PDBsum entry 5z3g

Ribosome

PDB id: 5z3g

Contents

Protein chains

247 a.a.

133 a.a.

336 a.a.

361 a.a.

256 a.a.

150 a.a.

239 a.a.

162 a.a.

191 a.a.

371 a.a.

226 a.a.

190 a.a.

108 a.a.

137 a.a.

175 a.a.

197 a.a.

136 a.a.

134 a.a.

392 a.a.

170 a.a.

202 a.a.

438 a.a.

169 a.a.

212 a.a.

82 a.a.

125 a.a.

154 a.a.

124 a.a.

106 a.a.

117 a.a.

67 a.a.

72 a.a.

DNA/RNA

PDB id:

5z3g

Name:

Ribosome

Title:

Cryo-em structure of a nucleolar pre-60s ribosome (rpf1-tap)

Structure:

25s rrna. Chain: a. 5.8s rrna. Chain: b. Its2 RNA. Chain: c. Ribosome biogenesis protein rlp7. Chain: d. Synonym: ribosomal protein l7-like.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Saccharomyces cerevisiae s288c. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Strain: atcc 204508 / s288c

Authors:

X.Zhu,D.Zhou,K.Ye

Key ref:

D.Zhou et al. (2019). Cryo-EM structure of an early precursor of large ribosomal subunit reveals a half-assembled intermediate. Protein Cell, 10, 120-130. PubMed id: 29557065 DOI: 10.1007/s13238-018-0526-7

Date:

06-Jan-18 Release date: 11-Apr-18

Protein chain

P40693  (RLP7_YEAST) -  Ribosome biogenesis protein RLP7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 322 a.a.

Struc: 247 a.a.

Protein chain

P53927  (NOP15_YEAST) -  Ribosome biogenesis protein 15 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 220 a.a.

Struc: 133 a.a.

Protein chain

P14126  (RL3_YEAST) -  Large ribosomal subunit protein uL3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 387 a.a.

Struc: 336 a.a.

Protein chain

P10664  (RL4A_YEAST) -  Large ribosomal subunit protein uL4A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 362 a.a.

Struc: 361 a.a.

Protein chain

P38779  (CIC1_YEAST) -  Proteasome-interacting protein CIC1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 376 a.a.

Struc: 256 a.a.

Protein chain

Q02326  (RL6A_YEAST) -  Large ribosomal subunit protein eL6A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 176 a.a.

Struc: 150 a.a.

Protein chain

P05737  (RL7A_YEAST) -  Large ribosomal subunit protein uL30A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 244 a.a.

Struc: 239 a.a.

Protein chain

P17076  (RL8A_YEAST) -  Large ribosomal subunit protein eL8A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 256 a.a.

Struc: 162 a.a.

Protein chain

P05738  (RL9A_YEAST) -  Large ribosomal subunit protein uL6A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 191 a.a.

Struc: 191 a.a.

Protein chain

P53261  (PESC_YEAST) -  Pescadillo homolog from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 605 a.a.

Struc: 371 a.a.

Protein chain

Q12522  (IF6_YEAST) -  Eukaryotic translation initiation factor 6 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 245 a.a.

Struc: 226 a.a.

Protein chain

P38805  (RPF1_YEAST) -  Ribosome production factor 1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 295 a.a.

Struc: 190 a.a.

Protein chain

Q12690  (RL13A_YEAST) -  Large ribosomal subunit protein eL13A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 199 a.a.

Struc: 108 a.a.

Protein chain

P36105  (RL14A_YEAST) -  Large ribosomal subunit protein eL14A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 138 a.a.

Struc: 137 a.a.

Protein chain

P05748  (RL15A_YEAST) -  Large ribosomal subunit protein eL15A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 204 a.a.

Struc: 175 a.a.

Protein chain

P26784  (RL16A_YEAST) -  Large ribosomal subunit protein uL13A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 199 a.a.

Struc: 197 a.a.

Protein chain

P05740  (RL17A_YEAST) -  Large ribosomal subunit protein uL22A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 184 a.a.

Struc: 136 a.a.

Protein chain

P0CX49  (RL18A_YEAST) -  Large ribosomal subunit protein eL18A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 186 a.a.

Struc: 134 a.a.

Protein chain

P53136  (NSA1_YEAST) -  Ribosome biogenesis protein NSA1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 463 a.a.

Struc: 392 a.a.

Protein chain

P0CX23  (RL20A_YEAST) -  Large ribosomal subunit protein eL20A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 172 a.a.

Struc: 170 a.a.

Protein chain

P35178  (RRP1_YEAST) -  Ribosomal RNA-processing protein 1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 278 a.a.

Struc: 202 a.a.

Protein chain

Q03532  (HAS1_YEAST) -  ATP-dependent RNA helicase HAS1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 505 a.a.

Struc: 438 a.a.

Protein chain

P10962  (MAK16_YEAST) -  Protein MAK16 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 306 a.a.

Struc: 169 a.a.

Protein chain

Q08235  (BRX1_YEAST) -  Ribosome biogenesis protein BRX1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 291 a.a.

Struc: 212 a.a.

Protein chain

P36049  (EBP2_YEAST) -  rRNA-processing protein EBP2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 427 a.a.

Struc: 82 a.a.

Protein chain

P05743  (RL26A_YEAST) -  Large ribosomal subunit protein uL24A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 127 a.a.

Struc: 125 a.a.

Protein chain

No UniProt id for this chain

Struc: 154 a.a.

Protein chain

P38061  (RL32_YEAST) -  Large ribosomal subunit protein eL32 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 130 a.a.

Struc: 124 a.a.

Protein chain

P05744  (RL33A_YEAST) -  Large ribosomal subunit protein eL33A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 107 a.a.

Struc: 106 a.a.

Protein chain

P0CX84  (RL35A_YEAST) -  Large ribosomal subunit protein uL29A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 120 a.a.

Struc: 117 a.a.

Protein chain

P05745  (RL36A_YEAST) -  Large ribosomal subunit protein eL36A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 100 a.a.

Struc: 67 a.a.

Protein chain

P49166  (RL37A_YEAST) -  Large ribosomal subunit protein eL37A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 88 a.a.

Struc: 72 a.a.

DNA/RNA chains

G-U-U-U-G-A-C-C-U-C-A-A-A-U-C-A-G-G-U-A-G-G-A-G-U-A-C-C-C-G-C-U-G-A-A-C-U-U-A- ... 1501 bases

A-A-A-C-U-U-U-C-A-A-C-A-A-C-G-G-A-U-C-U-C-U-U-G-G-U-U-C-U-C-G-C-A-U-C-G-A-U-G- 156 bases

C-C-U-U-C-U-C-A-A-A-C-A-U-U-C-U-G-U-U-U-G-G-U-A-G-U-G-A-G-U-G-A-U-A-C-U-C-U-U- 65 bases

Enzyme reactions

• Enzyme class: Chain Y: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1007/s13238-018-0526-7

Protein Cell 10:120-130 (2019)

PubMed id: 29557065

Cryo-EM structure of an early precursor of large ribosomal subunit reveals a half-assembled intermediate.

D.Zhou, X.Zhu, S.Zheng, D.Tan, M.Q.Dong, K.Ye.

ABSTRACT

Assembly of eukaryotic ribosome is a complicated and dynamic process that involves a series of intermediates. It is unknown how the highly intertwined structure of 60S large ribosomal subunits is established. Here, we report the structure of an early nucleolar pre-60S ribosome determined by cryo-electron microscopy at 3.7 Å resolution, revealing a half-assembled subunit. Domains I, II and VI of 25S/5.8S rRNA pack tightly into a native-like substructure, but domains III, IV and V are not assembled. The structure contains 12 assembly factors and 19 ribosomal proteins, many of which are required for early processing of large subunit rRNA. The Brx1-Ebp2 complex would interfere with the assembly of domains IV and V. Rpf1, Mak16, Nsa1 and Rrp1 form a cluster that consolidates the joining of domains I and II. Our structure reveals a key intermediate on the path to establishing the global architecture of 60S subunits.