PDBsum entry 4byt

Ribosome

PDB id: 4byt

Contents

Protein chains

97 a.a.

81 a.a.

63 a.a.

53 a.a.

60 a.a.

71 a.a.

318 a.a.

159 a.a.

206 a.a.

214 a.a.

217 a.a.

223 a.a.

260 a.a.

206 a.a.

226 a.a.

184 a.a.

188 a.a.

185 a.a.

96 a.a.

155 a.a.

124 a.a.

150 a.a.

127 a.a.

124 a.a.

141 a.a.

120 a.a.

145 a.a.

143 a.a.

107 a.a.

87 a.a.

129 a.a.

144 a.a.

134 a.a.

70 a.a.

Metals

_ZN ×4

PDB id:

4byt

Name:

Ribosome

Title:

Cryo-em reconstruction of the 80s-eif5b-met-itrnamet eukaryotic translation initiation complex

Structure:

40s ribosomal protein s27-a. Chain: 1. Synonym: rp61, ys20. 40s ribosomal protein s26-a. Chain: 0. 40s ribosomal protein s29-a. Chain: 3. Synonym: s36, ys29. 40s ribosomal protein s28-a.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Organism_taxid: 4932

Authors:

I.S.Fernandez,X.C.Bai,T.Hussain,A.C.Kelley,J.R.Lorsch,V.Rama S.H.W.Scheres

Key ref:

I.S.Fernández et al. (2013). Molecular architecture of a eukaryotic translational initiation complex. Science, 342, 1240585. PubMed id: 24200810 DOI: 10.1126/science.1240585

Date:

20-Jul-13 Release date: 20-Nov-13

Protein chain

P39938  (RS26A_YEAST) -  Small ribosomal subunit protein eS26A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 119 a.a.

Struc: 97 a.a.

Protein chain

P35997  (RS27A_YEAST) -  Small ribosomal subunit protein eS27A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 82 a.a.

Struc: 81 a.a.

Protein chain

Q3E7X9  (RS28A_YEAST) -  Small ribosomal subunit protein eS28A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 67 a.a.

Struc: 63 a.a.

Protein chain

P41057  (RS29A_YEAST) -  Small ribosomal subunit protein uS14A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 56 a.a.

Struc: 53 a.a.

Protein chain

P0CX33  (RS30A_YEAST) -  Small ribosomal subunit protein eS30A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 63 a.a.

Struc: 60 a.a.

Protein chain

P05759  (RS31_YEAST) -  Ubiquitin-ribosomal protein eS31 fusion protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 152 a.a.

Struc: 71 a.a.*

Protein chain

P38011  (GBLP_YEAST) -  Small ribosomal subunit protein RACK1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 319 a.a.

Struc: 318 a.a.

Protein chain

P39015  (STM1_YEAST) -  Suppressor protein STM1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 273 a.a.

Struc: 159 a.a.*

Protein chain

P32905  (RSSA1_YEAST) -  Small ribosomal subunit protein uS2A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 252 a.a.

Struc: 206 a.a.

Protein chain

P33442  (RS3A1_YEAST) -  Small ribosomal subunit protein eS1A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 255 a.a.

Struc: 214 a.a.

Protein chain

P25443  (RS2_YEAST) -  Small ribosomal subunit protein uS5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 254 a.a.

Struc: 217 a.a.

Protein chain

P05750  (RS3_YEAST) -  Small ribosomal subunit protein uS3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 240 a.a.

Struc: 223 a.a.

Protein chain

P0CX35  (RS4A_YEAST) -  Small ribosomal subunit protein eS4A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 261 a.a.

Struc: 260 a.a.

Protein chain

P26783  (RS5_YEAST) -  Small ribosomal subunit protein uS7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 225 a.a.

Struc: 206 a.a.

Protein chain

P0CX37  (RS6A_YEAST) -  Small ribosomal subunit protein eS6A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 236 a.a.

Struc: 226 a.a.

Protein chain

P26786  (RS7A_YEAST) -  Small ribosomal subunit protein eS7A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 190 a.a.

Struc: 184 a.a.

Protein chain

P0CX39  (RS8A_YEAST) -  Small ribosomal subunit protein eS8A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 200 a.a.

Struc: 188 a.a.

Protein chain

O13516  (RS9A_YEAST) -  Small ribosomal subunit protein uS4A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 197 a.a.

Struc: 185 a.a.

Protein chain

Q08745  (RS10A_YEAST) -  Small ribosomal subunit protein eS10A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 105 a.a.

Struc: 96 a.a.

Protein chain

P0CX47  (RS11A_YEAST) -  Small ribosomal subunit protein uS17A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 156 a.a.

Struc: 155 a.a.

Protein chain

P48589  (RS12_YEAST) -  Small ribosomal subunit protein eS12 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 143 a.a.

Struc: 124 a.a.

Protein chain

P05756  (RS13_YEAST) -  Small ribosomal subunit protein uS15 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 151 a.a.

Struc: 150 a.a.

Protein chain

P06367  (RS14A_YEAST) -  Small ribosomal subunit protein uS11A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 137 a.a.

Struc: 127 a.a.

Protein chain

Q01855  (RS15_YEAST) -  Small ribosomal subunit protein uS19 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 142 a.a.

Struc: 124 a.a.

Protein chain

P0CX51  (RS16A_YEAST) -  Small ribosomal subunit protein uS9A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 143 a.a.

Struc: 141 a.a.

Protein chain

P02407  (RS17A_YEAST) -  Small ribosomal subunit protein eS17A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 136 a.a.

Struc: 120 a.a.

Protein chain

P0CX55  (RS18A_YEAST) -  Small ribosomal subunit protein uS13A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 146 a.a.

Struc: 145 a.a.

Protein chain

P07280  (RS19A_YEAST) -  Small ribosomal subunit protein eS19A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 144 a.a.

Struc: 143 a.a.

Protein chain

P38701  (RS20_YEAST) -  Small ribosomal subunit protein uS10 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 121 a.a.

Struc: 107 a.a.

Protein chain

P0C0V8  (RS21A_YEAST) -  Small ribosomal subunit protein eS21A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 87 a.a.

Struc: 87 a.a.

Protein chain

P0C0W1  (RS22A_YEAST) -  Small ribosomal subunit protein uS8A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 130 a.a.

Struc: 129 a.a.

Protein chain

P0CX29  (RS23A_YEAST) -  Small ribosomal subunit protein uS12A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 145 a.a.

Struc: 144 a.a.

Protein chain

P0CX31  (RS24A_YEAST) -  Small ribosomal subunit protein eS24A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 135 a.a.

Struc: 134 a.a.

Protein chain

Q3E792  (RS25A_YEAST) -  Small ribosomal subunit protein eS25A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 108 a.a.

Struc: 70 a.a.

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

DOI no: 10.1126/science.1240585

Science 342:1240585 (2013)

PubMed id: 24200810

Molecular architecture of a eukaryotic translational initiation complex.

I.S.Fernández, X.C.Bai, T.Hussain, A.C.Kelley, J.R.Lorsch, V.Ramakrishnan, S.H.Scheres.

ABSTRACT

The last step in eukaryotic translational initiation involves the joining of the large and small subunits of the ribosome, with initiator transfer RNA (Met-tRNA(i)(Met)) positioned over the start codon of messenger RNA in the P site. This step is catalyzed by initiation factor eIF5B. We used recent advances in cryo-electron microscopy (cryo-EM) to determine a structure of the eIF5B initiation complex to 6.6 angstrom resolution from <3% of the population, comprising just 5143 particles. The structure reveals conformational changes in eIF5B, initiator tRNA, and the ribosome that provide insights into the role of eIF5B in translational initiation. The relatively high resolution obtained from such a small fraction of a heterogeneous sample suggests a general approach for characterizing the structure of other dynamic or transient biological complexes.