_ B: Ribosome biogenesis protein Nop10            SCOP domains
               CATH domains 2apoB00 B:403-457 Nop10-like SnoRNP                     CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee......ee.........................hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                 2apo B 403 EmRmKKCPKCGLYTLKEICPKCGEKTVIPKPPKFSLEDRWGKYRRmLKRALKNKN 457
                             | |   412       422       432       442     | 452     
                             | |                                       448-MSE     
                           404-MSE                                                 
                             406-MSE
   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, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TRUB_METJA | Q57612)
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:0000495    box H/ACA snoRNA 3'-end processing    Any process involved in forming the mature 3' end of a box H/ACA snoRNA molecule.
    GO:1990481    mRNA pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine in an mRNA molecule.
    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:0031118    rRNA pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine in an rRNA molecule.
    GO:0031120    snRNA pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine in an snRNA molecule.
    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.
cellular component
    GO:0031429    box H/ACA snoRNP complex    A box H/ACA RNP complex that is located in the nucleolus.

Chain B   (NOP10_METJA | P81303)
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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  2apo
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  NOP10_METJA | P81303
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  TRUB_METJA | Q57612
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 Related Entries

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

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        NOP10_METJA | P81303: 2aqc

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