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- PDB-1fka: STRUCTURE OF FUNCTIONALLY ACTIVATED SMALL RIBOSOMAL SUBUNIT AT 3.... -

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Basic information

Entry
Database: PDB / ID: 1fka
TitleSTRUCTURE OF FUNCTIONALLY ACTIVATED SMALL RIBOSOMAL SUBUNIT AT 3.3 A RESOLUTION
Components
  • (30S RIBOSOMAL PROTEIN ...) x 19
  • 16S RIBOSOMAL RNA
KeywordsRIBOSOME / 30S RIBOSOMAL SUBUNIT / PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal Protein S8; Chain: A, domain 1 - #30 / RNA-binding S4 domain / Ribosomal Protein S7 / Ribosomal protein S7/S5 ...Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal Protein S8; Chain: A, domain 1 - #30 / RNA-binding S4 domain / Ribosomal Protein S7 / Ribosomal protein S7/S5 / Ribosomal protein S6/Translation elongation factor EF1B / Dna Ligase; domain 1 - #10 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S15/NS1, RNA-binding / Double Stranded RNA Binding Domain - #20 / Ribosomal Protein S8; Chain: A, domain 1 / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Double Stranded RNA Binding Domain / Dna Ligase; domain 1 / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S4, bacterial-type / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / : / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Few Secondary Structures / Irregular / Ribosomal protein S7, conserved site / Ribosomal protein S19 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9 / Ribosomal protein S19 signature. / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S7 signature. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal protein S8 / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / S4 RNA-binding domain / Ribosomal protein S5, C-terminal domain / RNA-binding S4 domain / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S8 signature. / S4 domain / Ribosomal protein S4 signature. / Ribosomal_S15 / Ribosomal protein S15 signature. / Ribosomal protein S15 / Ribosomal protein S7p/S5e / S4 RNA-binding domain profile. / Ribosomal protein S15 / S15/NS1, RNA-binding / Helix Hairpins / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
OCTADECATUNGSTENYL DIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein bS6 ...OCTADECATUNGSTENYL DIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsSchluenzen, F. / Tocilj, A. / Zarivach, R. / Harms, J. / Gluehmann, M. / Janell, D. / Bashan, A. / Bartels, H. / Agmon, I. / Franceschi, F. / Yonath, A.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2000
Title: Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution.
Authors: Schluenzen, F. / Tocilj, A. / Zarivach, R. / Harms, J. / Gluehmann, M. / Janell, D. / Bashan, A. / Bartels, H. / Agmon, I. / Franceschi, F. / Yonath, A.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Refining the overall structure and subdomain orientation of ribosomal protein S4 delta 41 with dipolar couplings measured by nmr in uniaxial liquid crystalline phases
Authors: MARKUS, M.A. / GERSTNER, R.B. / DRAPER, D.E. / Torchia, D.A.
#2: Journal: Nature / Year: 1992
Title: The structure of ribosomal protein s5 reveals sites of interaction with 16S rRNA
Authors: RAMAKRISHNAN, V. / WHITE, S.W.
#3: Journal: Embo J. / Year: 1994
Title: Crystal structure of the ribosomal protein S6 from Thermus thermophilus
Authors: LINDAHL, M. / SVENSSON, L.A. / LILJAS, A. / SEDELNIKOVA, S.E. / ELISEIKINA, I.A. / FOMENKOVA, N.P. / NEVSKAYA, N. / NIKONOV, S.V. / GARBER, M.B. / MURANOVA, T.A. / RYKONOVA, A.I.
#4: Journal: Structure / Year: 1997
Title: The structure of ribosomal protein S7 at 1.9 A resolution reveals a beta-hairpin motif that binds double-stranded nucleic acids
Authors: WIMBERLY, B.T. / WHITE, S.W. / RAMAKRISHNAN, V.
#5: Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of ribosomal protein S8 from Thermus thermophilus reveals a high degree of structural conservation of a specific RNA binding site
Authors: NEVSKAYA, N. / TISHCHENKO, S. / NIKULIN, A. / AL-KARADAGHI, S. / LILJAS, A. / EHRESMANN, B. / EHRESMANN, C. / GARBER, M.B. / NIKONOV, S.
#6: Journal: Structure / Year: 1998
Title: Conformational variability of the N-terminal helix in the structure of ribosomal protein S15
Authors: CLEMONS, W.M. / DAVIES, C. / WHITE, S.W. / RAMAKRISHNAN, V.
#7: Journal: Science / Year: 2000
Title: Structure of the S15, S6, S18-rRNA complex: assembly of the 30S ribosome central domain
Authors: AGALAROV, S.C. / PRASAD, G.S. / FUNKE, P.M. / STOUT, C.D. / WILLIAMSON, J.R.
#8: Journal: J.Mol.Biol. / Year: 1999
Title: Solution structure of the ribosomal protein S19 from Thermus thermophilus
Authors: HELGSTRAND, M. / RAK, A.V. / ALLARD, P. / DAVYDOVA, N. / GARBER, M.B. / HARD, T.
History
DepositionAug 9, 2000Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 4, 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 ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16S RIBOSOMAL RNA
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)725,01227
Polymers694,47020
Non-polymers30,5417
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)406.300, 406.300, 173.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

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Components

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30S RIBOSOMAL PROTEIN ... , 19 types, 19 molecules BCDEFGHIJKLMNOPQRST

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


Mass: 9464.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#3: Protein 30S RIBOSOMAL PROTEIN S3 / / Coordinate model: Cα atoms only


Mass: 14996.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#4: Protein 30S RIBOSOMAL PROTEIN S4 /


Mass: 24373.447 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 /


Mass: 17583.416 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 /


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 /


Mass: 17335.170 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 /


Mass: 15868.570 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: 7592.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#10: Protein 30S RIBOSOMAL PROTEIN S10 / / Coordinate model: Cα atoms only


Mass: 6060.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#11: Protein 30S RIBOSOMAL PROTEIN S11 / / Coordinate model: Cα atoms only


Mass: 5975.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#12: Protein 30S RIBOSOMAL PROTEIN S12 / / Coordinate model: Cα atoms only


Mass: 8783.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#13: Protein 30S RIBOSOMAL PROTEIN S13 / / Coordinate model: Cα atoms only


Mass: 6571.091 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#14: Protein/peptide 30S RIBOSOMAL PROTEIN S14 / / Coordinate model: Cα atoms only


Mass: 2230.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#15: Protein 30S RIBOSOMAL PROTEIN S15 /


Mass: 10622.417 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: 6230.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#17: Protein 30S RIBOSOMAL PROTEIN S17 /


Mass: 7166.825 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#18: Protein 30S RIBOSOMAL PROTEIN S18 /


Mass: 10244.272 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 /


Mass: 10605.464 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 /


Mass: 8102.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)

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RNA chain / Non-polymers , 2 types, 8 molecules A

#1: RNA chain 16S RIBOSOMAL RNA /


Mass: 492673.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 155076
#21: Chemical
ChemComp-WO2 / OCTADECATUNGSTENYL DIPHOSPHATE


Mass: 4363.030 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: O62P2W18

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.14 Å3/Da / Density % sol: 76.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: MPD, Spermidine, MgCl2, NH4Cl, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1NH4Cl11
2MgCl211
3spermidine11
4MPD11
5MPD12
Crystal grow
*PLUS
Details: Tsiboli, P., (1994) Eur. J. Biochem., 226, 169.
Components of the solutions
*PLUS
IDCrystal-ID
11
21
31
41
51

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.3→35 Å / Num. all: 206724 / Num. obs: 206724 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 21.9
Reflection shellResolution: 3.3→3.52 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.441 / % possible all: 77.1

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 3.3→35 Å / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 0 / Stereochemistry target values: none
RfactorNum. reflection% reflectionSelection details
Rfree0.305 15852 10 %random
Rwork0.304 ---
all-213490 --
obs-159051 74.5 %-
Refinement stepCycle: LAST / Resolution: 3.3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6068 28902 7 0 34977
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 3 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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