PDBsum entry 4kzy

Ribosome

PDB id: 4kzy

Contents

Protein chains

208 a.a.

215 a.a.

226 a.a.

227 a.a.

263 a.a.

191 a.a.

237 a.a.

190 a.a.

206 a.a.

182 a.a.

98 a.a.

158 a.a.

124 a.a.

150 a.a.

136 a.a.

127 a.a.

141 a.a.

126 a.a.

137 a.a.

141 a.a.

104 a.a.

82 a.a.

129 a.a.

142 a.a.

126 a.a.

75 a.a.

107 a.a.

84 a.a.

64 a.a.

53 a.a.

59 a.a.

71 a.a.

313 a.a.

85 a.a.

82 a.a.

DNA/RNA

PDB id:

4kzy

Name:

Ribosome

Title:

Rabbit 40s ribosomal subunit in complex with eif1 and eif1a.

Structure:

40s ribosomal protein sa. Chain: a. 40s ribosomal protein s3a. Chain: b. 40s ribosomal protein s2. Chain: c. 40s ribosomal protein s3. Chain: d. 40s ribosomal protein s4x.

Source:

Oryctolagus cuniculus. European rabbit,japanese white rabbit,domestic rabbit,rabbits. Organism_taxid: 9986. Rabbit. Homo sapiens. Organism_taxid: 9606. Gene: eif1. Expressed in: escherichia coli.

Resolution:

7.01Å R-factor: 0.365 R-free: 0.348

Authors:

I.B.Lomakin,T.A.Steitz

Key ref:

I.B.Lomakin and T.A.Steitz (2013). The initiation of mammalian protein synthesis and mRNA scanning mechanism. Nature, 500, 307-311. PubMed id: 23873042 DOI: 10.1038/nature12355

Date:

30-May-13 Release date: 24-Jul-13

Protein chain

G1TGI6  (G1TGI6_RABIT) -  Small ribosomal subunit protein uS2 from Oryctolagus cuniculus

Seq: 297 a.a.

Struc: 208 a.a.*

Protein chain

G1TN72  (G1TN72_RABIT) -  Small ribosomal subunit protein eS1 from Oryctolagus cuniculus

Seq: 264 a.a.

Struc: 215 a.a.

Protein chain

G1U2Z9  (G1U2Z9_RABIT) -  Small ribosomal subunit protein uS5 from Oryctolagus cuniculus

Seq: 218 a.a.

Struc: 226 a.a.*

Protein chain

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

Seq: 243 a.a.

Struc: 227 a.a.

Protein chain

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

Seq: 263 a.a.

Struc: 263 a.a.

Protein chain

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

Seq: 204 a.a.

Struc: 191 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: 190 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: 182 a.a.

Protein chain

G1T168  (G1T168_RABIT) -  Small ribosomal subunit protein eS10 from Oryctolagus cuniculus

Seq: 165 a.a.

Struc: 98 a.a.

Protein chain

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

Seq: 158 a.a.

Struc: 158 a.a.

Protein chain

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

Seq: 132 a.a.

Struc: 124 a.a.

Protein chain

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

Seq: 151 a.a.

Struc: 150 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: 127 a.a.

Protein chain

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

Seq: 146 a.a.

Struc: 141 a.a.

Protein chain

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

Seq: 135 a.a.

Struc: 126 a.a.

Protein chain

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

Seq: 152 a.a.

Struc: 137 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: 104 a.a.

Protein chain

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

Seq: 83 a.a.

Struc: 82 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: 142 a.a.

Protein chain

G1TS40  (G1TS40_RABIT) -  40S ribosomal protein S24 from Oryctolagus cuniculus

Seq: 133 a.a.

Struc: 126 a.a.

Protein chain

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

Seq: 124 a.a.

Struc: 75 a.a.

Protein chain

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

Seq: 115 a.a.

Struc: 107 a.a.

Protein chain

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

Seq: 84 a.a.

Struc: 84 a.a.

Protein chain

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

Seq: 69 a.a.

Struc: 64 a.a.

Protein chain

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

Seq: 56 a.a.

Struc: 53 a.a.

Protein chain

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

Seq: 133 a.a.

Struc: 59 a.a.

Protein chain

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

Seq: 156 a.a.

Struc: 71 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

P41567  (EIF1_HUMAN) -  Eukaryotic translation initiation factor 1 from Homo sapiens

Seq: 113 a.a.

Struc: 85 a.a.

Protein chain

P47813  (IF1AX_HUMAN) -  Eukaryotic translation initiation factor 1A, X-chromosomal from Homo sapiens

Seq: 144 a.a.

Struc: 82 a.a.

* PDB and UniProt seqs differ at 69 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- ... 1840 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/nature12355

Nature 500:307-311 (2013)

PubMed id: 23873042

The initiation of mammalian protein synthesis and mRNA scanning mechanism.

I.B.Lomakin, T.A.Steitz.

ABSTRACT

During translation initiation in eukaryotes, the small ribosomal subunit binds messenger RNA at the 5' end and scans in the 5' to 3' direction to locate the initiation codon, form the 80S initiation complex and start protein synthesis. This simple, yet intricate, process is guided by multiple initiation factors. Here we determine the structures of three complexes of the small ribosomal subunit that represent distinct steps in mammalian translation initiation. These structures reveal the locations of eIF1, eIF1A, mRNA and initiator transfer RNA bound to the small ribosomal subunit and provide insights into the details of translation initiation specific to eukaryotes. Conformational changes associated with the captured functional states reveal the dynamics of the interactions in the P site of the ribosome. These results have functional implications for the mechanism of mRNA scanning.