6YLH image
Entry Detail
PDB ID:
6YLH
EMDB ID:
Keywords:
Title:
Rix1-Rea1 pre-60S particle - full composite structure
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2020-04-07
Release Date:
2020-07-29
Method Details:
Experimental Method:
Resolution:
3.10 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:25S rRNA
Chain IDs:A (auth: 1)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Description:5.8S rRNA
Chain IDs:B (auth: 2)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Description:5S rRNA
Chain IDs:C (auth: 3)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Probable metalloprotease ARX1
Chain IDs:D (auth: 4)
Chain Length:593
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:rRNA-processing protein CGR1
Chain IDs:E (auth: 5)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Pre-rRNA-processing protein RIX1
Chain IDs:GB (auth: 6), HB (auth: 7)
Chain Length:763
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L2-A
Chain IDs:F (auth: A)
Chain Length:149
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L3
Chain IDs:G (auth: B)
Chain Length:647
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L4-A
Chain IDs:H (auth: C)
Chain Length:175
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L5
Chain IDs:I (auth: D)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L6-A
Chain IDs:J (auth: E)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L7-A
Chain IDs:K (auth: F)
Chain Length:244
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L8-A
Chain IDs:L (auth: G)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L9-A
Chain IDs:M (auth: H)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Bud site selection protein 20
Chain IDs:N (auth: I)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L11-A
Chain IDs:O (auth: J)
Chain Length:174
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Pre-rRNA-processing protein IPI1
Chain IDs:P (auth: K)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L13-A
Chain IDs:Q (auth: L)
Chain Length:51
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L14-A
Chain IDs:R (auth: M)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L15-A
Chain IDs:S (auth: N)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L16-A
Chain IDs:T (auth: O)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L17-A
Chain IDs:U (auth: P)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L18-A
Chain IDs:V (auth: Q)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L19-A
Chain IDs:W (auth: R)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L20-A
Chain IDs:X (auth: S)
Chain Length:172
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L21-A
Chain IDs:Y (auth: T)
Chain Length:767
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L22-A
Chain IDs:Z (auth: U)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L23-A
Chain IDs:AA (auth: V)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Ribosome assembly factor MRT4
Chain IDs:BA (auth: W)
Chain Length:555
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L25
Chain IDs:CA (auth: X)
Chain Length:515
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L26-A
Chain IDs:DA (auth: Y)
Chain Length:245
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27-A
Chain IDs:EA (auth: Z)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L28
Chain IDs:FA (auth: a)
Chain Length:149
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Nucleolar GTP-binding protein 1
Chain IDs:GA (auth: b)
Chain Length:647
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein ALB1
Chain IDs:HA (auth: c)
Chain Length:175
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L31-A
Chain IDs:IA (auth: d)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L32
Chain IDs:JA (auth: e)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L33-A
Chain IDs:KA (auth: f)
Chain Length:244
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L34-A
Chain IDs:LA (auth: g)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L35-A
Chain IDs:MA (auth: h)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36-A
Chain IDs:NA (auth: i)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L37-A
Chain IDs:OA (auth: j)
Chain Length:174
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L38
Chain IDs:PA (auth: k)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L39
Chain IDs:QA (auth: l)
Chain Length:51
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Nucleolar GTP-binding protein 2
Chain IDs:RA (auth: m)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L30
Chain IDs:SA (auth: n)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L1-A
Chain IDs:TA (auth: o)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L43-A
Chain IDs:UA (auth: p)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L12-A
Chain IDs:VA (auth: q)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein NSA2
Chain IDs:WA (auth: r)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Nuclear GTP-binding protein NUG1
Chain IDs:XA (auth: s)
Chain Length:172
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Protein SDA1
Chain IDs:YA (auth: t)
Chain Length:767
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein RLP24
Chain IDs:ZA (auth: u)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Midasin
Chain IDs:DB (auth: v)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Pre-rRNA-processing protein IPI3
Chain IDs:EB (auth: w), FB (auth: 0)
Chain Length:555
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Ribosome assembly protein 4
Chain IDs:AB (auth: x)
Chain Length:515
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 6
Chain IDs:BB (auth: y)
Chain Length:245
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:UPF0642 protein YBL028C
Chain IDs:CB (auth: z)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Primary Citation
Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis.
Mol.Cell 79 615 628.e5 (2020)
PMID: 32668200 DOI: 10.1016/j.molcel.2020.06.032

Abstact

Ribosome assembly is driven by numerous assembly factors, including the Rix1 complex and the AAA ATPase Rea1. These two assembly factors catalyze 60S maturation at two distinct states, triggering poorly understood large-scale structural transitions that we analyzed by cryo-electron microscopy. Two nuclear pre-60S intermediates were discovered that represent previously unknown states after Rea1-mediated removal of the Ytm1-Erb1 complex and reveal how the L1 stalk develops from a pre-mature nucleolar to a mature-like nucleoplasmic state. A later pre-60S intermediate shows how the central protuberance arises, assisted by the nearby Rix1-Rea1 machinery, which was solved in its pre-ribosomal context to molecular resolution. This revealed a Rix12-Ipi32 tetramer anchored to the pre-60S via Ipi1, strategically positioned to monitor this decisive remodeling. These results are consistent with a general underlying principle that temporarily stabilized immature RNA domains are successively remodeled by assembly factors, thereby ensuring failsafe assembly progression.

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Primary Citation of related structures