PDBsum entry 5x8r

Ribosome

PDB id: 5x8r

Contents

Protein chains

227 a.a.

213 a.a.

171 a.a.

111 a.a.

149 a.a.

134 a.a.

133 a.a.

98 a.a.

118 a.a.

123 a.a.

110 a.a.

62 a.a.

80 a.a.

78 a.a.

64 a.a.

78 a.a.

105 a.a.

44 a.a.

108 a.a.

84 a.a.

199 a.a.

190 a.a.

99 a.a.

37 a.a.

154 a.a.

DNA/RNA

PDB id:

5x8r

Name:

Ribosome

Title:

Structure of the 30s small subunit of chloroplast ribosome from spinach

Structure:

30s ribosomal protein s2, chloroplastic. Chain: b. 30s ribosomal protein s3, chloroplastic. Chain: c. 30s ribosomal protein s5, chloroplastic. Chain: e. 30s ribosomal protein s6 alpha, chloroplastic. Chain: f. 30s ribosomal protein s7, chloroplastic.

Source:

Spinacia oleracea. Spinach. Organism_taxid: 3562. Organism_taxid: 3562

Authors:

T.Ahmed,J.Shi,S.Bhushan

Key ref:

T.Ahmed et al. (2017). Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation. Nucleic Acids Res, 45, 8581-8595. PubMed id: 28582576

Date:

03-Mar-17 Release date: 07-Jun-17

Protein chain

P08242  (RR2_SPIOL) -  Small ribosomal subunit protein uS2c from Spinacia oleracea

Seq: 236 a.a.

Struc: 227 a.a.

Protein chain

P09595  (RR3_SPIOL) -  Small ribosomal subunit protein uS3c from Spinacia oleracea

Seq: 218 a.a.

Struc: 213 a.a.

Protein chain

Q9ST69  (RR5_SPIOL) -  Small ribosomal subunit protein uS5c from Spinacia oleracea

Seq: 308 a.a.

Struc: 171 a.a.

Protein chain

P82403  (RR6_SPIOL) -  Small ribosomal subunit protein bS6c alpha from Spinacia oleracea

Seq: 211 a.a.

Struc: 111 a.a.

Protein chain

P82129  (RR7_SPIOL) -  Small ribosomal subunit protein uS7cz/uS7cy from Spinacia oleracea

Seq: 155 a.a.

Struc: 149 a.a.

Protein chain

P09597  (RR8_SPIOL) -  Small ribosomal subunit protein uS8c from Spinacia oleracea

Seq: 134 a.a.

Struc: 134 a.a.

Protein chain

P82278  (RR9_SPIOL) -  Small ribosomal subunit protein uS9c from Spinacia oleracea

Seq: 208 a.a.

Struc: 133 a.a.

Protein chain

P82162  (RR10_SPIOL) -  Small ribosomal subunit protein uS10c from Spinacia oleracea

Seq: 195 a.a.

Struc: 98 a.a.

Protein chain

P06506  (RR11_SPIOL) -  Small ribosomal subunit protein uS11c from Spinacia oleracea

Seq: 138 a.a.

Struc: 118 a.a.

Protein chain

P62128  (RR12_SPIOL) -  Small ribosomal subunit protein uS12cz/uS12cy from Spinacia oleracea

Seq: 123 a.a.

Struc: 123 a.a.

Protein chain

B8AQA7  (B8AQA7_ORYSI) -  30S ribosomal protein S13, chloroplastic from Oryza sativa subsp. indica

Seq: 171 a.a.

Struc: 110 a.a.

Protein chain

Q9M3I4  (RR15_SPIOL) -  Small ribosomal subunit protein uS15c from Spinacia oleracea

Seq: 90 a.a.

Struc: 62 a.a.

Protein chain

P28807  (RR16_SPIOL) -  Small ribosomal subunit protein bS16c from Spinacia oleracea

Seq: 88 a.a.

Struc: 80 a.a.

Protein chain

P82137  (RR17_SPIOL) -  Small ribosomal subunit protein uS17c from Spinacia oleracea

Seq: 165 a.a.

Struc: 78 a.a.

Protein chain

Q9M3K7  (RR18_SPIOL) -  Small ribosomal subunit protein bS18c from Spinacia oleracea

Seq: 101 a.a.

Struc: 64 a.a.

Protein chain

P06508  (RR19_SPIOL) -  Small ribosomal subunit protein uS19c from Spinacia oleracea

Seq: 92 a.a.

Struc: 78 a.a.

Protein chain

P82130  (RR20_SPIOL) -  Small ribosomal subunit protein bS20c from Spinacia oleracea

Seq: 183 a.a.

Struc: 105 a.a.

Protein chain

P82024  (RR21_SPIOL) -  Small ribosomal subunit protein bS21c from Spinacia oleracea

Seq: 180 a.a.

Struc: 44 a.a.

Protein chain

P19954  (PRSP1_SPIOL) -  Ribosome-binding factor PSRP1, chloroplastic from Spinacia oleracea

Seq: 302 a.a.

Struc: 108 a.a.

Protein chain

P82412  (RRP3_SPIOL) -  Small ribosomal subunit protein cS23 from Spinacia oleracea

Seq: 179 a.a.

Struc: 84 a.a.

Protein chain

P13788  (RR4_SPIOL) -  Small ribosomal subunit protein uS4c from Spinacia oleracea

Seq: 201 a.a.

Struc: 199 a.a.

Protein chain

P82277  (RRP2_SPIOL) -  Small ribosomal subunit protein cS22 from Spinacia oleracea

Seq: 260 a.a.

Struc: 190 a.a.

Protein chain

P06507  (RR14_SPIOL) -  Small ribosomal subunit protein uS14c from Spinacia oleracea

Seq: 100 a.a.

Struc: 99 a.a.

Protein chain

P47910  (RR31_SPIOL) -  Small ribosomal subunit protein bTHXc from Spinacia oleracea

Seq: 101 a.a.

Struc: 37 a.a.

Protein chain

P29344  (RR1_SPIOL) -  Small ribosomal subunit protein bS1c from Spinacia oleracea

Seq: 411 a.a.

Struc: 154 a.a.*

* PDB and UniProt seqs differ at 21 residue positions (black crosses)

DNA/RNA chain

U-C-A-U-G-G-A-G-A-G-U-U-C-G-A-U-C-C-U-G-G-C-U-C-A-G-G-A-U-G-A-A-C-G-C-U-G-G-C- ... 1480 bases

Enzyme reactions

• Enzyme class: Chains b, c, e, f, g, h, i, j, k, l, m, o, p, q, r, s, t, u, y, w, d, v, n, x, 8: E.C.?

Nucleic Acids Res 45:8581-8595 (2017)

PubMed id: 28582576

Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation.

T.Ahmed, J.Shi, S.Bhushan.

ABSTRACT

Chloroplastic translation is mediated by a bacterial-type 70S chloroplast ribosome. During the evolution, chloroplast ribosomes have acquired five plastid-specific ribosomal proteins or PSRPs (cS22, cS23, bTHXc, cL37 and cL38) which have been suggested to play important regulatory roles in translation. However, their exact locations on the chloroplast ribosome remain elusive due to lack of a high-resolution structure, hindering our progress to understand their possible roles. Here we present a cryo-EM structure of the 70S chloroplast ribosome from spinach resolved to 3.4 Å and focus our discussion mainly on the architecture of the 30S small subunit (SSU) which is resolved to 3.7 Å. cS22 localizes at the SSU foot where it seems to compensate for the deletions in 16S rRNA. The mRNA exit site is highly remodeled due to the presence of cS23 suggesting an alternative mode of translation initiation. bTHXc is positioned at the SSU head and appears to stabilize the intersubunit bridge B1b during thermal fluctuations. The translation factor plastid pY binds to the SSU on the intersubunit side and interacts with the conserved nucleotide bases involved in decoding. Most of the intersubunit bridges are conserved compared to the bacteria, except for a new bridge involving uL2c and bS6c.