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(-) Description

Title :  CRYSTAL STRUCTURE OF E.COLI RIBOSOMAL PROTEIN L25 COMPLEXED WITH A 5S RRNA FRAGMENT AT 1.8 A RESOLUTION
 
Authors :  M. Lu, T. A. Steitz
Date :  21 Nov 99  (Deposition) - 02 Dec 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  M,N,P
Keywords :  Protein-Rna Complex, Ribosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Lu, T. A. Steitz
Structure Of Escherichia Coli Ribosomal Protein L25 Complexed With A 5S Rrna Fragment At 1. 8-A Resolution.
Proc. Natl. Acad. Sci. Usa V. 97 2023 2000
PubMed-ID: 10696113  |  Reference-DOI: 10.1073/PNAS.97.5.2023
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5S RRNA
    Chains: M
    Engineered: YES
    Fragment: LOOP E-HELIX IV FRAGMENT
    Other Details: A FRAGMENT OF 5S RRNA IN 50S RIBOSOMAL SUBUNIT
    Other Details - Source: THIS SEQUENCE OCCURS NATURALLY IN E.COLI
    Synthetic: YES
 
Molecule 2 - 5S RRNA
    Chains: N
    Engineered: YES
    Fragment: LOOP E-HELIX IV FRAGMENT
    Other Details: A FRAGMENT OF 5S RRNA IN 50S RIBOSOMAL SUBUNIT
    Other Details - Source: THIS SEQUENCE OCCURS NATURALLY IN E.COLI
    Synthetic: YES
 
Molecule 3 - RIBOSOMAL PROTEIN L25
    Chains: P
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PL25
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: PROTEIN FROM THE LARGE RIBOSOMAL SUBUNIT

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : MNP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1MG5Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREU M:95 , HOH M:518 , HOH M:525 , HOH M:529 , HOH N:520 , HOH P:131BINDING SITE FOR RESIDUE MG M 501
2AC2SOFTWAREG M:100 , MG M:505 , HOH M:510 , HOH M:541 , HOH M:552 , HOH M:571 , HOH N:539BINDING SITE FOR RESIDUE MG M 502
3AC3SOFTWAREHOH M:550 , HOH M:569 , HOH M:583 , HOH M:584 , HOH M:586BINDING SITE FOR RESIDUE MG M 503
4AC4SOFTWAREHOH M:536 , HOH N:507 , HOH N:527 , HOH N:528 , HOH N:530 , HOH N:568BINDING SITE FOR RESIDUE MG N 504
5AC5SOFTWAREG M:102 , MG M:502 , HOH M:507 , HOH M:510 , HOH M:527 , HOH M:535 , HOH M:552BINDING SITE FOR RESIDUE MG M 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1DFU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DFU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DFU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1DFU)

(-) Exons   (0, 0)

(no "Exon" information available for 1DFU)

(-) 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 M from PDB  Type:RNA  Length:19
                                                   
                 1dfu M  91 CCCAUGCGAGAGUAGGGAC 109
                                   100         


Chain N from PDB  Type:RNA  Length:19
                                                   
                 1dfu N  68 UGCCGAUGGUAGUGUGGGG  86
                                    77         


Chain P from PDB  Type:PROTEIN  Length:94
 aligned with RL25_ECOLI | P68919 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:94
                                    10        20        30        40        50        60        70        80        90    
           RL25_ECOLI     1 MFTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEVLTIVVDGKEIKVKAQDVQRHPYKPKLQHIDFVRA  94
               SCOP domains d1dfup_ P: Ribosomal protein L25                                                               SCOP domains
               CATH domains 1dfuP00 P:1-94 Ribosomal Protein L25; Chain P                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.ee....hhhhhhhhhhh.eeeeeee......eeeeeehhhhhhhhhhhhhhh...eeee..ee..eeeeeeee......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 1dfu P   1 MFTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEVLTIVVDGKEIKVKAQDVQRHPYKPKLQHIDFVRA  94
                                    10        20        30        40        50        60        70        80        90
   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, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DFU)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain P   (RL25_ECOLI | P68919)
molecular function
    GO:0008097    5S rRNA binding    Interacting selectively and non-covalently with 5S ribosomal RNA, the smallest RNA constituent of a ribosome.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0019843    rRNA binding    Interacting selectively and non-covalently with ribosomal RNA.
    GO:0003735    structural constituent of ribosome    The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA 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 or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0022625    cytosolic large ribosomal subunit    The large subunit of a ribosome located in the cytosol.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0005840    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.

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  RL25_ECOLI | P68919
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 Related Entries

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

UniProtKB/Swiss-Prot
        RL25_ECOLI | P68919: 1b75 1d6k 1ml5 2j28 2rdo 3bbx 3j5l 3j7z 3j8g 3j9y 3j9z 3ja1 3jbu 3jbv 3jcd 3jce 3jcj 3jcn 487d 4csu 4u1u 4u1v 4u20 4u24 4u25 4u26 4u27 4uy8 4v47 4v48 4v4h 4v4q 4v4v 4v4w 4v50 4v52 4v53 4v54 4v55 4v56 4v57 4v5b 4v5h 4v5y 4v64 4v65 4v66 4v69 4v6c 4v6d 4v6e 4v6k 4v6l 4v6m 4v6n 4v6o 4v6p 4v6q 4v6r 4v6s 4v6t 4v6v 4v6y 4v6z 4v70 4v71 4v72 4v73 4v74 4v75 4v76 4v77 4v78 4v79 4v7a 4v7b 4v7c 4v7d 4v7i 4v7s 4v7t 4v7u 4v7v 4v85 4v89 4v9c 4v9d 4v9o 4v9p 4wf1 4woi 4www 4ybb 5ady 5afi 5aka 5gad 5gae 5gaf 5gag 5gah 5h5u 5iqr 5it8 5j5b 5j7l 5j88 5j8a 5j91 5jc9 5jte 5ju8 5kcr 5kcs 5kps 5kpv 5kpw 5kpx 5l3p 5lza 5lzb 5lzc 5lzd 5lze 5lzf 5mdv 5mdw 5mdy 5mdz 5mgp 5u4i

(-) Related Entries Specified in the PDB File

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