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Structure of a rare, non-standard sequence k-turn bound by L7Ae protein
Biology and Chemistry Report
4C4W
  •   Structure Details   Hide

    Structure Keywords

    Keywords RNA BINDING PROTEIN/RNA
    Text RNA BINDING PROTEIN-RNA COMPLEX, RNA BINDING PROTEIN, KINK TURN

    Polymeric Molecules

    Chain A,B,E,F
    Description U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A 
    Fragment RRM 1 DOMAIN, RESIDUES 1-102 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 11740.8 
    Source Method genetically manipulated  
    Entity Name U1 SNRNP A, U1-A, U1A 
    Chain C,G
    Description 50S RIBOSOMAL PROTEIN L7AE 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 13522.7 
    Source Method genetically manipulated  
    Chain D,H
    Description TSKT-23 
    Fragment KINK TURN MOTIF, RESIDUES 1-35 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polyribonucleotide 
    Formula Weight 11196.8 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    2HP  DIHYDROGENPHOSPHATE ION  H2 O4 P   96.99  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B,E,F SNRPA_HUMAN P09012     
    C,G RL7A_ARCFU O29494     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B,E,F
    GO ID   Ontology GO Term Definition
    398   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. 
    166   Nucleotide Binding  Interacting Selectively and Non Covalently with a Nucleotide Any Compound Consisting of a Nucleoside That Is Esterified with (ortho)phosphate or an Oligophosphate At Any Hydroxyl Group On the Ribose or Deoxyribose. 
    3676   Nucleic Acid Binding  Interacting Selectively and Non Covalently with Any Nucleic Acid. 
    17069   Snrna Binding  Interacting Selectively and Non Covalently with a Small Nuclear RNA (snrna). 
    Chain C,G
    GO ID   Ontology GO Term Definition
    1682   TRNA 5' Leader Removal  Generation of the Mature 5' End of the TRNA Usually Via an Endonucleolytic Cleavage by Rnase P. 
    6412   Translation  The Cellular Metabolic Process in Which a Protein Is Formed Using the Sequence of a Mature MRNA Molecule to Specify the Sequence of Amino Acids in a Polypeptide Chain. Translation Is Mediated by the Ribosome and Begins with the Formation of a Ternary Complex Between Aminoacylated Initiator Methionine TRNA GTP and Initiation Factor 2 Which Subsequently Associates with the Small Subunit of the Ribosome and an Mrna. Translation Ends with the Release of a Polypeptide Chain From the Ribosome. 
    8033   TRNA Processing  The Process in Which a Pre TRNA Molecule Is Converted to a Mature TRNA Ready For Addition of an Aminoacyl Group. 
    42254   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. 
    90501   RNA Phosphodiester Bond Hydrolysis  The RNA Metabolic Process in Which the Phosphodiester Bonds Between Ribonucleotides Are Cleaved by Hydrolysis. 
    90502   RNA Phosphodiester Bond Hydrolysis Endonucleolytic  The Chemical Reactions and Pathways Involving the Hydrolysis of Internal 3' 5' Phosphodiester Bonds in One or Two Strands of Ribonucleotides. 
    5622   Intracellular  The Living Contents of a Cell; the Matter Contained Within (but Not Including) the Plasma Membrane Usually Taken to Exclude Large Vacuoles and Masses of Secretory or Ingested Material. in Eukaryotes It Includes the Nucleus and Cytoplasm. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5840   Ribosome  An Intracellular Organelle About 200 a in Diameter Consisting of RNA and Protein. It Is the Site of Protein Biosynthesis Resulting From Translation of Messenger RNA (mrna). It Consists of Two Subunits One Large and One Small Each Containing Only Protein and Rna. Both the Ribosome and Its Subunits Are Characterized by Their Sedimentation Coefficients Expressed in Svedberg Units (symbol: S). Hence the Prokaryotic Ribosome (70s) Comprises a Large (50s) Subunit and a Small (30s) Subunit While the Eukaryotic Ribosome (80s) Comprises a Large (60s) Subunit and a Small (40s) Subunit. Two Sites On the Ribosomal Large Subunit Are Involved in Translation Namely the Aminoacyl Site (a Site) and Peptidyl Site (p Site). Ribosomes From Prokaryotes Eukaryotes Mitochondria and Chloroplasts Have Characteristically Distinct Ribosomal Proteins. 
    30529   Ribonucleoprotein Complex  A Macromolecular Complex Containing Both Protein and RNA Molecules. 
    3723   RNA Binding  Interacting Selectively and Non Covalently with an RNA Molecule or a Portion Thereof. 
    3735   Structural Constituent of Ribosome  The Action of a Molecule That Contributes to the Structural Integrity of the Ribosome. 
    4526   Ribonuclease P Activity  Catalysis of the Endonucleolytic Cleavage of RNA Removing 5' Extra Nucleotides From TRNA Precursor. 
    19843   RRNA Binding  Interacting Selectively and Non Covalently with Ribosomal Rna. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain C,G
    Scientific Name Archaeoglobus fulgidus  
    Strain DSM 4304
    ATCC Source Atcc 49558
    Host Scientific Name Escherichia coli  
    Host Variant Gold Plyss
    Host Strain Bl21(de3)
    Host Vector Type Plasmid


    Chain A,B,E,F
    Common Name Human
    Scientific Name Homo sapiens  
    Host Scientific Name Escherichia coli  
    Host Variant Gold Plyss
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name PT7


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    19 19q13.1 6626     small nuclear ribonucleoprotein polypeptide A SNRPA    
    - - 1483981     50S ribosomal protein L7Ae RPL7AE    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs11558817 LS-SNP   dbSNP   A 29 S - > Y Helix 2% (Buried) 19 41263249
    rs11558817 LS-SNP   dbSNP   A 29 S - > Y Helix 2% (Buried) 19 41263249
    rs144586987 LS-SNP   dbSNP   A 38 G - > C Bend 36% (Intermediate) 19 41263275
    rs144586987 LS-SNP   dbSNP   A 38 G - > C Bend 36% (Intermediate) 19 41263275
    rs143591779 LS-SNP   dbSNP   A 51 M - > T Turn 29% (Intermediate) 19 41263315
    rs143591779 LS-SNP   dbSNP   A 51 M - > T Turn 29% (Intermediate) 19 41263315
    rs2230694 LS-SNP   dbSNP   A 80 K - > N Bend 30% (Intermediate) 19 41263403
    rs2230694 LS-SNP   dbSNP   A 80 K - > N Bend 30% (Intermediate) 19 41263403
    rs138535346 LS-SNP   dbSNP   A 100 T - > S Coil 72% (Exposed) 19 41265387
    rs138535346 LS-SNP   dbSNP   A 100 T - > S Coil 72% (Exposed) 19 41265387