PDBsum entry 6p4h

Ribosome

PDB id: 6p4h

Contents

Protein chains

217 a.a.

213 a.a.

221 a.a.

228 a.a.

262 a.a.

184 a.a.

237 a.a.

185 a.a.

206 a.a.

185 a.a.

96 a.a.

143 a.a.

117 a.a.

149 a.a.

136 a.a.

119 a.a.

142 a.a.

132 a.a.

141 a.a.

141 a.a.

100 a.a.

83 a.a.

129 a.a.

141 a.a.

124 a.a.

70 a.a.

98 a.a.

83 a.a.

62 a.a.

55 a.a.

57 a.a.

68 a.a.

313 a.a.

25 a.a.

DNA/RNA

PDB id:

6p4h

Name:

Ribosome

Title:

Structure of a mammalian small ribosomal subunit in complex with the israeli acute paralysis virus ires (class 2)

Structure:

18s rrna. Chain: 2. Us2. Chain: b. Synonym: 37 kda laminin receptor precursor,37lrp,37/67 kda laminin receptor,lrp/lr,67 kda laminin receptor,67lr,laminin receptor 1,lamr, laminin-binding protein precursor p40,lbp/p40. Es1. Chain: c.

Source:

Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986. Israeli acute paralysis virus. Organism_taxid: 294365. Expressed in: synthetic construct. Expression_system_taxid: 32630. Organism_taxid: 9986

Authors:

F.J.Acosta-Reyes,R.Neupane,J.Frank,I.S.Fernandez

Key ref:

F.Acosta-Reyes et al. (2019). The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs. EMBO J, 38, e102226. PubMed id: 31609474 DOI: 10.15252/embj.2019102226

Date:

27-May-19 Release date: 18-Sep-19

Protein chain

G1TLT8  (G1TLT8_RABIT) -  Small ribosomal subunit protein uS2 from Oryctolagus cuniculus

Seq: 295 a.a.

Struc: 217 a.a.*

Protein chain

G1SS70  (G1SS70_RABIT) -  Small ribosomal subunit protein eS1 from Oryctolagus cuniculus

Seq: 264 a.a.

Struc: 213 a.a.

Protein chain

G1SWM1  (G1SWM1_RABIT) -  Small ribosomal subunit protein uS5 from Oryctolagus cuniculus

Seq: 292 a.a.

Struc: 221 a.a.*

Protein chain

G1TNM3  (G1TNM3_RABIT) -  Small ribosomal subunit protein uS3 from Oryctolagus cuniculus

Seq: 243 a.a.

Struc: 228 a.a.

Protein chain

G1TK17  (G1TK17_RABIT) -  Small ribosomal subunit protein eS4 from Oryctolagus cuniculus

Seq: 263 a.a.

Struc: 262 a.a.

Protein chain

G1TFM5  (G1TFM5_RABIT) -  Small ribosomal subunit protein uS7 from Oryctolagus cuniculus

Seq: 204 a.a.

Struc: 184 a.a.

Protein chain

G1TM55  (G1TM55_RABIT) -  Small ribosomal subunit protein eS6 from Oryctolagus cuniculus

Seq: 249 a.a.

Struc: 237 a.a.

Protein chain

G1SVB0  (G1SVB0_RABIT) -  Small ribosomal subunit protein eS7 from Oryctolagus cuniculus

Seq: 194 a.a.

Struc: 185 a.a.

Protein chain

G1TJW1  (G1TJW1_RABIT) -  Small ribosomal subunit protein eS8 from Oryctolagus cuniculus

Seq: 208 a.a.

Struc: 206 a.a.*

Protein chain

B7NZS8  (RS9_RABIT) -  Small ribosomal subunit protein uS4 from Oryctolagus cuniculus

Seq: 194 a.a.

Struc: 185 a.a.

Protein chain

G1TPV3  (G1TPV3_RABIT) -  Small ribosomal subunit protein eS10 from Oryctolagus cuniculus

Seq: 165 a.a.

Struc: 96 a.a.

Protein chain

G1TRM4  (G1TRM4_RABIT) -  Small ribosomal subunit protein uS17 from Oryctolagus cuniculus

Seq: 158 a.a.

Struc: 143 a.a.

Protein chain

G1SFR8  (G1SFR8_RABIT) -  Small ribosomal subunit protein eS12 from Oryctolagus cuniculus

Seq: 132 a.a.

Struc: 117 a.a.

Protein chain

G1SP51  (G1SP51_RABIT) -  Small ribosomal subunit protein uS15 from Oryctolagus cuniculus

Seq: 151 a.a.

Struc: 149 a.a.

Protein chain

G1T1F0  (G1T1F0_RABIT) -  Small ribosomal subunit protein uS11 from Oryctolagus cuniculus

Seq: 151 a.a.

Struc: 136 a.a.

Protein chain

G1U0Q2  (G1U0Q2_RABIT) -  Small ribosomal subunit protein uS19 from Oryctolagus cuniculus

Seq: 145 a.a.

Struc: 119 a.a.

Protein chain

G1SGX4  (G1SGX4_RABIT) -  Small ribosomal subunit protein uS9 from Oryctolagus cuniculus

Seq: 146 a.a.

Struc: 142 a.a.

Protein chain

G1TU13  (G1TU13_RABIT) -  Small ribosomal subunit protein eS17 from Oryctolagus cuniculus

Seq: 135 a.a.

Struc: 132 a.a.

Protein chain

G1TPG3  (G1TPG3_RABIT) -  Small ribosomal subunit protein uS13 from Oryctolagus cuniculus

Seq: 152 a.a.

Struc: 141 a.a.

Protein chain

G1TN62  (G1TN62_RABIT) -  Small ribosomal subunit protein eS19 from Oryctolagus cuniculus

Seq: 145 a.a.

Struc: 141 a.a.

Protein chain

G1SIZ2  (G1SIZ2_RABIT) -  Small ribosomal subunit protein uS10 from Oryctolagus cuniculus

Seq: 119 a.a.

Struc: 100 a.a.

Protein chain

G1TM82  (G1TM82_RABIT) -  Small ribosomal subunit protein eS21 from Oryctolagus cuniculus

Seq: 83 a.a.

Struc: 83 a.a.*

Protein chain

G1TG89  (G1TG89_RABIT) -  Small ribosomal subunit protein uS8 from Oryctolagus cuniculus

Seq: 130 a.a.

Struc: 129 a.a.

Protein chain

G1SZ47  (G1SZ47_RABIT) -  Small ribosomal subunit protein uS12 from Oryctolagus cuniculus

Seq: 143 a.a.

Struc: 141 a.a.

Protein chain

G1T3D8  (G1T3D8_RABIT) -  40S ribosomal protein S24 from Oryctolagus cuniculus

Seq: 131 a.a.

Struc: 124 a.a.

Protein chain

G1TDB3  (G1TDB3_RABIT) -  Small ribosomal subunit protein eS25 from Oryctolagus cuniculus

Seq: 124 a.a.

Struc: 70 a.a.

Protein chain

G1TFE8  (G1TFE8_RABIT) -  Small ribosomal subunit protein eS26 from Oryctolagus cuniculus

Seq: 115 a.a.

Struc: 98 a.a.

Protein chain

G1TZ76  (G1TZ76_RABIT) -  Small ribosomal subunit protein eS27 from Oryctolagus cuniculus

Seq: 84 a.a.

Struc: 83 a.a.

Protein chain

G1TIB4  (G1TIB4_RABIT) -  Small ribosomal subunit protein eS28 from Oryctolagus cuniculus

Seq: 69 a.a.

Struc: 62 a.a.

Protein chain

G1U7M4  (G1U7M4_RABIT) -  Small ribosomal subunit protein uS14 from Oryctolagus cuniculus

Seq: 56 a.a.

Struc: 55 a.a.

Protein chain

G1T8A2  (G1T8A2_RABIT) -  Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein from Oryctolagus cuniculus

Seq: 133 a.a.

Struc: 57 a.a.

Protein chain

G1SK22  (G1SK22_RABIT) -  Ubiquitin-ribosomal protein eS31 fusion protein from Oryctolagus cuniculus

Seq: 156 a.a.

Struc: 68 a.a.

Protein chain

G1SJB4  (G1SJB4_RABIT) -  Small ribosomal subunit protein RACK1 from Oryctolagus cuniculus

Seq: 317 a.a.

Struc: 313 a.a.

Protein chain

A0A087WNH4  (RS32_RABIT) -  Small ribosomal subunit protein eS32 from Oryctolagus cuniculus

Seq: 25 a.a.

Struc: 25 a.a.

* PDB and UniProt seqs differ at 12 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- ... 1697 bases

C-A-U-C-A-U-U-C-U-A-U-G-G-U-U-A-C-C-C-A-U-C-A-U-U-A-G-A-G-G-A-A-A-U-U-U-C-C-A- 203 bases

Enzyme reactions

• Enzyme class: Chain E: 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: 10.15252/embj.2019102226

EMBO J 38:e102226 (2019)

PubMed id: 31609474

The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs.

F.Acosta-Reyes, R.Neupane, J.Frank, I.S.Fernández.

ABSTRACT

Colony collapse disorder (CCD) is a multi-faceted syndrome decimating bee populations worldwide, and a group of viruses of the widely distributed Dicistroviridae family have been identified as a causing agent of CCD. This family of viruses employs non-coding RNA sequences, called internal ribosomal entry sites (IRESs), to precisely exploit the host machinery for viral protein production. Using single-particle cryo-electron microscopy (cryo-EM), we have characterized how the IRES of Israeli acute paralysis virus (IAPV) intergenic region captures and redirects translating ribosomes toward viral RNA messages. We reconstituted two in vitro reactions targeting a pre-translocation and a post-translocation state of the IAPV-IRES in the ribosome, allowing us to identify six structures using image processing classification methods. From these, we reconstructed the trajectory of IAPV-IRES from the early small subunit recruitment to the final post-translocated state in the ribosome. An early commitment of IRES/ribosome complexes for global pre-translocation mimicry explains the high efficiency observed for this IRES. Efforts directed toward fighting CCD by targeting the IAPV-IRES using RNA-interference technology are underway, and the structural framework presented here may assist in further refining these approaches.