6EM4 image
Entry Detail
PDB ID:
6EM4
Keywords:
Title:
State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Biological Source:
PDB Version:
Deposition Date:
2017-10-01
Release Date:
2017-12-27
Method Details:
Experimental Method:
Resolution:
4.10 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:25S ribosomal RNA
Chain IDs:CA (auth: 1)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Description:5.8S ribosomal RNA
Chain IDs:DA (auth: 2)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Protein MAK16
Chain IDs:C (auth: 3)
Chain Length:306
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Ribosomal RNA-processing protein 1
Chain IDs:D (auth: 4)
Chain Length:278
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein NSA1
Chain IDs:E (auth: 5)
Chain Length:463
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polyribonucleotide
Description:internal transcribed spacer 1
Chain IDs:JA (auth: 6)
Chain Length:232
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein BRX1
Chain IDs:F (auth: A)
Chain Length:291
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L3
Chain IDs:K (auth: B)
Chain Length:387
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L4-A
Chain IDs:L (auth: C)
Chain Length:362
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:ATP-dependent RNA helicase HAS1
Chain IDs:EA (auth: D)
Chain Length:505
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L6-A
Chain IDs:N (auth: E)
Chain Length:176
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L7-A
Chain IDs:B (auth: F)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L8-A
Chain IDs:P (auth: G)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein ERB1
Chain IDs:KA (auth: H)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:rRNA-processing protein EBP2
Chain IDs:G (auth: J)
Chain Length:427
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Proteasome-interacting protein CIC1
Chain IDs:FA (auth: K)
Chain Length:376
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L13-A
Chain IDs:T (auth: L)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L14-A
Chain IDs:U (auth: M)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L15-A
Chain IDs:V (auth: N)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L16-A
Chain IDs:W (auth: O)
Chain Length:220
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L17-A
Chain IDs:X (auth: P)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L18-A
Chain IDs:Y (auth: Q)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L20-A
Chain IDs:Z (auth: S)
Chain Length:172
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L23-A
Chain IDs:AA (auth: V)
Chain Length:231
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L26-A
Chain IDs:BA (auth: Y)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L32
Chain IDs:M (auth: e)
Chain Length:176
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L33-A
Chain IDs:O (auth: f)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L35-A
Chain IDs:Q (auth: h)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36-B
Chain IDs:R (auth: i)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L37-A
Chain IDs:S (auth: j)
Chain Length:427
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Pescadillo homolog
Chain IDs:GA (auth: n)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein 15
Chain IDs:HA (auth: o)
Chain Length:220
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein RLP7
Chain IDs:IA (auth: t)
Chain Length:322
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein RLP24
Chain IDs:H (auth: u)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Nucleolar protein 16
Chain IDs:I (auth: v)
Chain Length:231
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Ribosome production factor 1
Chain IDs:A (auth: x)
Chain Length:295
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 6
Chain IDs:J (auth: y)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Ligand Molecules
Primary Citation
Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes.
Cell 171 1599 1610.e14 (2017)
PMID: 29245012 DOI: 10.1016/j.cell.2017.11.039

Abstact

Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural information, this process is poorly understood. Using cryo-EM, we solved structures of early 60S biogenesis intermediates at 3.3 Å to 4.5 Å resolution, thereby providing insights into their sequential folding and assembly pathway. Besides revealing distinct immature rRNA conformations, we map 25 assembly factors in six different assembly states. Notably, the Nsa1-Rrp1-Rpf1-Mak16 module stabilizes the solvent side of the 60S subunit, and the Erb1-Ytm1-Nop7 complex organizes and connects through Erb1's meandering N-terminal extension, eight assembly factors, three ribosomal proteins, and three 25S rRNA domains. Our structural snapshots reveal the order of integration and compaction of the six major 60S domains within early nucleolar 60S particles developing stepwise from the solvent side around the exit tunnel to the central protuberance.

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Primary Citation of related structures