PDBsum entry 1vx5

Ribosome

PDB id: 1vx5

Contents

Protein chains

208 a.a.

213 a.a.

218 a.a.

227 a.a.

262 a.a.

191 a.a.

237 a.a.

189 a.a.

206 a.a.

185 a.a.

98 a.a.

157 a.a.

124 a.a.

150 a.a.

136 a.a.

96 a.a.

141 a.a.

129 a.a.

137 a.a.

141 a.a.

104 a.a.

82 a.a.

129 a.a.

141 a.a.

126 a.a.

75 a.a.

98 a.a.

83 a.a.

64 a.a.

52 a.a.

57 a.a.

71 a.a.

313 a.a.

DNA/RNA

Obsolete entry

PDB id:

1vx5

Name:

Ribosome

Title:

Structure of the 80s mammalian ribosome bound to eef2. This entry contains the small ribosomal subunit.

Structure:

18s ribosomal RNA. Chain: 2. Ribosomal protein us2. Chain: a. Ribosomal protein es1. Chain: b. Ribosomal protein us5. Chain: c. Ribosomal protein us3.

Source:

Sus scrofa. Pig. Organism_taxid: 9823. Organ: pancreas. Organ: pancreas

Authors:

R.M.Voorhees,I.S.Fernandez,S.H.W.Scheres,R.S.Hegde

Key ref:

R.M.Voorhees et al. (2014). Structure of the mammalian ribosome-Sec61 complex to 3.4 Å resolution. Cell, 157, 1632-1643. PubMed id: 24930395 DOI: 10.1016/j.cell.2014.05.024

Date:

19-May-14 Release date: 18-Jun-14

Protein chain

Q4GWZ2  (RSSA_PIG) -  40S ribosomal protein SA from Sus scrofa

Seq: 295 a.a.

Struc: 208 a.a.

Protein chain

B6V8C8  (B6V8C8_PIG) -  40S ribosomal protein S3a from Sus scrofa

Seq: 264 a.a.

Struc: 213 a.a.

Protein chain

No UniProt id for this chain

Struc: 218 a.a.

Protein chain

Q0Z8U2  (RS3_PIG) -  40S ribosomal protein S3 from Sus scrofa

Seq: 243 a.a.

Struc: 227 a.a.

Protein chain

F1RQ91  (F1RQ91_PIG) -  40S ribosomal protein S4 from Sus scrofa

Seq: 242 a.a.

Struc: 262 a.a.*

Protein chain

F2Z5E6  (F2Z5E6_PIG) -  40S ribosomal protein S5 from Sus scrofa

Seq: 204 a.a.

Struc: 191 a.a.

Protein chain

No UniProt id for this chain

Struc: 237 a.a.

Protein chain

I3L5B2  (I3L5B2_PIG) -  40S ribosomal protein S7 from Sus scrofa

Seq: 184 a.a.

Struc: 189 a.a.*

Protein chain

F2Z5F5  (F2Z5F5_PIG) -  40S ribosomal protein S8 from Sus scrofa

Seq: 208 a.a.

Struc: 206 a.a.

Protein chain

No UniProt id for this chain

Struc: 185 a.a.

Protein chain

F1RZ28  (F1RZ28_PIG) -  S10_plectin domain-containing protein from Sus scrofa

Seq: 244 a.a.

Struc: 98 a.a.*

Protein chain

F2Z4Y8  (F2Z4Y8_PIG) -  40S ribosomal protein S11 from Sus scrofa

Seq: 158 a.a.

Struc: 157 a.a.

Protein chain

No UniProt id for this chain

Struc: 124 a.a.

Protein chain

No UniProt id for this chain

Struc: 150 a.a.

Protein chain

No UniProt id for this chain

Struc: 136 a.a.

Protein chain

P62844  (RS15_PIG) -  40S ribosomal protein S15 from Sus scrofa

Seq: 145 a.a.

Struc: 96 a.a.

Protein chain

Q29201  (RS16_PIG) -  40S ribosomal protein S16 from Sus scrofa

Seq: 146 a.a.

Struc: 141 a.a.

Protein chain

Q6QAP7  (RS17_PIG) -  40S ribosomal protein S17 from Sus scrofa

Seq: 135 a.a.

Struc: 129 a.a.

Protein chain

P62272  (RS18_PIG) -  40S ribosomal protein S18 from Sus scrofa

Seq: 152 a.a.

Struc: 137 a.a.

Protein chain

F1RGG1  (F1RGG1_PIG) -  40S ribosomal protein S19 from Sus scrofa

Seq: 155 a.a.

Struc: 141 a.a.

Protein chain

A1XQU9  (RS20_PIG) -  40S ribosomal protein S20 from Sus scrofa

Seq: 119 a.a.

Struc: 104 a.a.

Protein chain

P63221  (RS21_PIG) -  40S ribosomal protein S21 from Sus scrofa

Seq: 83 a.a.

Struc: 82 a.a.

Protein chain

No UniProt id for this chain

Struc: 129 a.a.

Protein chain

Q6SA96  (RS23_PIG) -  40S ribosomal protein S23 from Sus scrofa

Seq: 143 a.a.

Struc: 141 a.a.

Protein chain

No UniProt id for this chain

Struc: 126 a.a.

Protein chain

No UniProt id for this chain

Struc: 75 a.a.

Protein chain

P49171  (RS26_PIG) -  40S ribosomal protein S26 from Sus scrofa

Seq: 115 a.a.

Struc: 98 a.a.

Protein chain

No UniProt id for this chain

Struc: 83 a.a.

Protein chain

Q6QAT1  (RS28_PIG) -  40S ribosomal protein S28 from Sus scrofa

Seq: 69 a.a.

Struc: 64 a.a.

Protein chain

Q6QAP6  (RS29_PIG) -  40S ribosomal protein S29 from Sus scrofa

Seq: 56 a.a.

Struc: 52 a.a.

Protein chain

No UniProt id for this chain

Struc: 57 a.a.

Protein chain

F2Z5U0  (F2Z5U0_PIG) -  40S ribosomal protein S27a from Sus scrofa

Seq: 130 a.a.

Struc: 71 a.a.*

Protein chain

P63246  (RACK1_PIG) -  Receptor of activated protein C kinase 1 from Sus scrofa

Seq: 317 a.a.

Struc: 313 a.a.

* PDB and UniProt seqs differ at 58 residue positions (black crosses)

DNA/RNA chain

U-A-C-C-U-G-G-U-U-G-A-U-C-C-U-G-C-C-A-G-U-A-G-C-A-U-A-U-G-C-U-U-G-U-C-U-C-A-A- ... 1742 bases

DOI no: 10.1016/j.cell.2014.05.024

Cell 157:1632-1643 (2014)

PubMed id: 24930395

Structure of the mammalian ribosome-Sec61 complex to 3.4 Å resolution.

R.M.Voorhees, I.S.Fernández, S.H.Scheres, R.S.Hegde.

ABSTRACT

Cotranslational protein translocation is a universally conserved process for secretory and membrane protein biosynthesis. Nascent polypeptides emerging from a translating ribosome are either transported across or inserted into the membrane via the ribosome-bound Sec61 channel. Here, we report structures of a mammalian ribosome-Sec61 complex in both idle and translating states, determined to 3.4 and 3.9 Å resolution. The data sets permit building of a near-complete atomic model of the mammalian ribosome, visualization of A/P and P/E hybrid-state tRNAs, and analysis of a nascent polypeptide in the exit tunnel. Unprecedented chemical detail is observed for both the ribosome-Sec61 interaction and the conformational state of Sec61 upon ribosome binding. Comparison of the maps from idle and translating complexes suggests how conformational changes to the Sec61 channel could facilitate translocation of a secreted polypeptide. The high-resolution structure of the mammalian ribosome-Sec61 complex provides a valuable reference for future functional and structural studies.