Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  THE STRUCTURE OF A RIBOSOMAL PROTEIN S8/SPC OPERON MRNA COMPLEX
 
Authors :  H. J. Merianos, J. Wang, P. B. Moore
Date :  29 Dec 03  (Deposition) - 25 May 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,G,H
Biol. Unit 1:  A,H  (1x)
Biol. Unit 2:  B,G  (1x)
Keywords :  Protein-Rna Complex, Ribosomal, Spc Operon, Transcription-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Merianos, J. Wang, P. B. Moore
The Structure Of A Ribosomal Protein S8/Spc Operon Mrna Complex.
Rna V. 10 954 2004
PubMed-ID: 15146079  |  Reference-DOI: 10.1261/RNA.7030704

(-) Compounds

Molecule 1 - 47-MER
    Chains: A, B
    Engineered: YES
    Other Details: RNA WAS PREPARED BY IN VITRO TRANSCIPTION, SEQUENCE FROM E. COLI SPC OPERON
    Synthetic: YES
 
Molecule 2 - 30S RIBOSOMAL PROTEIN S8
    Chains: H, G
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABGH
Biological Unit 1 (1x): A  H
Biological Unit 2 (1x):  BG 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 17)

Asymmetric Unit (1, 17)
No.NameCountTypeFull Name
1ZN17Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREG B:1BINDING SITE FOR RESIDUE ZN B 50
2AC2SOFTWAREG A:8BINDING SITE FOR RESIDUE ZN A 52
3AC3SOFTWAREG A:2BINDING SITE FOR RESIDUE ZN A 53
4AC4SOFTWAREGLU G:41BINDING SITE FOR RESIDUE ZN G 131
5AC5SOFTWAREG A:1BINDING SITE FOR RESIDUE ZN A 54
6AC6SOFTWAREG A:1BINDING SITE FOR RESIDUE ZN A 55
7AC7SOFTWAREG B:2BINDING SITE FOR RESIDUE ZN B 53

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S03)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S03)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S03)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_S8PS00053 Ribosomal protein S8 signature.RS8_ECOLI100-117
 		  2G:99-116
H:99-116
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_S8PS00053 Ribosomal protein S8 signature.RS8_ECOLI100-117
 		  1-
H:99-116
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_S8PS00053 Ribosomal protein S8 signature.RS8_ECOLI100-117
 		  1G:99-116
-

(-) Exons   (0, 0)

(no "Exon" information available for 1S03)

(-) 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:RNA  Length:47
                                                                               
                 1s03 A   1 GGACGAUGGCGAAACUGCAUGAGGCAAUUCAUGCAAGUCCCUCGUCC  47
                                    10        20        30        40       


Chain B from PDB  Type:RNA  Length:47
                                                                               
                 1s03 B   1 GGACGAUGGCGAAACUGCAUGAGGCAAUUCAUGCAAGUCCCUCGUCC  47
                                    10        20        30        40       


Chain G from PDB  Type:PROTEIN  Length:126
 aligned with RS8_ECOLI | P0A7W7 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:126
                                    14        24        34        44        54        64        74        84        94       104       114       124      
            RS8_ECOLI     5 DPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELELTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAGLGGEIICYVA 130
               SCOP domains d1s03g_ G: Ribosomal protein S8                                                                                                SCOP domains
               CATH domains 1s03G01 G:4-71  [code=3.30.1370.30, no name defined]                1s03G02 G:72-129  [code=3.30.1490.10, no name defined]     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhh..eeeeee......eeeeee...........eee........eehhhhh........eeeeee..eeeehhhhhhhh..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------RIBOSOMAL_S8      ------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1s03 G   4 DPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELELTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAGLGGEIICYVA 129
                                    13        23        33        43        53        63        73        83        93       103       113       123      


Chain H from PDB  Type:PROTEIN  Length:127
 aligned with RS8_ECOLI | P0A7W7 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:127
                                    13        23        33        43        53        63        73        83        93       103       113       123       
            RS8_ECOLI     4 QDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELELTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAGLGGEIICYVA 130
               SCOP domains d1s03h_ H: Ribosomal protein S8                                                                                                 SCOP domains
               CATH domains 1s03H01 H:3-71  [code=3.30.1370.30, no name defined]                 1s03H02 H:72-129  [code=3.30.1490.10, no name defined]     CATH domains
           Pfam domains (1) -Ribosomal_S8-1s03H01 H:4-128                                                                                                 - Pfam domains (1)
           Pfam domains (2) -Ribosomal_S8-1s03H02 H:4-128                                                                                                 - Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhh..eeeeeee.....eeeeee...........eee........eehhhhh........eeeeee..eeeehhhhhhhh..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------RIBOSOMAL_S8      ------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s03 H   3 QDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELELTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAGLGGEIICYVA 129
                                    12        22        32        42        52        62        72        82        92       102       112       122
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Ribosomal_S8] (19)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain G,H   (RS8_ECOLI | P0A7W7)
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:0043488    regulation of mRNA stability    Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0022627    cytosolic small ribosomal subunit    The small subunit of a ribosome located in the cytosol.
    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.

 Visualization

(-) Interactive Views

Asymmetric 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
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1s03)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  1s03
    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_ECOLI | P0A7W7
    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_ECOLI | P0A7W7
    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_ECOLI | P0A7W7: 1eg0 1m5g 2ykr 3iy8 3j9y 3j9z 3ja1 3jbu 3jbv 3jcd 3jce 3jcj 3jcn 4a2i 4adv 4u1u 4u1v 4u20 4u24 4u25 4u26 4u27 4v47 4v48 4v4h 4v4q 4v4v 4v4w 4v50 4v52 4v53 4v54 4v55 4v56 4v57 4v5b 4v5h 4v5y 4v64 4v65 4v66 4v69 4v6c 4v6d 4v6e 4v6k 4v6l 4v6m 4v6n 4v6o 4v6p 4v6q 4v6r 4v6s 4v6t 4v6v 4v6y 4v6z 4v70 4v71 4v72 4v73 4v74 4v75 4v76 4v77 4v78 4v79 4v7a 4v7b 4v7c 4v7d 4v7i 4v7s 4v7t 4v7u 4v7v 4v85 4v89 4v9c 4v9d 4v9o 4v9p 4wf1 4woi 4www 4ybb 5afi 5h5u 5iqr 5it8 5j5b 5j7l 5j88 5j8a 5j91 5jc9 5jte 5ju8 5kcr 5kcs 5kps 5kpv 5kpw 5kpx 5l3p 5lza 5lzb 5lzc 5lzd 5lze 5lzf 5mdv 5mdw 5mdy 5mdz 5me0 5me1 5mgp 5my1 5no2 5no3 5no4 5u4i

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1S03)