5APO image
Entry Detail
PDB ID:
5APO
Keywords:
Title:
Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and C-terminally tagged Rei1
Biological Source:
PDB Version:
Deposition Date:
2015-09-17
Release Date:
2015-12-16
Method Details:
Experimental Method:
Resolution:
3.41 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:25S ribosomal RNA
Chain IDs:A (auth: 5)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polyribonucleotide
Description:5S ribosomal RNA
Chain IDs:B (auth: 7)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polyribonucleotide
Description:5.8S ribosomal RNA
Chain IDs:C (auth: 8)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L2-A
Chain IDs:D (auth: A)
Chain Length:149
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L3
Chain IDs:E (auth: B)
Chain Length:59
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L4-A
Chain IDs:F (auth: C)
Chain Length:362
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L5
Chain IDs:G (auth: D)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S RIBOSOMAL PROTEIN EL6
Chain IDs:H (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:I (auth: F)
Chain Length:244
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L8-A
Chain IDs:J (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:K (auth: H)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L10
Chain IDs:L (auth: I)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L11-A
Chain IDs:M (auth: J)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L13-A
Chain IDs:N (auth: L)
Chain Length:51
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L14-A
Chain IDs:O (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:P (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:Q (auth: O)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L17-A
Chain IDs:R (auth: P)
Chain Length:92
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L18-A
Chain IDs:S (auth: Q)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L19-A
Chain IDs:T (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:U (auth: S)
Chain Length:172
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L21-A
Chain IDs:V (auth: T)
Chain Length:160
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L22-A
Chain IDs:W (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:X (auth: V)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L24-A
Chain IDs:Y (auth: W)
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L25
Chain IDs:Z (auth: X)
Chain Length:616
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L26-A
Chain IDs:AA (auth: Y)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27-A
Chain IDs:BA (auth: Z)
Chain Length:95
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L28
Chain IDs:CA (auth: a)
Chain Length:149
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L29
Chain IDs:DA (auth: b)
Chain Length:59
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L30
Chain IDs:EA (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:FA (auth: d)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L32
Chain IDs:GA (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:HA (auth: f)
Chain Length:244
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L34-A
Chain IDs:IA (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:JA (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:KA (auth: i)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L37-A
Chain IDs:LA (auth: j)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L38
Chain IDs:MA (auth: k)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L39
Chain IDs:NA (auth: l)
Chain Length:51
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Ubiquitin-60S ribosomal protein L40
Chain IDs:OA (auth: m)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L42-A
Chain IDs:PA (auth: o)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L43-A
Chain IDs:QA (auth: p)
Chain Length:92
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:60S acidic ribosomal protein P0
Chain IDs:RA (auth: q)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Probable metalloprotease ARX1
Chain IDs:SA (auth: x)
Chain Length:616
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:CYTOPLASMIC 60S SUBUNIT BIOGENESIS FACTOR REI1
Chain IDs:TA (auth: y)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:ALB1
Chain IDs:UA (auth: z)
Chain Length:95
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Primary Citation
Insertion of the Biogenesis Factor Rei1 Probes the Ribosomal Tunnel during 60S Maturation.
Cell(Cambridge,Mass.) 164 91 102 (2016)
PMID: 26709046 DOI: 10.1016/j.cell.2015.11.027

Abstact

Eukaryotic ribosome biogenesis depends on several hundred assembly factors to produce functional 40S and 60S ribosomal subunits. The final phase of 60S subunit biogenesis is cytoplasmic maturation, which includes the proofreading of functional centers of the 60S subunit and the release of several ribosome biogenesis factors. We report the cryo-electron microscopy (cryo-EM) structure of the yeast 60S subunit in complex with the biogenesis factors Rei1, Arx1, and Alb1 at 3.4 Å resolution. In addition to the network of interactions formed by Alb1, the structure reveals a mechanism for ensuring the integrity of the ribosomal polypeptide exit tunnel. Arx1 probes the entire set of inner-ring proteins surrounding the tunnel exit, and the C terminus of Rei1 is deeply inserted into the ribosomal tunnel, where it forms specific contacts along almost its entire length. We provide genetic and biochemical evidence that failure to insert the C terminus of Rei1 precludes subsequent steps of 60S maturation.

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