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(-) Description

Title :  STRUCTURE OF RIBOSOMAL PROTEIN L1-MRNA COMPLEX AT 2.1 RESOLUTION.
 
Authors :  S. Tishchenko, E. Nikonova, A. Nikulin, N. Nevskaya, S. Volchkov, W. Piendl, M. Garber, S. Nikonov
Date :  01 Aug 06  (Deposition) - 19 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ribosomal Protein L1, Mrna, Rna-Protein Complex, Structural Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Tishchenko, E. Nikonova, A. Nikulin, N. Nevskaya, S. Volchkov, W. Piendl, M. Garber, S. Nikonov
Structure Of The Ribosomal Protein L1-Mrna Complex At 2. 1 A Resolution: Common Features Of Crystal Packing Of L1-Rna Complexes.
Acta Crystallogr. , Sect. D V. 62 1545 2006
PubMed-ID: 17139090  |  Reference-DOI: 10.1107/S0907444906041655
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 36-MER
    Chains: B
    Engineered: YES
    Other Details: RNA WAS PREPARED FROM THE PLASMID IN CELL- FREE (IN VITRO) SYSTEM WITHOUT LIVING ORGANISM
    Synthetic: YES
 
Molecule 2 - 50S RIBOSOMAL PROTEIN L1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PACA-L1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RPL1
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Strain: VK1

 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
1BU11Ligand/Ion1,4-BUTANEDIOL
2K1Ligand/IonPOTASSIUM ION
3MG1Ligand/IonMAGNESIUM ION
4MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:42 , THR A:216 , THR A:217 , U B:30 , U B:31BINDING SITE FOR RESIDUE K A 229
2AC2SOFTWAREHOH B:210 , HOH B:217 , HOH B:232 , HOH B:237 , HOH B:257 , HOH B:282BINDING SITE FOR RESIDUE MG B 202
3AC3SOFTWAREGLY A:69 , SER A:179 , PHE A:180 , PRO A:181 , HOH A:276 , HOH A:310BINDING SITE FOR RESIDUE BU1 A 230

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HW8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2HW8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HW8)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_L1PS01199 Ribosomal protein L1 signature.RL1_THETH121-140  1A:120-139

(-) Exons   (0, 0)

(no "Exon" information available for 2HW8)

(-) 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:228
 aligned with RL1_THETH | P27150 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:228
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221        
            RL1_THETH     2 PKHGKRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS 229
               SCOP domains d2hw8a1 A:1-228 Ribosomal protein L1                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhh.....eehhhhhhhhhhhh.......eeeeeeee.....hhhhh.eeeee..........eeee...hhhhhhhh....eeehhhhhhhhhhh.....eeee...hhhhhhhhhhhhhh......hhhhh....hhhhhhhhhhh.eeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhh..........eeeeeeee.....eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------RIBOSOMAL_L1        ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2hw8 A   1 PKHGKRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVmGAVGSKmGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTmGPSVRINPHS 228
                                    10        20        30        40        50        60        70        80        90       100       110       120      |130       140       150       160       170       180       190       200       210       220        
                                                                                                                                                 120-MSE  |                                                                                        218-MSE      
                                                                                                                                                        127-MSE                                                                                                 


Chain B from PDB  Type:RNA  Length:36
                                                                    
                 2hw8 B   2 GGGGUGAAGGAGGCUUCGGCCGCGAAACUUCACCCC  37
                                    11        21        31
   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: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2HW8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HW8)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RL1_THETH | P27150)
molecular function
    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.
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
biological process
    GO:0006417    regulation of translation    Any process that modulates 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:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0015934    large ribosomal subunit    The larger of the two subunits of a ribosome. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site).
    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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  2hw8
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  RL1_THETH | P27150
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 Related Entries

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

UniProtKB/Swiss-Prot
        RL1_THETH | P27150: 1ad2 1eg0 1zho 2oum 2ov7 2vpl 3tg8 3u4m 3u56 3umy 487d 4f9t 4qg3 4qgb 4qvi 4reo 5ib7 5ib8 5ibb 5imq 5imr 5j8b

(-) Related Entries Specified in the PDB File

1u63 THE CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L1 FROM METHANOCOCCUS JANNASCHII IN COMPLEX WITH A SPECIFIC FRAGMENT OF ITS MRNA.
1zho THE CRYSTAL STRUCTURE AT 2.6 A OF RIBOSOMAL PROTEIN L1 FROM THERMUS THERMOPHILUS IN COMPLEX WITH A 38 NT FRAGMENT OF L1 MRNA FROM METHANOCCOCUS VANNIELII. SPACE GROUP IS P21.