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- PDB-1i95: CRYSTAL STRUCTURE OF THE 30S RIBOSOMAL SUBUNIT FROM THERMUS THERM... -

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Basic information

Entry
Database: PDB / ID: 1i95
TitleCRYSTAL STRUCTURE OF THE 30S RIBOSOMAL SUBUNIT FROM THERMUS THERMOPHILUS IN COMPLEX WITH EDEINE
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • 16S RRNA
KeywordsRIBOSOME / 30S ribosome / antibiotics / edeine
Function / homology
Function and homology information


ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic ...ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein S14, type Z / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type ...30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein S14, type Z / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / : / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / K homology domain superfamily, prokaryotic type / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S15 signature. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S4/S9 / K homology domain-like, alpha/beta / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S10p/S20e / Ribosomal protein S11 / Ribosomal protein S10 domain
Similarity search - Domain/homology
EDEINE B / OCTADECATUNGSTENYL DIPHOSPHATE / : / : / : / : / : / : / : / : ...EDEINE B / OCTADECATUNGSTENYL DIPHOSPHATE / : / : / : / : / : / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 4.5 Å
AuthorsPioletti, M. / Schluenzen, F. / Harms, J. / Zarivach, R. / Gluehmann, M. / Avila, H. / Bartels, H. / Jacobi, C. / Hartsch, T. / Yonath, A. / Franceschi, F.
Citation
Journal: EMBO J. / Year: 2001
Title: Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3.
Authors: Pioletti, M. / Schlunzen, F. / Harms, J. / Zarivach, R. / Gluhmann, M. / Avila, H. / Bashan, A. / Bartels, H. / Auerbach, T. / Jacobi, C. / Hartsch, T. / Yonath, A. / Franceschi, F.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2000
Title: Structure of Functionally Activated Small Ribosomal Subunit at 3.3 A Resolution
Authors: Schluenzen, F. / Tocilj, A. / Zarivach, R. / Harms, J. / Gluehmann, M. / Janell, D. / Bashan, A. / Bartels, H. / Agmon, I. / Franceschi, F. / Yonath, A.
History
DepositionMar 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2001Provider: 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16S RRNA
B: 30S RIBOSOMAL PROTEIN S2
C: 30S RIBOSOMAL PROTEIN S3
D: 30S RIBOSOMAL PROTEIN S4
E: 30S RIBOSOMAL PROTEIN S5
F: 30S RIBOSOMAL PROTEIN S6
G: 30S RIBOSOMAL PROTEIN S7
H: 30S RIBOSOMAL PROTEIN S8
I: 30S RIBOSOMAL PROTEIN S9
J: 30S RIBOSOMAL PROTEIN S10
K: 30S RIBOSOMAL PROTEIN S11
L: 30S RIBOSOMAL PROTEIN S12
M: 30S RIBOSOMAL PROTEIN S13
N: 30S RIBOSOMAL PROTEIN S14
O: 30S RIBOSOMAL PROTEIN S15
P: 30S RIBOSOMAL PROTEIN S16
Q: 30S RIBOSOMAL PROTEIN S17
R: 30S RIBOSOMAL PROTEIN S18
S: 30S RIBOSOMAL PROTEIN S19
T: 30S RIBOSOMAL PROTEIN S20
U: 30S RIBOSOMAL PROTEIN THX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)842,639113
Polymers778,82121
Non-polymers63,81892
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)407.100, 407.100, 174.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain 16S RRNA


Mass: 491510.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 155076

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30S RIBOSOMAL PROTEIN ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTU

#2: Protein 30S RIBOSOMAL PROTEIN S2 / Coordinate model: Cα atoms only


Mass: 29186.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 13446664, UniProt: P80371*PLUS
#3: Protein 30S RIBOSOMAL PROTEIN S3 / Coordinate model: Cα atoms only


Mass: 26619.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 13446666, UniProt: P80372*PLUS
#4: Protein 30S RIBOSOMAL PROTEIN S4 / Coordinate model: Cα atoms only


Mass: 24242.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80373
#5: Protein 30S RIBOSOMAL PROTEIN S5 / Coordinate model: Cα atoms only


Mass: 17452.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P27152, UniProt: Q5SHQ5*PLUS
#6: Protein 30S RIBOSOMAL PROTEIN S6 / Coordinate model: Cα atoms only


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P23370, UniProt: Q5SLP8*PLUS
#7: Protein 30S RIBOSOMAL PROTEIN S7 / Coordinate model: Cα atoms only


Mass: 17919.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P17291
#8: Protein 30S RIBOSOMAL PROTEIN S8 / Coordinate model: Cα atoms only


Mass: 15886.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P24319, UniProt: P0DOY9*PLUS
#9: Protein 30S RIBOSOMAL PROTEIN S9 / Coordinate model: Cα atoms only


Mass: 14429.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 13446668, UniProt: P80374*PLUS
#10: Protein 30S RIBOSOMAL PROTEIN S10 / Coordinate model: Cα atoms only


Mass: 11823.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80375, UniProt: Q5SHN7*PLUS
#11: Protein 30S RIBOSOMAL PROTEIN S11 / Coordinate model: Cα atoms only


Mass: 13606.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 4519421, UniProt: P80376*PLUS
#12: Protein 30S RIBOSOMAL PROTEIN S12 / Coordinate model: Cα atoms only


Mass: 14506.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P17293, UniProt: Q5SHN3*PLUS
#13: Protein 30S RIBOSOMAL PROTEIN S13 / Coordinate model: Cα atoms only


Mass: 14207.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 4519420, UniProt: P80377*PLUS
#14: Protein 30S RIBOSOMAL PROTEIN S14 / Coordinate model: Cα atoms only


Mass: 7027.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P24320, UniProt: P0DOY6*PLUS
#15: Protein 30S RIBOSOMAL PROTEIN S15 / Coordinate model: Cα atoms only


Mass: 10447.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80378, UniProt: Q5SJ76*PLUS
#16: Protein 30S RIBOSOMAL PROTEIN S16 / Coordinate model: Cα atoms only


Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 12056104, UniProt: Q5SJH3*PLUS
#17: Protein 30S RIBOSOMAL PROTEIN S17 / Coordinate model: Cα atoms only


Mass: 12144.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P24321, UniProt: P0DOY7*PLUS
#18: Protein 30S RIBOSOMAL PROTEIN S18 / Coordinate model: Cα atoms only


Mass: 10113.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 6739549, UniProt: Q5SLQ0*PLUS
#19: Protein 30S RIBOSOMAL PROTEIN S19 / Coordinate model: Cα atoms only


Mass: 10474.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80381, UniProt: Q5SHP2*PLUS
#20: Protein 30S RIBOSOMAL PROTEIN S20 / Coordinate model: Cα atoms only


Mass: 11604.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 11125386, UniProt: P80380*PLUS
#21: Protein/peptide 30S RIBOSOMAL PROTEIN THX / Coordinate model: Cα atoms only


Mass: 3218.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 11125387, UniProt: Q5SIH3*PLUS

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Non-polymers , 4 types, 92 molecules

#22: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 75 / Source method: obtained synthetically / Formula: Mg
#23: Chemical
ChemComp-WO2 / OCTADECATUNGSTENYL DIPHOSPHATE


Mass: 4363.030 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: O62P2W18
#24: Chemical ChemComp-EDE / EDEINE B


Mass: 781.900 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H59N11O10
#25: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.63 Å3/Da / Density % sol: 73.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: MPD, magnesium chloride, spermidine, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291.K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2MgCl211
3spermidine11
4MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / Details: or 19 degrees centigrade
Components of the solutions
*PLUS
IDCrystal-IDSol-ID
21
31
41
11reservoir

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033 Å
DetectorType: SBC / Detector: CCD / Date: Sep 1, 2000
RadiationMonochromator: double crystal monochromator, Si(111) double crystal monochromator, Si(222)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 4.5→35 Å / Num. all: 66468 / Num. obs: 66468 / % possible obs: 76.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.8
Reflection shellResolution: 4.5→4.58 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.5 / % possible all: 68.2

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 4.5→35 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflectionSelection details
Rfree0.244 6640 RANDOM
Rwork0.237 --
all0.238 66468 -
obs0.238 66468 -
Refinement stepCycle: LAST / Resolution: 4.5→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2410 32534 1280 0 36224

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