PDBsum entry: 1q81

Ribosome

PDB id: 1q81

Contents

Protein chains

237 a.a. *

337 a.a. *

246 a.a. *

140 a.a. *

172 a.a. *

119 a.a. *

29 a.a. *

156 a.a. *

142 a.a. *

132 a.a. *

145 a.a. *

194 a.a. *

186 a.a. *

115 a.a. *

143 a.a. *

95 a.a. *

150 a.a. *

81 a.a. *

119 a.a. *

53 a.a. *

65 a.a. *

154 a.a. *

82 a.a. *

142 a.a. *

73 a.a. *

56 a.a. *

46 a.a. *

92 a.a. *

DNA/RNA

Ligands

__C-__C

PPU

Metals

_CL ×22

_NA ×86

_MG ×117

_CD ×5

__K ×2

Waters ×7869

* Residue conservation analysis

PDB id:

1q81

Name:

Ribosome

Title:

Crystal structure of minihelix with 3' puromycin bound to a- site of the 50s ribosomal subunit.

Structure:

23s ribosomal RNA. Chain: a. 5s ribosomal RNA. Chain: b. Minihelix-puromycin. Chain: 5. Engineered: yes. Other_details: a-substrate analogue contains puromycin-5'- monophosphate.

Source:

Haloarcula marismortui. Organism_taxid: 2238. Synthetic: yes. Other_details: minihelix-puromycin synthesized by dharmacon pharmaceuticals. Organism_taxid: 2238

Biol. unit:

31mer (from PQS)

Resolution:

2.95Å R-factor: 0.210 R-free: 0.259

Authors:

J.L.Hansen,T.M.Schmeing,P.B.Moore,T.A.Steitz

Key ref:

J.L.Hansen et al. (2002). Structural insights into peptide bond formation. Proc Natl Acad Sci U S A, 99, 11670-11675. PubMed id: 12185246 DOI: 10.1073/pnas.172404099

Date:

20-Aug-03 Release date: 07-Oct-03

Protein chain

P20276  (RL2_HALMA) -  50S ribosomal protein L2P

Seq: 240 a.a.

Struc: 237 a.a.*

Protein chain

P20279  (RL3_HALMA) -  50S ribosomal protein L3P

Seq: 338 a.a.

Struc: 337 a.a.

Protein chain

P12735  (RL4_HALMA) -  50S ribosomal protein L4P

Seq: 246 a.a.

Struc: 246 a.a.*

Protein chain

P14124  (RL5_HALMA) -  50S ribosomal protein L5P

Seq: 177 a.a.

Struc: 140 a.a.

Protein chain

P14135  (RL6_HALMA) -  50S ribosomal protein L6P

Seq: 178 a.a.

Struc: 172 a.a.

Protein chain

P12743  (RL7A_HALMA) -  50S ribosomal protein L7Ae

Seq: 120 a.a.

Struc: 119 a.a.*

Protein chain

P15825  (RLA0_HALMA) -  50S ribosomal protein L10E

Seq: 348 a.a.

Struc: 29 a.a.*

Protein chain

P60617  (RL10_HALMA) -  50S ribosomal protein L10e

Seq: 177 a.a.

Struc: 156 a.a.*

Protein chain

P29198  (RL13_HALMA) -  50S ribosomal protein L13P

Seq: 145 a.a.

Struc: 142 a.a.

Protein chain

P22450  (RL14_HALMA) -  50S ribosomal protein L14P

Seq: 132 a.a.

Struc: 132 a.a.

Protein chain

P12737  (RL15_HALMA) -  50S ribosomal protein L15P

Seq: 165 a.a.

Struc: 145 a.a.

Protein chain

P60618  (RL15E_HALMA) -  50S ribosomal protein L15e

Seq: 196 a.a.

Struc: 194 a.a.*

Protein chain

P14123  (RL18_HALMA) -  50S ribosomal protein L18P

Seq: 187 a.a.

Struc: 186 a.a.

Protein chain

P12733  (RL18E_HALMA) -  50S ribosomal protein L18e

Seq: 116 a.a.

Struc: 115 a.a.

Protein chain

P14119  (RL19_HALMA) -  50S ribosomal protein L19e

Seq: 149 a.a.

Struc: 143 a.a.*

Protein chain

P12734  (RL21_HALMA) -  50S ribosomal protein L21e

Seq: 96 a.a.

Struc: 95 a.a.

Protein chain

P10970  (RL22_HALMA) -  50S ribosomal protein L22P

Seq: 155 a.a.

Struc: 150 a.a.

Protein chain

P12732  (RL23_HALMA) -  50S ribosomal protein L23P

Seq: 85 a.a.

Struc: 81 a.a.

Protein chain

P10972  (RL24_HALMA) -  50S ribosomal protein L24P

Seq: 120 a.a.

Struc: 119 a.a.

Protein chain

P14116  (RL24E_HALMA) -  50S ribosomal protein L24e

Seq: 67 a.a.

Struc: 53 a.a.

Protein chain

P10971  (RL29_HALMA) -  50S ribosomal protein L29P

Seq: 71 a.a.

Struc: 65 a.a.

Protein chain

P14121  (RL30_HALMA) -  50S ribosomal protein L30P

Seq: 154 a.a.

Struc: 154 a.a.

Protein chain

P18138  (RL31_HALMA) -  50S ribosomal protein L31e

Seq: 92 a.a.

Struc: 82 a.a.

Protein chain

P12736  (RL32_HALMA) -  50S ribosomal protein L32e

Seq: 241 a.a.

Struc: 142 a.a.

Protein chain

P60619  (RL37A_HALMA) -  50S ribosomal protein L37Ae

Seq: 92 a.a.

Struc: 73 a.a.*

Protein chain

P32410  (RL37_HALMA) -  50S ribosomal protein L37e

Seq: 57 a.a.

Struc: 56 a.a.

Protein chain

P22452  (RL39_HALMA) -  50S ribosomal protein L39e

Seq: 50 a.a.

Struc: 46 a.a.*

Protein chain

P32411  (RL44_HALMA) -  50S ribosomal protein L44E

Seq: 92 a.a.

Struc: 92 a.a.

* PDB and UniProt seqs differ at 185 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (4 terms)
• Biological process: ribosome biogenesis (3 terms)
• Biochemical function: structural constituent of ribosome (7 terms)

DOI no: 10.1073/pnas.172404099

Proc Natl Acad Sci U S A 99:11670-11675 (2002)

PubMed id: 12185246

Structural insights into peptide bond formation.

J.L.Hansen, T.M.Schmeing, P.B.Moore, T.A.Steitz.

ABSTRACT

The large ribosomal subunit catalyzes peptide bond formation and will do so by using small aminoacyl- and peptidyl-RNA fragments of tRNA. We have refined at 3-A resolution the structures of both A and P site substrate and product analogues, as well as an intermediate analogue, bound to the Haloarcula marismortui 50S ribosomal subunit. A P site substrate, CCA-Phe-caproic acid-biotin, binds equally to both sites, but in the presence of sparsomycin binds only to the P site. The CCA portions of these analogues are bound identically by either the A or P loop of the 23S rRNA. Combining the separate P and A site substrate complexes into one model reveals interactions that may occur when both are present simultaneously. The alpha-NH(2) group of an aminoacylated fragment in the A site forms one hydrogen bond with the N3 of A2486 (2451) and may form a second hydrogen bond either with the 2' OH of the A-76 ribose in the P site or with the 2' OH of A2486 (2451). These interactions position the alpha amino group adjacent to the carbonyl carbon of esterified P site substrate in an orientation suitable for a nucleophilic attack.

Selected figure(s)

Figure 1.
Fig. 1. Chemical structures of peptidyl transferase substrate analogues. (A) CCA-pcb is active as a P site substrate and binds to only the P site in the presence of the antibiotic, sparsomycin. (B) An aminoacylated RNA minihelix binds to the A site. (C) CCdA-phosphate-puromycin is an intermediate analogue containing A and P site-binding components. (D) CC-puromycin-phenylalanine-caproic acid-biotin and deacylated CCA are products of the peptidyl transferase reaction.

Figure 2.
Fig. 2. Experimental electron density maps. (A) An F[o] F[o] electron density map (blue net) contoured at 4.0 shows density corresponding to CCA-pcb (green) in the P site and sparsomycin (yellow). Additional density corresponds to altered conformations of nucleotides such as A2637 (orange). (B) F[o] F[o] electron density map of CCA-pcb shows that in the absence of sparsomycin, the P site substrate is bound equally between the P site (green) and the A site (red).

Figures were selected by the author.