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(-) Description

Title :  CRYSTAL STRUCTURE (II) OF NOVA-1 KH1/KH2 DOMAIN TANDEM WITH 25NT RNA HAIRPIN
 
Authors :  L. Malinina, M. Teplova, K. Musunuru, A. Teplov, J. C. Darnell, S. K. Bur R. B. Darnell, D. J. Patel
Date :  11 Aug 05  (Deposition) - 24 Oct 06  (Release) - 02 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Rna Complex, Kh Domain, Hairpin, Rna-Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Teplova, L. Malinina, J. C. Darnell, J. Song, M. Lu, R. Abagyan, K. Musunuru, A. Teplov, S. K. Burley, R. B. Darnell, D. J. Patel
Protein-Rna And Protein-Protein Recognition By Dual Kh1/2 Domains Of The Neuronal Splicing Factor Nova-1.
Structure V. 19 930 2011
PubMed-ID: 21742260  |  Reference-DOI: 10.1016/J.STR.2011.05.002

(-) Compounds

Molecule 1 - 5'-R(*CP*(5BU) P*CP*GP*CP*GP*GP*AP*UP*CP*AP*GP*UP*CP*AP*CP*CP*CP*AP*AP*GP*CP*GP*AP*G )-3'
    ChainsB
    EngineeredYES
    SyntheticYES
 
Molecule 2 - NEURO-ONCOLOGICAL VENTRAL ANTIGEN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentKH1/KH2 DOMAINS
    GeneNOVA1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNOVA-1, RNA-BINDING PROTEIN NOVA-1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
15BU1Mod. Nucleotide5-BROMO-URIDINE-5'-MONOPHOSPHATE
2K1Ligand/IonPOTASSIUM ION
3MG2Ligand/IonMAGNESIUM ION
4MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREG B:206 , G B:207 , MG B:302 , HOH B:321 , HOH B:322 , HOH B:332 , HOH B:334BINDING SITE FOR RESIDUE K B 301
2AC2SOFTWAREG B:207 , K B:301 , HOH B:303 , HOH B:321 , HOH B:334BINDING SITE FOR RESIDUE MG B 302
3AC3SOFTWAREG B:206 , HOH B:323 , HOH B:332 , HOH B:333BINDING SITE FOR RESIDUE MG B 306

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KH_TYPE_1PS50084 Type-1 KH domain profile.NOVA1_HUMAN49-119
174-240
424-491
  2A:5-72
A:103-169
-

(-) Exons   (0, 0)

(no "Exon" information available for 2ANR)

(-) 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:155
 aligned with NOVA1_HUMAN | P51513 from UniProtKB/Swiss-Prot  Length:510

    Alignment length:213
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246   
          NOVA1_HUMAN    37 GSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKLSKSKDFYPGTTERVCLIQGTVEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRIKQTLPSSPTTTKSSPSDPMTTSRANQVKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINLQERVVTVSGEPEQNRKAVELIIQKIQEDPQ 249
               SCOP domains d2          anra1 A:3-76 automated matches                                             ------                 ---                        ---d2anra2 A:106-178 automated matches                                       SCOP domains
               CATH domains 2a          nrA01 A:3-82  [code=3.30.1370.10, no n   ame defined]                                             2an                        rA02 A:100-178  [code=3.30.1370.10, no na    me defined]                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..----------.eeeeeeeehhhhhhhhh..hhhhhhhhhhhh.eeee.---..........eeeeeeeehhhhhhhhhhhhhhhhh.....-----------------hhh------------------------h.eeeeeeehhhhhhhhh..hhhhhhhhhhh..eeee....----..eeeeeee.hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------KH_TYPE_1  PDB: A:5-72 UniProt: 49-119                                 ------------------------------------------------------KH_TYPE_1  PDB: A:103-169 UniProt: 174-240                         --------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2anr A   3 GS----------QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLS---KSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREmPQN-----------------PDR------------------------ANQVKIIVPNSTAGLIIGKGGATVKAImEQSGAWVQLSQKP----LQNRVVTVSGEPEQNRKAVELIIQKIQEDPQ 178
                             |       -  |     12        22        32        42   |    49        59        69        79  |      -         -| |      -         -       105       115       125    |  135       | -  |    155       165       175   
                             4          5                                   42  43                                  79-MSE              100 |                      103                        130-MSE      143  148                              
                                                                                                                                          102                                                                                                    

Chain B from PDB  Type:RNA  Length:25
                                                         
                 2anr B 201 CuCGCGGAUCAGUCACCCAAGCGAG 225
                             |     210       220     
                           202-5BU                   

   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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NOVA1_HUMAN | P51513)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
biological process
    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:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:0007626    locomotory behavior    The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.
    GO:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
    GO:0051252    regulation of RNA metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA.
    GO:0050684    regulation of mRNA processing    Any process that modulates the frequency, rate or extent of mRNA processing, those processes involved in the conversion of a primary mRNA transcript into a mature mRNA prior to its translation into polypeptide.
    GO:0021510    spinal cord development    The process whose specific outcome is the progression of the spinal cord over time, from its formation to the mature structure. The spinal cord primarily conducts sensory and motor nerve impulses between the brain and the peripheral nervous tissues.
cellular component
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NOVA1_HUMAN | P515131dt4 2ann

(-) Related Entries Specified in the PDB File

2ann CRYSTAL STRUCTURE (1) OF NOVA-1 KH1/KH2 TANDEM WITH 25NT RNA HAIRPIN