7UG6 image
Deposition Date 2022-03-24
Release Date 2022-12-21
Last Version Date 2024-06-12
Entry Detail
PDB ID:
7UG6
Keywords:
RIBOSOME
Title:
Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922
Biological Source:
Source Organism:
Saccharomyces cerevisiae S288C (Taxon ID: 559292)
Host Organism:
Saccharomyces cerevisiae S288C
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.90 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7UG6 validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:25S rRNA
Chain IDs:A (auth: 1)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:B (auth: 2)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:C (auth: 3)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:D (auth: 7)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P14120 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2-A
Gene (Uniprot):RPL2A
Chain IDs:E (auth: A)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX45 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:F (auth: B)
Chain Length:387
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P14126 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4-A
Gene (Uniprot):RPL4A
Chain IDs:G (auth: C)
Chain Length:175
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P10664 Pfam ID:PF00573, PF14374
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Gene (Uniprot):RPL5
Chain IDs:H (auth: D)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P26321 Pfam ID:PF17144, PF14204
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6-A
Gene (Uniprot):RPL6A
Chain IDs:I (auth: E)
Chain Length:176
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q02326 Pfam ID:PF01159
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-A
Gene (Uniprot):RPL7A
Chain IDs:J (auth: F)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05737 Pfam ID:PF08079, PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8-A
Gene (Uniprot):RPL8A
Chain IDs:K (auth: G)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P17076 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9-A
Gene (Uniprot):RPL9A
Chain IDs:L (auth: H)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05738 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Bud site selection protein 20
Gene (Uniprot):BUD20
Chain IDs:M (auth: I)
Chain Length:166
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q08004 Pfam ID:PF12171
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11-A
Gene (Uniprot):RPL11A
Chain IDs:N (auth: J)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0C0W9 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13-A
Gene (Uniprot):RPL13A
Chain IDs:O (auth: L)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q12690 Pfam ID:PF01294
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14-A
Gene (Uniprot):RPL14A
Chain IDs:P (auth: M)
Chain Length:519
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P36105 Pfam ID:PF00467, PF01929
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15-A
Gene (Uniprot):RPL15A
Chain IDs:Q (auth: N)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05748 Pfam ID:PF00827
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16-A
Gene (Uniprot):RPL16A
Chain IDs:R (auth: O)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P26784 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17-A
Gene (Uniprot):RPL17A
Chain IDs:S (auth: P)
Chain Length:92
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05740 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18-A
Gene (Uniprot):RPL18A
Chain IDs:T (auth: Q)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX49 Pfam ID:PF17135
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19-A
Gene (Uniprot):RPL19A
Chain IDs:U (auth: R)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX82 Pfam ID:PF01280
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L20-A
Gene (Uniprot):RPL20A
Chain IDs:V (auth: S)
Chain Length:520
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX23 Pfam ID:PF01775
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21-A
Gene (Uniprot):RPL21A
Chain IDs:W (auth: T)
Chain Length:160
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q02753 Pfam ID:PF01157
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22-A
Gene (Uniprot):RPL22A
Chain IDs:X (auth: U)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05749 Pfam ID:PF01776
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23-A
Gene (Uniprot):RPL23A
Chain IDs:Y (auth: V)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX41 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome assembly factor MRT4
Gene (Uniprot):MRT4
Chain IDs:Z (auth: W)
Chain Length:203
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P33201 Pfam ID:PF00466, PF17777
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Gene (Uniprot):RPL25
Chain IDs:AA (auth: X)
Chain Length:514
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P04456 Pfam ID:PF03939, PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26-A
Gene (Uniprot):RPL26A
Chain IDs:BA (auth: Y)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05743 Pfam ID:PF16906, PF00467
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27-A
Gene (Uniprot):RPL27A
Chain IDs:CA (auth: Z)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0C2H6 Pfam ID:PF01777
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:DA (auth: a)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P02406 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar GTP-binding protein 1
Gene (Uniprot):NOG1
Chain IDs:EA (auth: b)
Chain Length:387
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q02892 Pfam ID:PF17835, PF06858, PF08155
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein ALB1
Gene (Uniprot):ALB1
Chain IDs:FA (auth: c)
Chain Length:175
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P47019 Pfam ID:PF09135
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31-A
Gene (Uniprot):RPL31A
Chain IDs:GA (auth: d)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0C2H8 Pfam ID:PF01198
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Gene (Uniprot):RPL32
Chain IDs:HA (auth: e)
Chain Length:176
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P38061 Pfam ID:PF01655
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L33-A
Gene (Uniprot):RPL33A
Chain IDs:IA (auth: f)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05744 Pfam ID:PF01247
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34-A
Gene (Uniprot):RPL34A
Chain IDs:JA (auth: g)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P87262 Pfam ID:PF01199
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35-A
Gene (Uniprot):RPL35A
Chain IDs:KA (auth: h)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX84 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36-A
Gene (Uniprot):RPL36A
Chain IDs:LA (auth: i)
Chain Length:166
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05745 Pfam ID:PF01158
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37-A
Gene (Uniprot):RPL37A
Chain IDs:MA (auth: j)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P49166 Pfam ID:PF01907
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Gene (Uniprot):RPL38
Chain IDs:NA (auth: k)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P49167 Pfam ID:PF01781
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):RPL39
Chain IDs:OA (auth: l)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P04650 Pfam ID:PF00832
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar GTP-binding protein 2
Gene (Uniprot):NOG2
Chain IDs:PA (auth: m)
Chain Length:519
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P53742 Pfam ID:PF08153, PF01926
Protein Blast
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
UniProt ID:P0CX25 Pfam ID:PF01780
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L12-A
Gene (Uniprot):RPL12A
Chain IDs:RA (auth: q)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX53 Pfam ID:PF03946, PF00298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein NSA2
Gene (Uniprot):NSA2
Chain IDs:SA (auth: r)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P40078 Pfam ID:PF01201
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nuclear GTP-binding protein NUG1
Gene (Uniprot):NUG1
Chain IDs:TA (auth: s)
Chain Length:520
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P40010 Pfam ID:PF08701, PF01926
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein RLP24
Gene (Uniprot):RLP24
Chain IDs:UA (auth: u)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q07915 Pfam ID:PF01246
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein RPF2
Gene (Uniprot):RPF2
Chain IDs:VA (auth: v)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P36160 Pfam ID:PF04427
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Regulator of ribosome biosynthesis
Gene (Uniprot):RRS1
Chain IDs:WA (auth: w)
Chain Length:203
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q08746 Pfam ID:PF04939
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome assembly protein 4
Gene (Uniprot):RSA4
Chain IDs:XA (auth: x)
Chain Length:514
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P25382 Pfam ID:PF08154, PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 6
Gene (Uniprot):TIF6
Chain IDs:YA (auth: y)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q12522 Pfam ID:PF01912
Protein Blast
Polymer Type:polypeptide(L)
Molecule:UPF0642 protein YBL028C
Gene (Uniprot):YBL0423
Chain IDs:ZA (auth: z)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P38202 Pfam ID:PF10338
Ligand Molecules
GDP
MG
Primary Citation
A single 2'-O-methylation of ribosomal RNA gates assembly of a functional ribosome.
Nat.Struct.Mol.Biol. 30 91 98 (2023)
PMID: 36536102 DOI: 10.1038/s41594-022-00891-8

Abstact

RNA modifications are widespread in biology and abundant in ribosomal RNA. However, the importance of these modifications is not well understood. We show that methylation of a single nucleotide, in the catalytic center of the large subunit, gates ribosome assembly. Massively parallel mutational scanning of the essential nuclear GTPase Nog2 identified important interactions with rRNA, particularly with the 2'-O-methylated A-site base Gm2922. We found that methylation of G2922 is needed for assembly and efficient nuclear export of the large subunit. Critically, we identified single amino acid changes in Nog2 that completely bypass dependence on G2922 methylation and used cryoelectron microscopy to directly visualize how methylation flips Gm2922 into the active site channel of Nog2. This work demonstrates that a single RNA modification is a critical checkpoint in ribosome biogenesis, suggesting that such modifications can play an important role in regulation and assembly of macromolecular machines.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
7UG6