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- PDB-1qd7: PARTIAL MODEL FOR 30S RIBOSOMAL SUBUNIT -

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Basic information

Entry
Database: PDB / ID: 1qd7
TitlePARTIAL MODEL FOR 30S RIBOSOMAL SUBUNIT
Components
  • CENTRAL FRAGMENT OF 16 S RNA
  • END FRAGMENT OF 16 S RNA
  • S15 RIBOSOMAL PROTEIN
  • S17 RIBOSOMAL PROTEIN
  • S20 RIBOSOMAL PROTEIN
  • S4 RIBOSOMAL PROTEIN
  • S5 RIBOSOMAL PROTEIN
  • S6 RIBOSOMAL PROTEIN
  • S7 RIBOSOMAL PROTEIN
  • S8 RIBOSOMAL PROTEIN
KeywordsRIBOSOME / 30S RIBOSOMAL SUBUNIT / LOW RESOLUTION MODEL
Function / homology
Function and homology information


ribosomal small subunit biogenesis / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / cytoplasm
Similarity search - Function
Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 ...Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Translation elongation factor EF1B/ribosomal protein S6 / : / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S5 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / 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 S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / S15/NS1, RNA-binding / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 ...RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein bS6
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 5.5 Å
AuthorsClemons Jr., W.M. / May, J.L.C. / Wimberly, B.T. / McCutcheon, J.P. / Capel, M.S. / Ramakrishnan, V.
Citation
Journal: Nature / Year: 1999
Title: Structure of a bacterial 30S ribosomal subunit at 5.5 A resolution.
Authors: Clemons Jr., W.M. / May, J.L. / Wimberly, B.T. / McCutcheon, J.P. / Capel, M.S. / Ramakrishnan, V.
#1: Journal: Embo J. / Year: 1998
Title: The crystal structure of ribosomal protein S4 reveals a two-domain molecule with an extensive RNA-binding surface: one domain shows structural homology to the ETS DNA-binding motif
Authors: Davies, C. / Gerstner, R.B. / Draper, D.E. / Ramakrishnan, V. / White, S.W.
#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, I.A. / Eliseikina, I.A. / Fomenkova, N.P. / Nevskaya, N. / Nikonov, S.V. / Garber, M.B. / Muranova, T.A. / Rykonova, A.I. / Amons, R.
#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. / Tischenko, S. / Nikulin, A. / Al-Karadaghi, S. / Liljas, A. / Ehresmann, B. / Ehresmann, C. / Garber, M. / Nikonov, S.
#6: Journal: Structure / Year: 1998
Title: Conformational variability of the N-terminal helix in the structure of ribosomal protein S15
Authors: Clemons Jr., W.M. / Davies, C.R. / White, S.W. / Ramakrishnan, V.
#7: Journal: Biochemistry / Year: 1996
Title: Solution structure of prokaryotic ribosomal protein S17 by high-resolution NMR spectroscopy
Authors: Jaishree, T.N. / Ramakrishnan, V. / White, S.W.
History
DepositionJul 9, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _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: CENTRAL FRAGMENT OF 16 S RNA
B: END FRAGMENT OF 16 S RNA
C: S4 RIBOSOMAL PROTEIN
D: S5 RIBOSOMAL PROTEIN
E: S6 RIBOSOMAL PROTEIN
F: S7 RIBOSOMAL PROTEIN
G: S8 RIBOSOMAL PROTEIN
H: S15 RIBOSOMAL PROTEIN
I: S17 RIBOSOMAL PROTEIN
J: S20 RIBOSOMAL PROTEIN


Theoretical massNumber of molelcules
Total (without water)175,57110
Polymers175,57110
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)401.6, 401.6, 174.5
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

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Components

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RNA chain , 2 types, 2 molecules AB

#1: RNA chain CENTRAL FRAGMENT OF 16 S RNA / Coordinate model: P atoms only


Mass: 53096.625 Da / Num. of mol.: 1 / Fragment: RESIDUES 563-912 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#2: RNA chain END FRAGMENT OF 16 S RNA / Coordinate model: P atoms only


Mass: 17211.391 Da / Num. of mol.: 1 / Fragment: RESIDUES 1400-1500 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)

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Protein , 8 types, 8 molecules CDEFGHIJ

#3: Protein S4 RIBOSOMAL PROTEIN / Coordinate model: Cα atoms only


Mass: 18624.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P81288
#4: Protein S5 RIBOSOMAL PROTEIN / Coordinate model: Cα atoms only


Mass: 15240.724 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P02357
#5: Protein S6 RIBOSOMAL PROTEIN / Coordinate model: Cα atoms only


Mass: 11619.337 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P23370, UniProt: Q5SLP8*PLUS
#6: Protein S7 RIBOSOMAL PROTEIN / Coordinate model: Cα atoms only


Mass: 15342.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P17291
#7: Protein S8 RIBOSOMAL PROTEIN / 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: P24319, UniProt: P0DOY9*PLUS
#8: Protein S15 RIBOSOMAL PROTEIN / Coordinate model: Cα atoms only


Mass: 10200.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P05766
#9: Protein S17 RIBOSOMAL PROTEIN / Coordinate model: Cα atoms only


Mass: 10081.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P23828
#10: Protein S20 RIBOSOMAL PROTEIN / Coordinate model: Cα atoms only


Mass: 8528.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion / Details: VAPOUR DIFFUSION AT 277 K, MPD, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2MPD12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Trakhanov, S.D., (1987) FEBS Lett., 220, 319.
Components of the solutions
*PLUS
IDConc.Crystal-IDSol-ID
115 %1reservoir
21

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.000, 1.700
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Mar 4, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.71
ReflectionHighest resolution: 5.5 Å / Num. all: 42000 / Num. obs: 42000 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 5 %
Reflection shellHighest resolution: 5.5 Å / Mean I/σ(I) obs: 5.1 / % possible all: 83
Reflection
*PLUS

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Processing

Software
NameClassification
SOLVEphasing
Omodel building
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD
Starting model: PROTEINS WERE FIT INTO MAP AS RIGID BODIES FROM KNOWN CRYSTAL OR NMR STRUCTURES OF ISOLATED PROTEINS EXCEPT FOR S20, FOR WHICH NO HIGH RESOLUTION STRUCTURE EXISTS. S20 WAS FIT AS ...Starting model: PROTEINS WERE FIT INTO MAP AS RIGID BODIES FROM KNOWN CRYSTAL OR NMR STRUCTURES OF ISOLATED PROTEINS EXCEPT FOR S20, FOR WHICH NO HIGH RESOLUTION STRUCTURE EXISTS. S20 WAS FIT AS THREE-HELIX BUNDLE.S4 SEE REFERENCE (1); S5 MODELED ACCORDING TO PDB CODE 1PKP;S6 MODELED ACCORDING TO PDB CODE 1RIS;S7 MODELED ACCORDING TO PDB CODE 1RSS;S8 MODELED ACCORDING TO PDB CODE 1AN7;S15 MODELED ACCORDING TO PDB CODE 1A23;S17 SEE REFERENCE (7);

1pkp

1ris

1rss

1an7

1a23


Highest resolution: 5.5 Å / Num. reflection all: 42000 / Num. reflection obs: 42000
Details: NO REFINEMENT WAS DONE EXCEPT FOR VISUAL MAP FITTING. THIS MODEL WAS MADE FROM A 5.5 ANGSTROM X-RAY MAP BY FITTING A-FORM RNA HELICES INTO REGIONS OF DOUBLE- HELICAL DENSITY. NO ATTEMPT HAS ...Details: NO REFINEMENT WAS DONE EXCEPT FOR VISUAL MAP FITTING. THIS MODEL WAS MADE FROM A 5.5 ANGSTROM X-RAY MAP BY FITTING A-FORM RNA HELICES INTO REGIONS OF DOUBLE- HELICAL DENSITY. NO ATTEMPT HAS BEEN MADE TO MAINTAIN PROPER STEREOCHEMISTRY OR EVEN PHOSPHATE-PHOSPHATE DISTANCES. IN PARTICULAR AT JUNCTIONS OF THE SHORT HELICES, THE CHAIN MAY BE UNREALISTIC
Refinement stepCycle: LAST / Highest resolution: 5.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms946 359 0 0 1305
Refinement
*PLUS
Highest resolution: 5.5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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