PDBsum entry 5a2q

Ribosome

PDB id: 5a2q

Contents

Protein chains

216 a.a.

213 a.a.

218 a.a.

225 a.a.

262 a.a.

189 a.a.

230 a.a.

186 a.a.

205 a.a.

180 a.a.

95 a.a.

151 a.a.

123 a.a.

149 a.a.

135 a.a.

120 a.a.

139 a.a.

132 a.a.

143 a.a.

145 a.a.

101 a.a.

82 a.a.

129 a.a.

141 a.a.

124 a.a.

72 a.a.

101 a.a.

82 a.a.

61 a.a.

55 a.a.

56 a.a.

72 a.a.

314 a.a.

24 a.a.

13 a.a.

62 a.a.

DNA/RNA

Metals

_MG ×98

_ZN ×3

Waters ×144

PDB id:

5a2q

Name:

Ribosome

Title:

Structure of the hcv ires bound to the human ribosome

Structure:

18s rrna. Chain: 2. Hcv ires. Chain: 3. Engineered: yes. Ribosomal protein us2. Chain: a. Ribosomal protein es1. Chain: b.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Cell_line: hek293-6e. Organ: kidney. Synthetic: yes. Hepatitis c virus. Organism_taxid: 11103. Organ: kidney

Authors:

N.Quade,M.Leiundgut,D.Boehringer,J.V.D.Heuvel,N.Ban

Key ref:

N.Quade et al. (2015). Cryo-EM structure of Hepatitis C virus IRES bound to the human ribosome at 3.9-Å resolution. Nat Commun, 6, 7646. PubMed id: 26155016 DOI: 10.1038/ncomms8646

Date:

21-May-15 Release date: 15-Jul-15

Protein chain

P08865  (RSSA_HUMAN) -  Small ribosomal subunit protein uS2 from Homo sapiens

Seq: 295 a.a.

Struc: 216 a.a.

Protein chain

P61247  (RS3A_HUMAN) -  Small ribosomal subunit protein eS1 from Homo sapiens

Seq: 264 a.a.

Struc: 213 a.a.

Protein chain

P15880  (RS2_HUMAN) -  Small ribosomal subunit protein uS5 from Homo sapiens

Seq: 293 a.a.

Struc: 218 a.a.

Protein chain

P23396  (RS3_HUMAN) -  Small ribosomal subunit protein uS3 from Homo sapiens

Seq: 243 a.a.

Struc: 225 a.a.

Protein chain

P62701  (RS4X_HUMAN) -  Small ribosomal subunit protein eS4, X isoform from Homo sapiens

Seq: 263 a.a.

Struc: 262 a.a.

Protein chain

P46782  (RS5_HUMAN) -  Small ribosomal subunit protein uS7 from Homo sapiens

Seq: 204 a.a.

Struc: 189 a.a.

Protein chain

P62753  (RS6_HUMAN) -  Small ribosomal subunit protein eS6 from Homo sapiens

Seq: 249 a.a.

Struc: 230 a.a.*

Protein chain

P62081  (RS7_HUMAN) -  Small ribosomal subunit protein eS7 from Homo sapiens

Seq: 194 a.a.

Struc: 186 a.a.

Protein chain

P62241  (RS8_HUMAN) -  Small ribosomal subunit protein eS8 from Homo sapiens

Seq: 208 a.a.

Struc: 205 a.a.

Protein chain

P46781  (RS9_HUMAN) -  Small ribosomal subunit protein uS4 from Homo sapiens

Seq: 194 a.a.

Struc: 180 a.a.

Protein chain

P46783  (RS10_HUMAN) -  Small ribosomal subunit protein eS10 from Homo sapiens

Seq: 165 a.a.

Struc: 95 a.a.

Protein chain

P62280  (RS11_HUMAN) -  Small ribosomal subunit protein uS17 from Homo sapiens

Seq: 158 a.a.

Struc: 151 a.a.

Protein chain

P25398  (RS12_HUMAN) -  Small ribosomal subunit protein eS12 from Homo sapiens

Seq: 132 a.a.

Struc: 123 a.a.

Protein chain

P62277  (RS13_HUMAN) -  Small ribosomal subunit protein uS15 from Homo sapiens

Seq: 151 a.a.

Struc: 149 a.a.

Protein chain

P62263  (RS14_HUMAN) -  Small ribosomal subunit protein uS11 from Homo sapiens

Seq: 151 a.a.

Struc: 135 a.a.

Protein chain

P62841  (RS15_HUMAN) -  Small ribosomal subunit protein uS19 from Homo sapiens

Seq: 145 a.a.

Struc: 120 a.a.

Protein chain

P62249  (RS16_HUMAN) -  Small ribosomal subunit protein uS9 from Homo sapiens

Seq: 146 a.a.

Struc: 139 a.a.

Protein chain

P08708  (RS17_HUMAN) -  Small ribosomal subunit protein eS17 from Homo sapiens

Seq: 135 a.a.

Struc: 132 a.a.

Protein chain

P62269  (RS18_HUMAN) -  Small ribosomal subunit protein uS13 from Homo sapiens

Seq: 152 a.a.

Struc: 143 a.a.

Protein chain

P39019  (RS19_HUMAN) -  Small ribosomal subunit protein eS19 from Homo sapiens

Seq: 145 a.a.

Struc: 145 a.a.

Protein chain

P60866  (RS20_HUMAN) -  Small ribosomal subunit protein uS10 from Homo sapiens

Seq: 119 a.a.

Struc: 101 a.a.

Protein chain

P63220  (RS21_HUMAN) -  Small ribosomal subunit protein eS21 from Homo sapiens

Seq: 83 a.a.

Struc: 82 a.a.

Protein chain

P62244  (RS15A_HUMAN) -  Small ribosomal subunit protein uS8 from Homo sapiens

Seq: 130 a.a.

Struc: 129 a.a.

Protein chain

P62266  (RS23_HUMAN) -  Small ribosomal subunit protein uS12 from Homo sapiens

Seq: 143 a.a.

Struc: 141 a.a.

Protein chain

P62847  (RS24_HUMAN) -  Small ribosomal subunit protein eS24 from Homo sapiens

Seq: 133 a.a.

Struc: 124 a.a.

Protein chain

P62851  (RS25_HUMAN) -  Small ribosomal subunit protein eS25 from Homo sapiens

Seq: 125 a.a.

Struc: 72 a.a.

Protein chain

P62854  (RS26_HUMAN) -  Small ribosomal subunit protein eS26 from Homo sapiens

Seq: 115 a.a.

Struc: 101 a.a.*

Protein chain

P42677  (RS27_HUMAN) -  Small ribosomal subunit protein eS27 from Homo sapiens

Seq: 84 a.a.

Struc: 82 a.a.

Protein chain

P62857  (RS28_HUMAN) -  Small ribosomal subunit protein eS28 from Homo sapiens

Seq: 69 a.a.

Struc: 61 a.a.

Protein chain

P62273  (RS29_HUMAN) -  Small ribosomal subunit protein uS14 from Homo sapiens

Seq: 56 a.a.

Struc: 55 a.a.

Protein chain

P62861  (RS30_HUMAN) -  Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein from Homo sapiens

Seq: 133 a.a.

Struc: 56 a.a.

Protein chain

P62979  (RS27A_HUMAN) -  Ubiquitin-ribosomal protein eS31 fusion protein from Homo sapiens

Seq: 156 a.a.

Struc: 72 a.a.*

Protein chain

P63244  (RACK1_HUMAN) -  Small ribosomal subunit protein RACK1 from Homo sapiens

Seq: 317 a.a.

Struc: 314 a.a.

Protein chain

P62945  (RL41_HUMAN) -  Small ribosomal subunit protein eS32 from Homo sapiens

Seq: 25 a.a.

Struc: 24 a.a.

Protein chain

P84098  (RL19_HUMAN) -  Large ribosomal subunit protein eL19 from Homo sapiens

Seq: 196 a.a.

Struc: 13 a.a.

Protein chain

P83731  (RL24_HUMAN) -  Large ribosomal subunit protein eL24 from Homo sapiens

Seq: 157 a.a.

Struc: 62 a.a.*

* PDB and UniProt seqs differ at 17 residue positions (black crosses)

DNA/RNA chains

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- ... 1665 bases

C-U-C-C-C-C-U-G-U-G-A-G-G-A-A-C-U-A-C-U-G-U-C-U-U-C-A-C-G-C-A-G-A-A-A-G-C-G-U- 257 bases

Enzyme reactions

• Enzyme class: Chain D: E.C.4.2.99.18 - DNA-(apurinic or apyrimidinic site) lyase.
• Reaction: 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)- 2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho- 2'-deoxyribonucleoside-DNA + H⁺

DOI no: 10.1038/ncomms8646

Nat Commun 6:7646 (2015)

PubMed id: 26155016

Cryo-EM structure of Hepatitis C virus IRES bound to the human ribosome at 3.9-Å resolution.

N.Quade, D.Boehringer, M.Leibundgut, J.van den Heuvel, N.Ban.

ABSTRACT

Hepatitis C virus (HCV), a widespread human pathogen, is dependent on a highly structured 5'-untranslated region of its mRNA, referred to as internal ribosome entry site (IRES), for the translation of all of its proteins. The HCV IRES initiates translation by directly binding to the small ribosomal subunit (40S), circumventing the need for many eukaryotic translation initiation factors required for mRNA scanning. Here we present the cryo-EM structure of the human 40S ribosomal subunit in complex with the HCV IRES at 3.9 Å resolution, determined by focused refinement of an 80S ribosome-HCV IRES complex. The structure reveals the molecular details of the interactions between the IRES and the 40S, showing that expansion segment 7 (ES7) of the 18S rRNA acts as a central anchor point for the HCV IRES. The structural data rationalizes previous biochemical and genetic evidence regarding the initiation mechanism of the HCV and other related IRESs.