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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 30S RIBOSOMAL PROTEIN S4E FROM THERMOPLASMA ACIDOPHILUM. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET TAR28.
 
Authors :  S. M. Vorobiev, M. Su, J. Seetharaman, R. L. Belote, C. Ciccosanti, D. Patel, J. Liu, B. Rost, T. B. Acton, R. Xiao, J. K. Everett, G. T. Montelione, L. Tong, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)
Date :  20 Oct 09  (Deposition) - 27 Oct 09  (Release) - 27 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  30S Ribosomal Protein S4E; Rps4E; Rs4E_theac; Tar28; Nesg, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Ribonucleoprotein, Ribosomal Protein, Rna-Binding, Rrna- Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Vorobiev, M. Su, J. Seetharaman, R. L. Belote, C. Ciccosanti, J. Liu, B. Rost, T. B. Acton, R. Xiao, J. K. Everett, G. T. Montelione, L. Tong, J. F. Hunt
Crystal Structure Of The 30S Ribosomal Protein S4E From Thermoplasma Acidophilum.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 30S RIBOSOMAL PROTEIN S4E
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET 21-23C
    Expression System Strain: BL21(DE3)+MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RPS4E, TA1259
    Mutation: YES
    Organism Scientific: THERMOPLASMA ACIDOPHILUM
    Organism Taxid: 2303

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3KBG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1S4PS50889 S4 RNA-binding domain profile.RS4E_THEAC38-99  1A:38-99
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1S4PS50889 S4 RNA-binding domain profile.RS4E_THEAC38-99  1A:38-99
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1S4PS50889 S4 RNA-binding domain profile.RS4E_THEAC38-99  2A:38-99

(-) Exons   (0, 0)

(no "Exon" information available for 3KBG)

(-) 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:192
 aligned with RS4E_THEAC | Q56230 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:194
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223    
           RS4E_THEAC    34 KDQSVTLLSIIRDYLKLSDKEREAARILANGLVKVDGKTVREKKFAVGFMDVIEINGESYRVVYNDQGALVLMKETKERASMKLLKVRSKVIAPGNRIQLGTHDGRTFITDDKSKKVGDVWAVSVPDMKISEIIKMQPGNKAYITAGSHVNQTGTISKIEAKEGSSANLVHFQEGFSTIKDHVFMIGSSKFSFV 227
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------S4-3kbgA01 A:47-86                      -Ribosomal_S4e-3kbgA02 A:88-164                                               --------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhhhhhhhhhhhhhhhhhhhhhhh..eee..ee......ee....eeee..eeeeeee.....eeeee...hhh.eeeeeeeeeeeehhheeeeee....eeee.........eeeee.....eeeee......eeee........eeeeeee......--.eeee...eeee...eeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----S4  PDB: A:38-99 UniProt: 38-99                               -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kbg A  34 KDQSVTLLSIIRDYLKLSDKEREAARILANGLVKVDGKTVREKKFAVGFmDVIEINGESYRVVYNDQGALVLmKETKERASmKLLKVRSKVIAPGNRIQLGTHDGRTFITDDKSIKVGDVLAVSVPDmKISEIIKmQPGNKAYITAGSHVNQTGTISKIEAKEGS--NLVHFQEGFSTIKDHVFmIGSSKFSFV 227
                                    43        53        63        73        83        93       103  |    113 |     123       133       143       153       163     | 173       183       193    |  203       213    |  223    
                                                                            83-MSE                106-MSE  115-MSE                                       161-MSE 169-MSE                      198  |              218-MSE     
                                                                                                                                                                                                 201
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  - → 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  (0, 0)

(no "SCOP Domain" information available for 3KBG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: S4 (23)
(-)
Clan: no clan defined [family: Ribosomal_S4e] (1)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (RS4E_THEAC | Q56230)
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: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.

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