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- PDB-1emi: STRUCTURE OF 16S RRNA IN THE REGION AROUND RIBOSOMAL PROTEIN S8. -

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Basic information

Entry
Database: PDB / ID: 1emi
TitleSTRUCTURE OF 16S RRNA IN THE REGION AROUND RIBOSOMAL PROTEIN S8.
Components
  • 16S RIBOSOMAL RNA
  • RIBOSOMAL PROTEIN S8
KeywordsRIBOSOME / RNA / rRNA / ribosomal protein / 16S rRNA / S8
Function / homology
Function and homology information


rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex
Similarity search - Function
: / Ribosomal protein S8 signature. / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein uS8 / 30S ribosomal protein S8
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 7.5 Å
AuthorsLancaster, L. / Culver, G.M. / Yusupova, G.Z. / Cate, J.H. / Yuspov, M.M. / Noller, H.F.
CitationJournal: RNA / Year: 2000
Title: 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.
Authors: Lancaster, L. / Culver, G.M. / Yusupova, G.Z. / Cate, J.H. / Yusupov, M.M. / Noller, H.F.
History
DepositionMar 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 16S RIBOSOMAL RNA
A: RIBOSOMAL PROTEIN S8


Theoretical massNumber of molelcules
Total (without water)67,5462
Polymers67,5462
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)508, 508, 803
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Cell settingtetragonal
Space group name H-MI422

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Components

#1: RNA chain 16S RIBOSOMAL RNA / Coordinate model: P atoms only


Mass: 51921.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: COORDINATES FOR THERMUS THERMOPHILUS 16S RRNA BUT SEQUENCE AND NUMBERING IS THAT OF E.COLI 16S RRNA
Source: (natural) Thermus thermophilus (bacteria)
#2: Protein RIBOSOMAL PROTEIN S8 / Coordinate model: Cα atoms only


Mass: 15624.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Type: ALS / Wavelength: 1.1051
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1051 Å / Relative weight: 1
ReflectionHighest resolution: 7.5 Å

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementHighest resolution: 7.5 Å
Details: All data collection parameters are as reported for 486D. The RNA model for the S8 region of 16S rRNA was built manually by fitting to the 7.8 A X-ray map of the Thermus thermophilus 70S ...Details: All data collection parameters are as reported for 486D. The RNA model for the S8 region of 16S rRNA was built manually by fitting to the 7.8 A X-ray map of the Thermus thermophilus 70S ribosome (Cate et al., Science 285, 2095-2104, 1999; see PDB 486D) using a single P pseudoatom for each nucleotide. Note that the nucleotide numbering corresponds to the nucleotide positions of E.coli 16S rRNA. Protein S8 from Thermus thermophilus (PDB 1AN7) was fitted to the 7.8 A map of the Thermus thermophilus 70S ribosome by splitting the protein into N- and C-terminal domains between residues 80 and 81. The two domains were fit separately, resulting in a small relative movement compared with the original X-ray structure. Only C-alpha positions are given in the PDB file.
Refinement stepCycle: LAST / Highest resolution: 7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms136 161 0 0 297

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