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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN TL5, ONE OF THE CTC FAMILY PROTEINS, COMPLEXED WITH A FRAGMENT OF 5S RRNA.
 
Authors :  R. V. Fedorov, V. A. Meshcheryakov, G. M. Gongadze, N. P. Fomenkova, N. A. Nevskaya, M. Selmer, M. Laurberg, O. Kristensen, S. Al- Karadaghi, A. Liljas, M. B. Garber, S. V. Nikonov
Date :  23 Jul 00  (Deposition) - 25 Jun 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  General Stress Protein Ctc, 5S Rrna-Protein Complex, Cadmium Ions, Ribosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Fedorov, V. Meshcheryakov, G. Gongadze, N. Fomenkova, N. Nevskaya, M. Selmer, M. Laurberg, O. Kristensen, S. Al-Karadaghi, A. Liljas, M. Garber, S. Nikonov
Structure Of Ribosomal Protein Tl5 Complexed With Rna Provides New Insights Into The Ctc Family Of Stress Proteins.
Acta Crystallogr. , Sect. D V. 57 968 2001
PubMed-ID: 11418764  |  Reference-DOI: 10.1107/S0907444901006291
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 19 NT FRAGMENT OF 5S RRNA
    Chains: B, E
    Engineered: YES
    Fragment: INCLUDES LOOP E AND HELIX IV
    Synthetic: YES
 
Molecule 2 - 21 NT FRAGMENT OF 5S RRNA
    Chains: C, F
    Engineered: YES
    Fragment: INCLUDES LOOP E AND HELIX IV
    Synthetic: YES
 
Molecule 3 - 50S RIBOSOMAL PROTEIN L25
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Other Details: BACTERIA
    Synonym: RIBOSOMAL PROTEIN TL5

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 30)

Asymmetric Unit (2, 30)
No.NameCountTypeFull Name
1CD13Ligand/IonCADMIUM ION
2MG17Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:54 , ASP A:123 , HOH A:305 , HOH A:306 , HOH A:307BINDING SITE FOR RESIDUE CD A 296
02AC2SOFTWAREMET A:1 , HIS A:55 , GLU A:135 , HOH A:342BINDING SITE FOR RESIDUE CD A 297
03AC3SOFTWAREHIS A:32 , SER A:92 , ASP A:93 , GLU A:94 , HOH A:304 , HOH A:308BINDING SITE FOR RESIDUE CD A 298
04AC4SOFTWARESER A:149 , HIS A:151 , ASP A:154 , HOH D:434BINDING SITE FOR RESIDUE CD A 299
05AC5SOFTWAREHIS A:151 , HOH A:318 , ASP D:93 , HOH D:434 , HOH D:435BINDING SITE FOR RESIDUE CD D 300
06AC6SOFTWAREHIS A:121 , GLU A:169 , HOH A:309 , HOH A:313BINDING SITE FOR RESIDUE CD A 301
07AC7SOFTWAREHIS A:121 , ASP A:123 , HOH A:309 , HOH A:311BINDING SITE FOR RESIDUE CD A 302
08AC8SOFTWAREHIS D:54 , ASP D:123 , HOH D:323 , HOH D:324 , HOH D:325 , HOH D:343BINDING SITE FOR RESIDUE CD D 303
09AC9SOFTWAREMET D:1 , HIS D:55 , GLU D:135 , HOH D:443BINDING SITE FOR RESIDUE CD D 304
10BC1SOFTWAREGLU A:168 , HIS D:32 , SER D:92 , GLU D:94 , HOH D:425BINDING SITE FOR RESIDUE CD D 305
11BC2SOFTWAREHIS D:151 , ASP D:154BINDING SITE FOR RESIDUE CD D 306
12BC3SOFTWAREHIS D:121 , GLU D:169 , HOH D:336 , HOH D:355BINDING SITE FOR RESIDUE CD D 307
13BC4SOFTWAREHIS D:121 , ASP D:123 , HOH D:328 , HOH D:336BINDING SITE FOR RESIDUE CD D 308
14BC5SOFTWAREA C:109 , HOH C:319 , HOH C:320 , HOH F:326 , HOH F:344BINDING SITE FOR RESIDUE MG C 309
15BC6SOFTWAREASP D:40 , HOH D:381 , HOH D:406 , HOH D:436BINDING SITE FOR RESIDUE MG D 310
16BC7SOFTWAREHOH B:10 , HOH B:12 , HOH B:13 , HOH B:17 , HOH B:251BINDING SITE FOR RESIDUE MG B 311
17BC8SOFTWAREHOH C:340 , HOH C:341 , HOH C:342BINDING SITE FOR RESIDUE MG C 312
18BC9SOFTWAREU B:80 , HOH D:380 , A E:78 , A F:99BINDING SITE FOR RESIDUE MG B 313
19CC1SOFTWAREG C:100 , HOH C:343 , HOH C:344 , HOH C:345 , HOH C:346 , HOH C:347BINDING SITE FOR RESIDUE MG C 314
20CC2SOFTWAREG E:75 , G E:76 , HOH E:331 , HOH E:348 , HOH E:349 , HOH F:357BINDING SITE FOR RESIDUE MG E 315
21CC3SOFTWAREU E:80 , HOH E:328 , HOH E:350 , U F:95 , G F:96 , HOH F:335BINDING SITE FOR RESIDUE MG F 316
22CC4SOFTWAREC F:97 , G F:98BINDING SITE FOR RESIDUE MG F 317
23CC5SOFTWAREC C:110BINDING SITE FOR RESIDUE MG C 318
24CC6SOFTWAREHOH D:437 , HOH E:351BINDING SITE FOR RESIDUE MG D 319
25CC7SOFTWAREGLU D:13 , HOH E:351 , A F:94BINDING SITE FOR RESIDUE MG D 320
26CC8SOFTWARETYR D:38 , HOH D:375 , G E:83 , HOH E:351BINDING SITE FOR RESIDUE MG E 321
27CC9SOFTWAREC F:110 , HOH F:344BINDING SITE FOR RESIDUE MG F 323
28DC1SOFTWAREG F:100 , HOH F:333 , HOH F:345 , HOH F:358 , HOH F:359 , HOH F:360BINDING SITE FOR RESIDUE MG F 324
29DC2SOFTWAREA F:108BINDING SITE FOR RESIDUE MG F 325

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1FEU)

(-) Sequences/Alignments

Asymmetric 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:185
 aligned with RL25_THETH | P56930 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     
           RL25_THETH     1 MEYRLKAYYREGEKPSALRRAGKLPGLMYNRHLNRKVYVDLVEFDKVFRQASIHHVIVLELPDGQSLPTLVRQVNLDKRRRRPEHVDFFVLSDEPVEMYVPLRFVGTPAGVRAGGVLQEIHRDILVKVSPRNIPEFIEVDVSGLEIGDSLHASDLKLPPGVELAVSPEETIAAVVPPEDVEKLAE 185
               SCOP domains d1feua_ A: Ribosomal protein TL5 (general stress protein CTC)                                                                                                                             SCOP domains
               CATH domains 1feuA01 A:1-91 Ribosomal Protein L25; Chain P                                              1feuA02 A:92-185 Ribosomal protein L25-like. Domain 2                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.ee....hhhhhhhh.eeeeeee....eeeeeeehhhhhhhhhhhh...eeeee.....eeeeeeeeeee......eeeeeeee.....eeeeeeeeee..hhhhhh..eeee...eeeeeehhhhh...eeee.......eeee.hhh......ee......eeeeee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1feu A   1 MEYRLKAYYREGEKPSALRRAGKLPGLMYNRHLNRKVYVDLVEFDKVFRQASIHHVIVLELPDGQSLPTLVRQVNLDKRRRRPEHVDFFVLSDEPVEMYVPLRFVGTPAGVRAGGVLQEIHRDILVKVSPRNIPEFIEVDVSGLEIGDSLHASDLKLPPGVELAVSPEETIAAVVPPEDVEKLAE 185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     


Chain B from PDB  Type:RNA  Length:19
                                                   
                 1feu B  69 GCCGAUGGUAGUGUGGGGU  87
                                    78         


Chain C from PDB  Type:RNA  Length:21
                                                     
                 1feu C  90 CCCCAUGCGAGAGUAGGGAAC 110
                                    99       109 


Chain D from PDB  Type:PROTEIN  Length:189
 aligned with RL25_THETH | P56930 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         
           RL25_THETH     1 MEYRLKAYYREGEKPSALRRAGKLPGLMYNRHLNRKVYVDLVEFDKVFRQASIHHVIVLELPDGQSLPTLVRQVNLDKRRRRPEHVDFFVLSDEPVEMYVPLRFVGTPAGVRAGGVLQEIHRDILVKVSPRNIPEFIEVDVSGLEIGDSLHASDLKLPPGVELAVSPEETIAAVVPPEDVEKLAEEAAA 189
               SCOP domains d1feud_ D: Ribosomal protein TL5 (general stress protein CTC)                                                                                                                                 SCOP domains
               CATH domains 1feuD01 D:1-91 Ribosomal Protein L25; Chain P                                              1feuD02 D:92-185 Ribosomal protein L25-like. Domain 2                                         ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhh.eeeeeeee..eeeeeeeehhhhhhhhhhhh...eeeee.....eeeeeeeeeee......eeeeeeee.....eeeeeeeeee..hhhhhh..eee....eeeeeehhhhh...eeee........eee.hhh......ee......eeeeee.....hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1feu D   1 MEYRLKAYYREGEKPSALRRAGKLPGLMYNRHLNRKVYVDLVEFDKVFRQASIHHVIVLELPDGQSLPTLVRQVNLDKRRRRPEHVDFFVLSDEPVEMYVPLRFVGTPAGVRAGGVLQEIHRDILVKVSPRNIPEFIEVDVSGLEIGDSLHASDLKLPPGVELAVSPEETIAAVVPPEDVEKLAEEAAA 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         


Chain E from PDB  Type:RNA  Length:19
                                                   
                 1feu E  69 GCCGAUGGUAGUGUGGGGU  87
                                    78         


Chain F from PDB  Type:RNA  Length:21
                                                     
                 1feu F  90 CCCCAUGCGAGAGUAGGGAAC 110
                                    99       109
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,D   (RL25_THETH | P56930)
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: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: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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