5APN image
Deposition Date 2015-09-17
Release Date 2015-12-16
Last Version Date 2024-10-16
Entry Detail
PDB ID:
5APN
Keywords:
Title:
Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and N-terminally tagged Rei1
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.91 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:25S rRNA
Chain IDs:A (auth: 5)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:B (auth: 7)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:C (auth: 8)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2-A
Gene (Uniprot):RPL2A
Chain IDs:D (auth: A)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:E (auth: B)
Chain Length:387
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4-A
Gene (Uniprot):RPL4A
Chain IDs:F (auth: C)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Gene (Uniprot):RPL5
Chain IDs:G (auth: D)
Chain Length:113
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6-A
Gene (Uniprot):RPL6A
Chain IDs:H (auth: E)
Chain Length:176
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-A
Gene (Uniprot):RPL7A
Chain IDs:I (auth: F)
Chain Length:244
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8-A
Gene (Uniprot):RPL8A
Chain IDs:J (auth: G)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9-A
Gene (Uniprot):RPL9A
Chain IDs:K (auth: H)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10
Gene (Uniprot):RPL10
Chain IDs:L (auth: I)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11-A
Gene (Uniprot):RPL11A
Chain IDs:M (auth: J)
Chain Length:174
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13-A
Gene (Uniprot):RPL13A
Chain IDs:N (auth: L)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14-A
Gene (Uniprot):RPL14A
Chain IDs:O (auth: M)
Chain Length:128
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15-A
Gene (Uniprot):RPL15A
Chain IDs:P (auth: N)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16-A
Gene (Uniprot):RPL16A
Chain IDs:Q (auth: O)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17-A
Gene (Uniprot):RPL17A
Chain IDs:R (auth: P)
Chain Length:92
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18-A
Gene (Uniprot):RPL18A
Chain IDs:S (auth: Q)
Chain Length:312
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19-A
Gene (Uniprot):RPL19A
Chain IDs:T (auth: R)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L20-A
Gene (Uniprot):RPL20A
Chain IDs:U (auth: S)
Chain Length:172
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21-A
Gene (Uniprot):RPL21A
Chain IDs:V (auth: T)
Chain Length:160
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22-A
Gene (Uniprot):RPL22A
Chain IDs:W (auth: U)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23-A
Gene (Uniprot):RPL23A
Chain IDs:X (auth: V)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L24-A
Gene (Uniprot):RPL24A
Chain IDs:Y (auth: W)
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Gene (Uniprot):RPL25
Chain IDs:Z (auth: X)
Chain Length:616
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26-A
Gene (Uniprot):RPL26A
Chain IDs:AA (auth: Y)
Chain Length:414
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27-A
Gene (Uniprot):RPL27A
Chain IDs:BA (auth: Z)
Chain Length:85
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:CA (auth: a)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Gene (Uniprot):RPL29
Chain IDs:DA (auth: b)
Chain Length:387
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:EA (auth: c)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31-A
Gene (Uniprot):RPL31A
Chain IDs:FA (auth: d)
Chain Length:113
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Gene (Uniprot):RPL32
Chain IDs:GA (auth: e)
Chain Length:176
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L33-A
Gene (Uniprot):RPL33A
Chain IDs:HA (auth: f)
Chain Length:244
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34-A
Gene (Uniprot):RPL34A
Chain IDs:IA (auth: g)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35-A
Gene (Uniprot):RPL35A
Chain IDs:JA (auth: h)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36-A
Gene (Uniprot):RPL36A
Chain IDs:KA (auth: i)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37-A
Gene (Uniprot):RPL37A
Chain IDs:LA (auth: j)
Chain Length:174
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Gene (Uniprot):RPL38
Chain IDs:MA (auth: k)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):RPL39
Chain IDs:NA (auth: l)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-60S ribosomal protein L40
Gene (Uniprot):RPL40A
Chain IDs:OA (auth: m)
Chain Length:128
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L42-A
Gene (Uniprot):RPL42A
Chain IDs:PA (auth: o)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43-A
Gene (Uniprot):RPL43A
Chain IDs:QA (auth: p)
Chain Length:92
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:60S acidic ribosomal protein P0
Gene (Uniprot):RPP0
Chain IDs:RA (auth: q)
Chain Length:312
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Probable metalloprotease ARX1
Gene (Uniprot):ARX1
Chain IDs:SA (auth: x)
Chain Length:616
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Cytoplasmic 60S subunit biogenesis factor REI1
Gene (Uniprot):REI1
Chain IDs:TA (auth: y)
Chain Length:414
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:ALB1
Chain IDs:UA (auth: z)
Chain Length:85
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 164 91 ? (2015)
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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures