Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF 16S RRNA IN THE REGION AROUND RIBOSOMAL PROTEIN S8.
 
Authors :  L. Lancaster, G. M. Culver, G. Z. Yusupova, J. H. Cate, M. M. Yuspov, H. F. Noller
Date :  16 Mar 00  (Deposition) - 12 Jun 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  7.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rna, Rrna, Ribosome, Ribosomal Protein, 16S Rrna, S8 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Lancaster, G. M. Culver, G. Z. Yusupova, J. H. Cate, M. M. Yusupov, H. F. Noller
The Location Of Protein S8 And Surrounding Elements Of 16S Rrna In The 70S Ribosome From Combined Use Of Directed Hydroxyl Radical Probing And X-Ray Crystallography.
Rna V. 6 717 2000
PubMed-ID: 10836793  |  Reference-DOI: 10.1017/S1355838200000303
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 16S RIBOSOMAL RNA
    Chains: B
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Other Details: COORDINATES FOR THERMUS THERMOPHILUS 16S RRNA BUT SEQUENCE AND NUMBERING IS THAT OF E.COLI 16S RRNA
 
Molecule 2 - RIBOSOMAL PROTEIN S8
    Chains: A
    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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1EMI)

(-) Sites  (0, 0)

(no "Site" information available for 1EMI)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_S8PS00053 Ribosomal protein S8 signature.RS8_THEAQ108-125  1A:108-125
RS8_THET8108-125  1A:108-125

(-) Exons   (0, 0)

(no "Exon" information available for 1EMI)

(-) 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:136
 aligned with RS8_THEAQ | A0A0M9AFS9 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:136
                                    12        22        32        42        52        62        72        82        92       102       112       122       132      
            RS8_THEAQ     3 TDPIADMLTRIRNATRVYKESTEVPASRFKEEILKILAREGFIKGYERVEVDGKPYLRIHLKYGPRRQGPDPRPEQVIKHIRRISRPGRRVYVGVKEIPRVRRGLGIAILSTPKGVLTDREARKLGVGGELICEVW 138
               SCOP domains d1emia_ A: 30S subunit                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................................................................................................................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------RIBOSOMAL_S8      ------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1emi A   3 TDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDREARKLGVGGELICEVW 138
                                    12        22        32        42        52        62        72        82        92       102       112       122       132      


Chain A from PDB  Type:PROTEIN  Length:136
 aligned with RS8_THET8 | P0DOY9 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:136
                                    12        22        32        42        52        62        72        82        92       102       112       122       132      
            RS8_THET8     3 TDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDREARKLGVGGELICEVW 138
               SCOP domains d1emia_ A: 30S subunit                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................................................................................................................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------RIBOSOMAL_S8      ------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1emi A   3 TDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDREARKLGVGGELICEVW 138
                                    12        22        32        42        52        62        72        82        92       102       112       122       132      


Chain B from PDB  Type:RNA  Length:161
                                                                                                                                                                                                 
                 1emi B 577 GCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUACGAAGACUGACGCUCAGGUGCGUCGACUUGGAGGUUGUGCUUCGUGGCUUCCGGAGCUAACGCGUUAAGUCGAC 879
                                   586       596       606       616       626       636       646       656     ||746       756       822       832     ||848       858       868       878 
                                                                                                               662|                  764|              838| ||                               
                                                                                                                743                   821               841 ||                               
                                                                                                                                                          843|                               
                                                                                                                                                           848
   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: Low resolution protein structures (283)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1EMI)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RS8_THEAQ | A0A0M9AFS9)

Chain A   (RS8_THET8 | P0DOY9)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1emi)
 
  Sites
(no "Sites" information available for 1emi)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1emi)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1emi
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RS8_THEAQ | A0A0M9AFS9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  RS8_THET8 | P0DOY9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  RS8_THEAQ | A0A0M9AFS9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  RS8_THET8 | P0DOY9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RS8_THEAQ | A0A0M9AFS9: 1jgo 1jgp 1jgq 1n34 1n36 2e5l 2uu9 2uua 2uub 2uuc 2uxb 2uxc 2uxd 2vqe 2vqf 2zm6 3t1h 3t1y 4b3m 4b3r 4b3s 4b3t 4dr1 4dr2 4dr3 4dr4 4dr5 4dr6 4dr7 4duy 4duz 4dv0 4dv1 4dv2 4dv3 4dv4 4dv5 4dv6 4dv7 4gkj 4gkk 4ji0 4ji1 4ji2 4ji3 4ji4 4ji5 4ji6 4ji7 4ji8 4jv5 4jya 4k0k 4khp 4lf4 4lf5 4lf6 4lf7 4lf8 4lf9 4lfa 4lfb 4lfc 4nxm 4nxn 4ox9 4v7k 4w2e 4wpo 4wqf 4wqu 4wqy 4wt8 4x62 4x64 4x65 4x66 4yhh 4yy3 5br8 5hau 5iwa 5j8b 5lmn 5lmo 5lmp 5lmq 5lmr 5lms 5lmt 5lmu 5lmv
        RS8_THET8 | P0DOY9: 1fjg 1fka 1hnw 1hnx 1hnz 1hr0 1i94 1i95 1i96 1i97 1ibk 1ibl 1ibm 1j5e 1jgo 1jgp 1jgq 1l1u 1ml5 1n32 1n33 1n34 1n36 1qd7 1vvj 1vy4 1vy5 1vy6 1vy7 1xmo 1xmq 1xnq 1xnr 2e5l 2f4v 2hhh 2uu9 2uua 2uub 2uuc 2uxb 2uxc 2uxd 2vqe 2vqf 2zm6 3oto 3t1h 3t1y 4aqy 4b3m 4b3r 4b3s 4b3t 4dr1 4dr2 4dr3 4dr4 4dr5 4dr6 4dr7 4duy 4duz 4dv0 4dv1 4dv2 4dv3 4dv4 4dv5 4dv6 4dv7 4gkj 4gkk 4ji0 4ji1 4ji2 4ji3 4ji4 4ji5 4ji6 4ji7 4ji8 4jv5 4jya 4k0k 4khp 4l47 4l71 4lel 4lf4 4lf5 4lf6 4lf7 4lf8 4lf9 4lfa 4lfb 4lfc 4lfz 4lnt 4lsk 4lt8 4nxm 4nxn 4ox9 4p6f 4p70 4tua 4tub 4tuc 4tud 4tue 4v42 4v49 4v4a 4v4g 4v4i 4v4p 4v4r 4v4s 4v4t 4v4x 4v4y 4v4z 4v51 4v5a 4v5c 4v5d 4v5e 4v5f 4v5g 4v5j 4v5k 4v5l 4v5m 4v5n 4v5p 4v5q 4v5r 4v5s 4v68 4v6a 4v6f 4v6g 4v7j 4v7k 4v7l 4v7m 4v7w 4v7x 4v7y 4v7z 4v87 4v8a 4v8b 4v8c 4v8d 4v8e 4v8f 4v8g 4v8h 4v8i 4v8j 4v8n 4v8o 4v8q 4v8u 4v8x 4v90 4v95 4v97 4v9a 4v9b 4v9h 4v9i 4v9r 4v9s 4w2e 4w2f 4w2g 4w2h 4w2i 4w4g 4wpo 4wq1 4wqf 4wqr 4wqu 4wqy 4wr6 4wra 4wro 4wsd 4wsm 4wt1 4wt8 4wu1 4wzd 4wzo 4x62 4x64 4x65 4x66 4y4o 4y4p 4yhh 4ypb 4yy3 4yzv 4z3s 4z8c 4zer 4zsn 5a9z 5aa0 5br8 5czp 5d8b 5dfe 5dox 5doy 5e7k 5e81 5el4 5el5 5el6 5el7 5f8k 5fdu 5fdv 5hau 5hcp 5hcq 5hcr 5hd1 5ib7 5ib8 5ibb 5imq 5imr 5iwa 5j30 5j3c 5j4b 5j4c 5j8b 5lmn 5lmo 5lmp 5lmq 5lmr 5lms 5lmt 5lmu 5lmv

(-) Related Entries Specified in the PDB File

486d X-RAY CRYSTAL STRUCTURES OF 70S RIBOSOME FUNCTIONAL COMPLEXES