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

(-) Description

Title :  CRYSTAL STRUCTURE OF P. ABYSSI RPS24
 
Authors :  P. Legrand, N. Pinaud, P. E. Gleizes, S. Fribourg
Date :  21 Aug 07  (Deposition) - 29 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ribosomal Protein, Ribonucleoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Choesmel, S. Fribourg, A. H. Aguissa-Toure, N. Pinaud, P. Legrand, H. T. Gazda, P. E. Gleizes
Mutation Of Ribosomal Protein Rps24 In Diamond- Blackfan Anemia Results In A Ribosome Biogenesis Disorder.
Hum. Mol. Genet. V. 17 1253 2008
PubMed-ID: 18230666  |  Reference-DOI: 10.1093/HMG/DDN015

(-) Compounds

Molecule 1 - 30S RIBOSOMAL PROTEIN S24E
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Organism Scientific: PYROCOCCUS ABYSSI
    Organism Taxid: 29292
    Synonym: RPS24

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2V94)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V94)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V94)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V94)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_S24EPS00529 Ribosomal protein S24e signature.RS24_PYRAB60-82
 		  2A:60-82
B:60-82
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_S24EPS00529 Ribosomal protein S24e signature.RS24_PYRAB60-82
 		  1A:60-82
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_S24EPS00529 Ribosomal protein S24e signature.RS24_PYRAB60-82
 		  1-
B:60-82

(-) Exons   (0, 0)

(no "Exon" information available for 2V94)

(-) 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:97
 aligned with RS24_PYRAB | Q9UY20 from UniProtKB/Swiss-Prot  Length:99

    Alignment length:97
                                1                                                                                            
                                |    6        16        26        36        46        56        66        76        86       
            RS24_PYRAB    - ----MEIKITEVKENKLIGRKEIYFEIYHPGEPTPSRKDVKGKLVAMLDLNPETTVIQYIRSYFGSYKSKGYAKYYYDKDRMLYIEPEYILIRDGII 93
               SCOP domains ----d2v94a1 A:1-93 Ribosomal protein S24e                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee....eeeeeeeee.......hhhhhhhhhhhhhh.hhh.eeeeeee......eeeeeeeee.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------RIBOSOMAL_S24E         ----------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                  2v94 A -3 FmLEmEIKITEVKENKLIGRKEIYFEIYHPGEPTPSRKDVKGKLVAmLDLNPETTVIQYIRSYFGSYKSKGYAKYYYDKDRmLYIEPEYILIRDGII 93
                             |  |    6        16        26        36      | 46        56        66        76 |      86       
                             |  |                                        43-MSE                             78-MSE           
                            -2-MSE                                                                                           
                                1-MSE                                                                                        


Chain B from PDB  Type:PROTEIN  Length:94
 aligned with RS24_PYRAB | Q9UY20 from UniProtKB/Swiss-Prot  Length:99

    Alignment length:94
                                    10        20        30        40        50        60        70        80        90    
            RS24_PYRAB    1 MEIKITEVKENKLIGRKEIYFEIYHPGEPTPSRKDVKGKLVAMLDLNPETTVIQYIRSYFGSYKSKGYAKYYYDKDRMLYIEPEYILIRDGIIE 94
               SCOP domains d2v94b1 B:1-93 Ribosomal protein S24e                                                        - SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------Ribosomal_S24e-2v94B01 B:19-94                                               Pfam domains (1)
           Pfam domains (2) ------------------Ribosomal_S24e-2v94B02 B:19-94                                               Pfam domains (2)
         Sec.struct. author .eeeeeeeeee....eeeeeeeee.......hhhhhhhhhhhhhh.hhh.eeeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------RIBOSOMAL_S24E         ------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  2v94 B  1 mEIKITEVKENKLIGRKEIYFEIYHPGEPTPSRKDVKGKLVAmLDLNPETTVIQYIRSYFGSYKSKGYAKYYYDKDRmLYIEPEYILIRDGIIE 94
                            |       10        20        30        40  |     50        60        70       |80        90    
                            1-MSE                                    43-MSE                             78-MSE
   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  (0, 0)

(no "CATH Domain" information available for 2V94)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Ribosomal_S24e] (3)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RS24_PYRAB | Q9UY20)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2v94)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2v94)
 
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 | Biol. Unit 1 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
  2v94
    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
  RS24_PYRAB | Q9UY20
    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
  RS24_PYRAB | Q9UY20
    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
        RS24_PYRAB | Q9UY20: 5jb3

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2V94)