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(-) Description

Title :  CRYSTAL STRUCTURE OF A CONSERVED RIBOSOMAL PROTEIN-RNA COMPLEX
 
Authors :  G. L. Conn, D. E. Draper, E. E. Lattman, A. G. Gittis
Date :  27 Apr 01  (Deposition) - 23 May 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Ribosome, Ribosomal Rna, Tertiary Structure, Rna-Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. L. Conn, A. G. Gittis, E. E. Lattman, V. K. Misra, D. E. Draper
A Compact Rna Tertiary Structure Contains A Buried Backbone-K+ Complex
J. Mol. Biol. V. 318 963 2002
PubMed-ID: 12054794  |  Reference-DOI: 10.1016/S0022-2836(02)00147-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSOMAL PROTEIN L11
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L11
    Organism Scientific: BACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
 
Molecule 2 - 58 NUCLEOTIDE RIBOSOMAL 23S RNA DOMAIN
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Fragment: NTS 1051-1108 FROM E. COLI 23S RRNA
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: RNA SYNTHESIZED BY IN VITRO TRANSCRIPTION USING T7 RNA POLYMERASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 29)

Asymmetric Unit (4, 29)
No.NameCountTypeFull Name
1GTP2Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
2K2Ligand/IonPOTASSIUM ION
3MG21Ligand/IonMAGNESIUM ION
4OS4Ligand/IonOSMIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
2K-1Ligand/IonPOTASSIUM ION
3MG-1Ligand/IonMAGNESIUM ION
4OS-1Ligand/IonOSMIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
2K-1Ligand/IonPOTASSIUM ION
3MG-1Ligand/IonMAGNESIUM ION
4OS-1Ligand/IonOSMIUM ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREU C:108BINDING SITE FOR RESIDUE MG C1159
02AC2SOFTWAREA C:148BINDING SITE FOR RESIDUE MG C1161
03AC3SOFTWAREA C:119 , A C:120 , C C:122 , A C:123BINDING SITE FOR RESIDUE K C1162
04AC4SOFTWAREA C:120 , G C:121 , C C:122BINDING SITE FOR RESIDUE MG C1163
05AC5SOFTWAREC C:152 , HOH C:2001BINDING SITE FOR RESIDUE MG C1164
06AC6SOFTWAREU C:115 , U C:116 , A D:336BINDING SITE FOR RESIDUE MG C1165
07AC7SOFTWAREGTP C:101 , U D:358BINDING SITE FOR RESIDUE MG C1166
08AC8SOFTWAREA C:123 , G C:143 , U C:144BINDING SITE FOR RESIDUE MG C1167
09AC9SOFTWAREA C:111BINDING SITE FOR RESIDUE MG C1168
10BC1SOFTWAREG C:137BINDING SITE FOR RESIDUE OS C1169
11BC2SOFTWAREG C:113BINDING SITE FOR RESIDUE MG C1172
12BC3SOFTWAREG D:321BINDING SITE FOR RESIDUE MG D1360
13BC4SOFTWAREG D:321 , A D:348BINDING SITE FOR RESIDUE MG D1361
14BC5SOFTWAREA D:319 , A D:320 , C D:322 , A D:323BINDING SITE FOR RESIDUE K D1362
15BC6SOFTWAREG D:313 , A D:320 , C D:322BINDING SITE FOR RESIDUE MG D1363
16BC7SOFTWAREGTP C:101 , GTP D:301BINDING SITE FOR RESIDUE MG D1364
17BC8SOFTWAREA D:311BINDING SITE FOR RESIDUE MG D1365
18BC9SOFTWAREU C:158 , GTP D:301BINDING SITE FOR RESIDUE MG D1366
19CC1SOFTWAREA D:323 , U D:344BINDING SITE FOR RESIDUE MG D1367
20CC2SOFTWAREG D:306BINDING SITE FOR RESIDUE MG D1368
21CC3SOFTWAREG D:312 , G D:313 , A D:320BINDING SITE FOR RESIDUE MG D1372

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HC8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HC8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HC8)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_L11PS00359 Ribosomal protein L11 signature.RL11_GEOSE118-133
 		  2A:61-75
B:261-275
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_L11PS00359 Ribosomal protein L11 signature.RL11_GEOSE118-133
 		  1A:61-75
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_L11PS00359 Ribosomal protein L11 signature.RL11_GEOSE118-133
 		  1-
B:261-275

(-) Exons   (0, 0)

(no "Exon" information available for 1HC8)

(-) 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:74
 aligned with RL11_GEOSE | P56210 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:74
                                    68        78        88        98       108       118       128    
           RL11_GEOSE    59 TFITKTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMRMIEGTARSMGIVVE 132
               SCOP domains d1hc8a_ A: Ribosomal protein L11, C-terminal domain                        SCOP domains
               CATH domains 1hc8A00 A:2-75  [code=1.10.10.250, no name defined]                        CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhh..............eee..hhhhhhhhhhhh........hhhhhhhhhhhhh..eeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------RIBOSOMAL_L11   PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 1hc8 A   2 TFITKTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMRMIEGTARSMGIVVE  75
                                    11        21        31        41        51        61        71    


Chain B from PDB  Type:PROTEIN  Length:70
 aligned with RL11_GEOSE | P56210 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:70
                                    72        82        92       102       112       122       132
           RL11_GEOSE    63 KTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMRMIEGTARSMGIVVE 132
               SCOP domains d1hc8b_ B: Ribosomal protein L11, C-terminal domain                    SCOP domains
               CATH domains 1hc8B00 B:206-275  [code=1.10.10.250, no name defined]                 CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh..............eee..hhhhhhhhhhhh........hhhhhhhhhhhhh..eeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------RIBOSOMAL_L11   PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 1hc8 B 206 KTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMRMIEGTARSMGIVVE 275
                                   215       225       235       245       255       265       275


Chain C from PDB  Type:RNA  Length:58
                                                                                          
                 1hc8 C 101 xCCAGGAUGUAGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACUGGU 158
                            |      110       120       130       140       150        
                          101-GTP                                                     


Chain D from PDB  Type:RNA  Length:58
                                                                                          
                 1hc8 D 301 xCCAGGAUGUAGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACUGGU 358
                            |      310       320       330       340       350        
                          301-GTP
   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 alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HC8)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RL11_GEOSE | P56210)
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.
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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  RL11_GEOSE | P56210
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 Related Entries

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

UniProtKB/Swiss-Prot
        RL11_GEOSE | P56210: 1aci 1c04 1fow 1fox 1foy 1ip8 1qa6 1y39 2fow

(-) Related Entries Specified in the PDB File

1aci L11 RIBOSOMAL PROTEIN RNA BINDING DOMAIN, NMR, 20 STRUCTURES
1c04 IDENTIFICATION OF KNOWN PROTEIN AND RNA STRUCTURES IN A 5 AMAP OF THE LARGE RIBOSOMAL SUBUNIT FROM HALOARCULAMARISMORTUI
1fow NMR STRUCTURE OF L11-C76, THE C-TERMINAL DOMAIN OF50S RIBOSOMAL PROTEIN L11, MINIMIZED AVERAGE STRUCTURE
1fox NMR STRUCTURE OF L11-C76, THE C-TERMINAL DOMAIN OF50S RIBOSOMAL PROTEIN L11, 33 STRUCTURES
1foy THE RNA BINDING DOMAIN OF RIBOSOMAL PROTEIN L11:THREE-DIMENSIONAL STRUCTURE OF THE RNA -BOUND FORM OF THEPROTEIN, NMR, MINIMIZED AVERAGE STRUCTURE
1qa6 CRYSTAL STRUCTURE OF A CONSERVED RIBOSOMAL PROTEIN-RNACOMPLEX
2fow THE RNA BINDING DOMAIN OF RIBOSOMAL PROTEIN L11:THREE-DIMENSIONAL STRUCTURE OF THE RNA -BOUND FORM OF THEPROTEIN, NMR, 26 STRUCTURES