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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HOMO SAPIENS MITOCHONDRIAL RIBOSOMAL DECODING SITE IN THE PRESENCE OF SRCL2 (A1555G MUTANT, BR-DERIVATIVE)
 
Authors :  J. Kondo, E. Westhof
Date :  14 Dec 07  (Deposition) - 24 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Ribosome, Decoding Site, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Kondo, E. Westhof
The Bacterial And Mitochondrial Ribosomal A-Site Molecular Switches Possess Different Conformational Substates
Nucleic Acids Res. V. 36 2654 2008
PubMed-ID: 18346970  |  Reference-DOI: 10.1093/NAR/GKN112
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - A SITE OF HUMAN MITOCHONDRIAL RIBOSOME, A CHAIN
    ChainsA, B, C
    EngineeredYES
    MutationYES
    SyntheticYES
 
Molecule 2 - A SITE OF HUMAN MITOCHONDRIAL RIBOSOME, B CHAIN
    ChainsD
    EngineeredYES
    MutationYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
15BU4Mod. Nucleotide5-BROMO-URIDINE-5'-MONOPHOSPHATE
2K2Ligand/IonPOTASSIUM ION
3PAR1Ligand/IonPAROMOMYCIN
4SR8Ligand/IonSTRONTIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
15BU2Mod. Nucleotide5-BROMO-URIDINE-5'-MONOPHOSPHATE
2K-1Ligand/IonPOTASSIUM ION
3PAR-1Ligand/IonPAROMOMYCIN
4SR-1Ligand/IonSTRONTIUM ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
15BU2Mod. Nucleotide5-BROMO-URIDINE-5'-MONOPHOSPHATE
2K-1Ligand/IonPOTASSIUM ION
3PAR1Ligand/IonPAROMOMYCIN
4SR-1Ligand/IonSTRONTIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH C:320 , HOH C:321 , HOH C:332BINDING SITE FOR RESIDUE PAR C 101
02AC2SOFTWAREHOH A:302 , HOH B:203 , HOH B:204 , HOH B:205 , HOH B:206 , HOH B:207BINDING SITE FOR RESIDUE SR B 201
03AC3SOFTWAREHOH C:304 , HOH D:204 , HOH D:205 , HOH D:206 , HOH D:207 , HOH D:208BINDING SITE FOR RESIDUE SR D 201
04AC4SOFTWAREHOH A:331 , HOH C:305 , HOH C:306 , HOH C:307 , HOH D:209 , HOH D:210BINDING SITE FOR RESIDUE SR C 201
05AC5SOFTWAREHOH A:303 , HOH A:304 , HOH B:208 , HOH B:209 , HOH B:210 , HOH C:302BINDING SITE FOR RESIDUE SR B 202
06AC6SOFTWAREHOH C:308 , HOH D:203 , HOH D:211 , HOH D:212 , HOH D:213 , HOH D:214BINDING SITE FOR RESIDUE SR D 202
07AC7SOFTWAREHOH C:309 , HOH C:310 , HOH C:311 , HOH D:215 , HOH D:216 , HOH D:217BINDING SITE FOR RESIDUE SR C 202
08AC8SOFTWAREHOH C:312 , HOH C:313 , HOH C:314 , HOH D:218 , HOH D:219 , HOH D:220BINDING SITE FOR RESIDUE SR C 203
09AC9SOFTWAREHOH A:306 , HOH B:211 , HOH D:231BINDING SITE FOR RESIDUE K C 301
10BC1SOFTWAREHOH B:224 , HOH C:315 , HOH C:317BINDING SITE FOR RESIDUE K A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BNQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BNQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BNQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BNQ)

(-) Exons   (0, 0)

(no "Exon" information available for 3BNQ)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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Chain A from PDB  Type:RNA  Length:23
                                                      
                  3bnq A  1 UUGCGUCACCuCGAGCAAGUCGC 23
                                    10|       20   
                                     11-5BU        

Chain B from PDB  Type:RNA  Length:23
                                                      
                  3bnq B  1 UUGCGUCACCuCGAGCAAGUCGC 23
                                    10|       20   
                                     11-5BU        

Chain C from PDB  Type:RNA  Length:23
                                                      
                  3bnq C  1 UUGCGUCACCuCGAGCAAGUCGC 23
                                    10|       20   
                                     11-5BU        

Chain D from PDB  Type:RNA  Length:21
                                                    
                  3bnq D  1 GCGUCACCuCGAGCAAGUCGC 21
                                    10        20 
                                    9-5BU        

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  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 3BNQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3BNQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BNQ)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3BNQ)

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 Related Entries

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(-) Related Entries Specified in the PDB File

3bnl 3bnn 3bno 3bnp 3bnr 3bns 3bnt