6ELZ image
Entry Detail
PDB ID:
6ELZ
EMDB ID:
Keywords:
Title:
State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Biological Source:
PDB Version:
Deposition Date:
2017-09-30
Release Date:
2017-12-27
Method Details:
Experimental Method:
Resolution:
3.30 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:25S ribosomal RNA
Chain IDs:A (auth: 1)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polyribonucleotide
Description:5.8S ribosomal RNA
Chain IDs:B (auth: 2)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polyribonucleotide
Description:Internal transcribed spacer 2
Chain IDs:C (auth: 6)
Chain Length:232
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein BRX1
Chain IDs:EA (auth: A)
Chain Length:291
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L3
Chain IDs:BA (auth: B)
Chain Length:647
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L4-A
Chain IDs:CA (auth: C)
Chain Length:362
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:ATP-dependent RNA helicase HAS1
Chain IDs:HA (auth: D)
Chain Length:505
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L6-A
Chain IDs:ZA (auth: E)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L7-A
Chain IDs:AA (auth: F)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L8-A
Chain IDs:AB (auth: G)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L9-A
Chain IDs:DA (auth: H)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Nucleolar complex-associated protein 3
Chain IDs:XA (auth: I)
Chain Length:663
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:rRNA-processing protein EBP2
Chain IDs:YA (auth: J)
Chain Length:427
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Proteasome-interacting protein CIC1
Chain IDs:FA (auth: K)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L13-A
Chain IDs:D (auth: L)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L14-A
Chain IDs:BB (auth: M)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L15-A
Chain IDs:E (auth: N)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L16-A
Chain IDs:T (auth: O)
Chain Length:220
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L17-A
Chain IDs:W (auth: P)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L18-A
Chain IDs:F (auth: Q)
Chain Length:618
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L19-A
Chain IDs:G (auth: R)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L20-A
Chain IDs:H (auth: S)
Chain Length:520
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L21-A
Chain IDs:I (auth: T)
Chain Length:322
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L22-A
Chain IDs:J (auth: U)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L23-A
Chain IDs:U (auth: V)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Ribosome assembly factor MRT4
Chain IDs:IA (auth: W)
Chain Length:841
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L25
Chain IDs:X
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L26-A
Chain IDs:Y
Chain Length:245
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27-A
Chain IDs:K (auth: Z)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L28
Chain IDs:V (auth: a)
Chain Length:291
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Nucleolar GTP-binding protein 1
Chain IDs:KA (auth: b)
Chain Length:647
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L30
Chain IDs:L (auth: c)
Chain Length:362
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L31-A
Chain IDs:M (auth: d)
Chain Length:505
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L32
Chain IDs:N (auth: e)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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 S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L34-A
Chain IDs:P (auth: g)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L35-A
Chain IDs:Z (auth: h)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36-A
Chain IDs:Q (auth: i)
Chain Length:663
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L37-A
Chain IDs:R (auth: j)
Chain Length:427
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L38
Chain IDs:S (auth: k)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosome subunit biogenesis protein NIP7
Chain IDs:JA (auth: l)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein ERB1
Chain IDs:GA (auth: m)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Pescadillo homolog
Chain IDs:MA (auth: n)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein 15
Chain IDs:LA (auth: o)
Chain Length:220
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein YTM1
Chain IDs:SA (auth: p)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:25S rRNA (cytosine(2870)-C(5))-methyltransferase
Chain IDs:TA (auth: q)
Chain Length:618
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein NSA2
Chain IDs:NA (auth: r)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Nuclear GTP-binding protein NUG1
Chain IDs:OA (auth: s)
Chain Length:520
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein RLP7
Chain IDs:PA (auth: t)
Chain Length:322
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein RLP24
Chain IDs:UA (auth: u)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Nucleolar protein 16
Chain IDs:VA (auth: v)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
Chain IDs:WA (auth: w)
Chain Length:841
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 6
Chain IDs:QA (auth: y)
Chain Length:245
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:UPF0642 protein YBL028C
Chain IDs:RA (auth: z)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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