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(-) Description

Title :  CRYSTAL STRUCTURE OF MUTANT RIBOSOMAL PROTEIN G219V TTHL1 IN COMPLEX WITH 80NT 23S RNA FROM THERMUS THERMOPHILUS
 
Authors :  A. G. Gabdulkhakov, N. A. Nevskaya, S. V. Nikonov
Date :  22 May 14  (Deposition) - 11 Feb 15  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Ribosomal Protein, Rrna, Rrna Binding, Ribosome, Ribosomal Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Tishchenko, O. Kostareva, A. Gabdulkhakov, A. Mikhaylina, E. Nikonova, N. Nevskaya, A. Sarskikh, W. Piendl, M. Garber, S. Nikono
Protein-Rna Affinity Of Ribosomal Protein L1 Mutants Does Not Correlate With The Number Of Intermolecular Interactions.
Acta Crystallogr. , Sect. D V. 71 376 2015
PubMed-ID: 25664749  |  Reference-DOI: 10.1107/S1399004714026248

(-) Compounds

Molecule 1 - 50S RIBOSOMAL PROTEIN L1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A-PL/TTHL1 G219V
    Expression System Strain: BL11(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PET11A-PL
    Gene: RPLA, RPL1
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
 
Molecule 2 - FRAGMENT OF 23S RRNA
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC18/RRNATTH
    Expression System Taxid: 562
    Expression System Vector Type: PUC18
    Fragment: 80 NT FRAGMENT OF 23S RRNA
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric/Biological Unit (4, 18)
No.NameCountTypeFull Name
1BME4Ligand/IonBETA-MERCAPTOETHANOL
2IPA8Ligand/IonISOPROPYL ALCOHOL
3SO45Ligand/IonSULFATE ION
4URE1Ligand/IonUREA

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:1 , LYS A:2 , HIS A:3 , ARG A:8 , ARG A:52 , ARG A:53 , SER A:54 , HOH A:483BINDING SITE FOR RESIDUE SO4 A 301
02AC2SOFTWARELYS A:46 , ARG A:210 , HOH A:466BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWARELYS A:205 , GLY A:206BINDING SITE FOR RESIDUE IPA A 303
04AC4SOFTWARESER A:63BINDING SITE FOR RESIDUE IPA A 304
05AC5SOFTWAREGLY A:95 , GLY A:96 , GLU A:97 , GLU A:98 , ILE A:99 , ASN A:225 , HOH A:430 , HOH A:463 , HOH B:2430BINDING SITE FOR RESIDUE IPA A 305
06AC6SOFTWAREGLY A:60 , THR A:61 , LYS A:141 , HIS A:199BINDING SITE FOR RESIDUE IPA A 306
07AC7SOFTWARELYS A:205 , ARG A:210BINDING SITE FOR RESIDUE IPA A 307
08AC8SOFTWAREGLN A:71 , LYS A:157BINDING SITE FOR RESIDUE IPA A 308
09AC9SOFTWAREPRO A:65BINDING SITE FOR RESIDUE IPA A 309
10BC1SOFTWAREGLU A:85 , GLY A:150 , GLU A:151 , ARG A:154BINDING SITE FOR RESIDUE BME A 310
11BC2SOFTWAREC B:2128 , C B:2129 , HOH B:2415BINDING SITE FOR RESIDUE SO4 B 2201
12BC3SOFTWAREG B:2112 , HOH B:2318 , HOH B:2425 , HOH B:2427BINDING SITE FOR RESIDUE SO4 B 2202
13BC4SOFTWAREC B:2161BINDING SITE FOR RESIDUE SO4 B 2203
14BC5SOFTWAREC B:2178 , C B:2179 , HOH B:2381BINDING SITE FOR RESIDUE BME B 2204
15BC6SOFTWAREC B:2174 , C B:2175 , A B:2176 , HOH B:2375 , HOH B:2382BINDING SITE FOR RESIDUE BME B 2205
16BC7SOFTWAREG B:2110 , U B:2180BINDING SITE FOR RESIDUE IPA B 2206
17BC8SOFTWAREC B:2138 , C B:2139 , HOH B:2333 , HOH B:2392 , HOH B:2470BINDING SITE FOR RESIDUE URE B 2207
18BC9SOFTWAREG B:2133 , G B:2157BINDING SITE FOR RESIDUE BME B 2208

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QG3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4QG3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QG3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QG3)

(-) Exons   (0, 0)

(no "Exon" information available for 4QG3)

(-) 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
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhh........hhhhhhhhhhhhh......eeeeeeee.....hhhhh.eeeee..........eeee...hhhhhhhhh...eeehhhhhhhhhh......eeee...hhhhhhhhhhhhhhhhh............hhhhhhhhhhh.eeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhhh.........eeeeeeee....eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4qg3 A    1 PKHGKRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMVPSVRINPHS  228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        


Chain B from PDB  Type:RNA  Length:80
                                                                                                                 
                4qg3 B 2105 GGGAUGCGUAGGAUAGGUGGGAGCCUGUGAACCCCCGCCUCCGGGUGGGGGGGAGGCGCCGGUGAAAUACCACCCUUCCC 2184
                                  2114      2124      2134      2144      2154      2164      2174      2184
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "SCOP Domain" information available for 4QG3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QG3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QG3)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RL1_THETH | P27150: 1ad2 1eg0 1zho 2hw8 2oum 2ov7 2vpl 3tg8 3u4m 3u56 3umy 487d 4f9t 4qgb 4qvi 4reo 5ib7 5ib8 5ibb 5imq 5imr 5j8b

(-) Related Entries Specified in the PDB File

1u63 THE STRUCTURE OF A RIBOSOMAL PROTEIN L1-MRNA COMPLEX
3u42 MUTANT RIBOSOMAL PROTEIN L1 FROM THERMUS THERMOPHILUS WITH THREONINE 217 REPLACED BY VALINE
3u4m CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN TTHL1 IN COMPLEX WITH 80NT 23S RNA FROM THERMUS THERMOPHILUS
3u56 CRYSTAL STRUCTURE OF MUTANT RIBOSOMAL PROTEIN T217V TTHL1 IN COMPLEX WITH 80NT 23S RNA FROM THERMUS THERMOPHILUS
3umy CRYSTAL STRUCTURE OF MUTANT RIBOSOMAL PROTEIN T217A TTHL1 IN COMPLEX WITH 80NT 23S RNA FROM THERMUS THERMOPHILUS
4qgb