PDBsum entry 4b6a

Ribosome

PDB id: 4b6a

Contents

Protein chains

252 a.a.

386 a.a.

361 a.a.

294 a.a.

157 a.a.

223 a.a.

231 a.a.

191 a.a.

213 a.a.

169 a.a.

150 a.a.

194 a.a.

137 a.a.

203 a.a.

217 a.a.

155 a.a.

185 a.a.

188 a.a.

172 a.a.

159 a.a.

98 a.a.

136 a.a.

135 a.a.

120 a.a.

126 a.a.

135 a.a.

148 a.a.

58 a.a.

100 a.a.

109 a.a.

127 a.a.

106 a.a.

112 a.a.

119 a.a.

99 a.a.

87 a.a.

77 a.a.

50 a.a.

52 a.a.

25 a.a.

105 a.a.

91 a.a.

143 a.a.

47 a.a.

380 a.a.

Metals

_ZN ×4

PDB id:

4b6a

Name:

Ribosome

Title:

Cryo-em structure of the 60s ribosomal subunit in complex with arx1 and rei1

Structure:

60s ribosomal protein l2-b. Chain: a. Synonym: l5, rp8, yl6. 60s ribosomal protein l3. Chain: b. Synonym: maintenance of killer protein 8, rp1, trichodermin resistance protein, yl1. 60s ribosomal protein l4-a. Chain: c.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 559292. Strain: s288c. Expressed in: escherichia coli. Expression_system_taxid: 562.

Authors:

B.J.Greber,D.Boehringer,C.Montellese,N.Ban

Key ref:

B.J.Greber et al. (2012). Cryo-EM structures of Arx1 and maturation factors Rei1 and Jjj1 bound to the 60S ribosomal subunit. Nat Struct Biol, 19, 1228-1233. PubMed id: 23142985

Date:

07-Aug-12 Release date: 31-Oct-12

Protein chain

P0CX46  (RL2B_YEAST) -  60S ribosomal protein L2-B from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 254 a.a.

Struc: 252 a.a.

Protein chain

P14126  (RL3_YEAST) -  60S ribosomal protein L3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 387 a.a.

Struc: 386 a.a.

Protein chain

P10664  (RL4A_YEAST) -  60S ribosomal protein L4-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 362 a.a.

Struc: 361 a.a.

Protein chain

P26321  (RL5_YEAST) -  60S ribosomal protein L5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 297 a.a.

Struc: 294 a.a.

Protein chain

Q02326  (RL6A_YEAST) -  60S ribosomal protein L6-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 176 a.a.

Struc: 157 a.a.

Protein chain

P05737  (RL7A_YEAST) -  60S ribosomal protein L7-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 244 a.a.

Struc: 223 a.a.

Protein chain

P17076  (RL8A_YEAST) -  60S ribosomal protein L8-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 256 a.a.

Struc: 231 a.a.

Protein chain

P05738  (RL9A_YEAST) -  60S ribosomal protein L9-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 191 a.a.

Struc: 191 a.a.

Protein chain

P41805  (RL10_YEAST) -  60S ribosomal protein L10 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 221 a.a.

Struc: 213 a.a.

Protein chain

Q3E757  (RL11B_YEAST) -  60S ribosomal protein L11-B from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 174 a.a.

Struc: 169 a.a.

Protein chain

No UniProt id for this chain

Struc: 150 a.a.

Protein chain

Q12690  (RL13A_YEAST) -  60S ribosomal protein L13-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 199 a.a.

Struc: 194 a.a.

Protein chain

P36105  (RL14A_YEAST) -  60S ribosomal protein L14-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 138 a.a.

Struc: 137 a.a.

Protein chain

P05748  (RL15A_YEAST) -  60S ribosomal protein L15-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 204 a.a.

Struc: 203 a.a.

Protein chain

P26784  (RL16A_YEAST) -  60S ribosomal protein L16-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 199 a.a.

Struc: 217 a.a.*

Protein chain

P05740  (RL17A_YEAST) -  60S ribosomal protein L17-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 184 a.a.

Struc: 155 a.a.

Protein chain

P0CX50  (RL18B_YEAST) -  60S ribosomal protein L18-B from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 186 a.a.

Struc: 185 a.a.

Protein chain

P0CX83  (RL19B_YEAST) -  60S ribosomal protein L19-B from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 189 a.a.

Struc: 188 a.a.

Protein chain

P0CX23  (RL20A_YEAST) -  60S ribosomal protein L20-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 172 a.a.

Struc: 172 a.a.

Protein chain

Q02753  (RL21A_YEAST) -  60S ribosomal protein L21-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 160 a.a.

Struc: 159 a.a.

Protein chain

P05749  (RL22A_YEAST) -  60S ribosomal protein L22-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 121 a.a.

Struc: 98 a.a.

Protein chain

P0CX41  (RL23A_YEAST) -  60S ribosomal protein L23-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 137 a.a.

Struc: 136 a.a.

Protein chain

P04449  (RL24A_YEAST) -  60S ribosomal protein L24-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 155 a.a.

Struc: 135 a.a.

Protein chain

P04456  (RL25_YEAST) -  60S ribosomal protein L25 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 142 a.a.

Struc: 120 a.a.

Protein chain

P05743  (RL26A_YEAST) -  60S ribosomal protein L26-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 127 a.a.

Struc: 126 a.a.

Protein chain

P0C2H6  (RL27A_YEAST) -  60S ribosomal protein L27-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 136 a.a.

Struc: 135 a.a.

Protein chain

P02406  (RL28_YEAST) -  60S ribosomal protein L28 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 149 a.a.

Struc: 148 a.a.

Protein chain

P05747  (RL29_YEAST) -  60S ribosomal protein L29 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 59 a.a.

Struc: 58 a.a.

Protein chain

P14120  (RL30_YEAST) -  60S ribosomal protein L30 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 105 a.a.

Struc: 100 a.a.

Protein chain

P0C2H8  (RL31A_YEAST) -  60S ribosomal protein L31-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 113 a.a.

Struc: 109 a.a.

Protein chain

P38061  (RL32_YEAST) -  60S ribosomal protein L32 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 130 a.a.

Struc: 127 a.a.

Protein chain

P05744  (RL33A_YEAST) -  60S ribosomal protein L33-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 107 a.a.

Struc: 106 a.a.

Protein chain

P87262  (RL34A_YEAST) -  60S ribosomal protein L34-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 121 a.a.

Struc: 112 a.a.

Protein chain

P0CX84  (RL35A_YEAST) -  60S ribosomal protein L35-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 120 a.a.

Struc: 119 a.a.

Protein chain

P05745  (RL36A_YEAST) -  60S ribosomal protein L36-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 100 a.a.

Struc: 99 a.a.

Protein chain

P49166  (RL37A_YEAST) -  60S ribosomal protein L37-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 88 a.a.

Struc: 87 a.a.

Protein chain

P49167  (RL38_YEAST) -  60S ribosomal protein L38 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 78 a.a.

Struc: 77 a.a.

Protein chain

P04650  (RL39_YEAST) -  60S ribosomal protein L39 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 51 a.a.

Struc: 50 a.a.

Protein chain

P0CH08  (RL40A_YEAST) -  Ubiquitin-60S ribosomal protein L40 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 128 a.a.

Struc: 52 a.a.

Protein chain

P0CX86  (RL41A_YEAST) -  60S ribosomal protein L41-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 25 a.a.

Struc: 25 a.a.

Protein chain

P0CX27  (RL44A_YEAST) -  60S ribosomal protein L42-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 106 a.a.

Struc: 105 a.a.

Protein chain

P0CX25  (RL43A_YEAST) -  60S ribosomal protein L43-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 92 a.a.

Struc: 91 a.a.

Protein chain

P05317  (RLA0_YEAST) -  60S acidic ribosomal protein P0 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 312 a.a.

Struc: 143 a.a.*

Protein chains

No UniProt id for this chain

Struc: 47 a.a.

Protein chain

No UniProt id for this chain

Struc: 380 a.a.

* PDB and UniProt seqs differ at 60 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chain t: E.C.3.-.-.-

Nat Struct Biol 19:1228-1233 (2012)

PubMed id: 23142985

Cryo-EM structures of Arx1 and maturation factors Rei1 and Jjj1 bound to the 60S ribosomal subunit.

B.J.Greber, D.Boehringer, C.Montellese, N.Ban.

ABSTRACT

Eukaryotic ribosome biogenesis requires many protein factors that facilitate the assembly, nuclear export and final maturation of 40S and 60S particles. We have biochemically characterized ribosomal complexes of the yeast 60S-biogenesis factor Arx1 and late-maturation factors Rei1 and Jjj1 and determined their cryo-EM structures. Arx1 was visualized bound to the 60S subunit together with Rei1, at 8.1-Å resolution, to reveal the molecular details of Arx1 binding whereby Arx1 arrests the eukaryotic-specific rRNA expansion segment 27 near the polypeptide tunnel exit. Rei1 and Jjj1, which have been implicated in Arx1 recycling, bind in the vicinity of Arx1 and form a network of interactions. We suggest that, in addition to the role of Arx1 during pre-60S nuclear export, the binding of Arx1 conformationally locks the pre-60S subunit and inhibits the premature association of nascent chain-processing factors to the polypeptide tunnel exit.