1QD7

PARTIAL MODEL FOR 30S RIBOSOMAL SUBUNIT

• PDB DOI:  https://doi.org/10.2210/pdb1QD7/pdb
• NAKB: 1QD7

• Classification: RIBOSOME
• Organism(s): Thermus thermophilus
• Mutation(s): No 


• Deposited: 1999-07-09 Released: 1999-08-31 
• Deposition Author(s): Clemons Jr., W.M., May, J.L.C., Wimberly, B.T., McCutcheon, J.P., Capel, M.S., Ramakrishnan, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 5.50 Å

Literature

Structure of a bacterial 30S ribosomal subunit at 5.5 A resolution.

Clemons Jr., W.M., May, J.L., Wimberly, B.T., McCutcheon, J.P., Capel, M.S., Ramakrishnan, V.

(1999) Nature 400: 833-840

• PubMed: 10476960 
• DOI: https://doi.org/10.1038/23631
• Primary Citation of Related Structures:  
  1QD7


• PubMed Abstract: 
  

The 30S ribosomal subunit binds messenger RNA and the anticodon stem-loop of transfer RNA during protein synthesis. A crystallographic analysis of the structure of the subunit from the bacterium Thermus thermophilus is presented. At a resolution of 5.5 A, the phosphate backbone of the ribosomal RNA is visible, as are the alpha-helices of the ribosomal proteins, enabling double-helical regions of RNA to be identified throughout the subunit, all seven of the small-subunit proteins of known crystal structure to be positioned in the electron density map, and the fold of the entire central domain of the small-subunit ribosomal RNA to be determined.

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Related Citations: 

• 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
  Davies, C., Gerstner, R.B., Draper, D.E., Ramakrishnan, V., White, S.W.
  (1998) EMBO J 17: 4545

• The structure of ribosomal protein S5 reveals sites of interaction with 16S rRNA
  Ramakrishnan, V., White, S.W.
  (1992) Nature 358: 768

• Crystal structure of the ribosomal protein S6 from Thermus thermophilus
  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.
  (1994) EMBO J 13: 1249

• The structure of ribosomal protein S7 at 1.9 A resolution reveals a beta- hairpin motif that binds double-stranded nucleic acids
  Wimberly, B.T., White, S.W., Ramakrishnan, V.
  (1997) Structure 5: 1187

• Crystal structure of ribosomal protein S8 from Thermus thermophilus reveals a high degree of structural conservation of a specific RNA binding site
  Nevskaya, N., Tischenko, S., Nikulin, A., Al-Karadaghi, S., Liljas, A., Ehresmann, B., Ehresmann, C., Garber, M., Nikonov, S.
  (1998) J Mol Biol 279: 233

• Conformational variability of the N-terminal helix in the structure of ribosomal protein S15
  Clemons Jr., W.M., Davies, C.R., White, S.W., Ramakrishnan, V.
  (1998) Structure 6: 429

• Solution structure of prokaryotic ribosomal protein S17 by high-resolution NMR spectroscopy
  Jaishree, T.N., Ramakrishnan, V., White, S.W.
  (1996) Biochemistry 35: 2845

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Organizational Affiliation: 

Department of Biochemistry, University of Utah School of Medicine, Salt Lake City 84103, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A1B1C1D1E1F1G1H1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 175.57 kDa 
• Atom Count: 1,305 
• Modelled Residue Count: 1,305 
• Deposited Residue Count: 1,305 
• Unique protein chains: 8
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
S4 RIBOSOMAL PROTEIN	C	159	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P81288 (Geobacillus stearothermophilus) Explore P81288  Go to UniProtKB:  P81288

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
S5 RIBOSOMAL PROTEIN	D	145	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P02357 (Geobacillus stearothermophilus) Explore P02357  Go to UniProtKB:  P02357

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
S6 RIBOSOMAL PROTEIN	E	97	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SLP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP8  Go to UniProtKB:  Q5SLP8

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
S7 RIBOSOMAL PROTEIN	F	135	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P17291  Go to UniProtKB:  P17291

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
S8 RIBOSOMAL PROTEIN	G	136	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P0DOY9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY9  Go to UniProtKB:  P0DOY9

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
S15 RIBOSOMAL PROTEIN	H	85	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P05766 (Geobacillus stearothermophilus) Explore P05766  Go to UniProtKB:  P05766

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
S17 RIBOSOMAL PROTEIN	I	89	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P23828 (Geobacillus stearothermophilus) Explore P23828  Go to UniProtKB:  P23828

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
S20 RIBOSOMAL PROTEIN	J	100	Thermus thermophilus	Mutation(s): 0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
CENTRAL FRAGMENT OF 16 S RNA	A	271	Thermus thermophilus

Entity ID: 2
Molecule	Chains	Length	Organism	Image
END FRAGMENT OF 16 S RNA	B	88	Thermus thermophilus

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 5.50 Å
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 401.6	α = 90
b = 401.6	β = 90
c = 174.5	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
O	model building
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-08-31 
Deposition Author(s): Clemons Jr., W.M., May, J.L.C., Wimberly, B.T., McCutcheon, J.P., Capel, M.S., Ramakrishnan, V.

Revision History  

• Version 1.0: 1999-08-31
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2023-08-16
  Changes: Data collection, Database references, Polymer sequence, Refinement description