7Z34 image
Deposition Date 2022-03-01
Release Date 2022-09-21
Last Version Date 2024-11-13
Entry Detail
PDB ID:
7Z34
Keywords:
RIBOSOME
Title:
Structure of pre-60S particle bound to DRG1(AFG2).
Biological Source:
Source Organism:
Saccharomyces cerevisiae S288C (Taxon ID: 559292)
Host Organism:
Saccharomyces cerevisiae BY4743
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.80 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7Z34 validation report
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Unknown peptide
Chain IDs:EB (auth: 0)
Chain Length:19
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polyribonucleotide
Molecule:35S pre-ribosomal RNA
Chain IDs:B (auth: 1)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:C (auth: 2)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:D (auth: 3)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable metalloprotease ARX1
Gene (Uniprot):ARX1
Chain IDs:E (auth: 4)
Chain Length:593
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q03862
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2-A
Gene (Uniprot):RPL2A
Chain IDs:F (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:ATPase family gene 2 protein
Gene (Uniprot):AFG2
Chain IDs:A (auth: Aa), RA (auth: m), SA (auth: n), XA (auth: t), AB (auth: w), BB (auth: x)
Chain Length:780
Number of Molecules:6
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P32794 Pfam ID:PF00004, PF17862
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:G (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:H (auth: C)
Chain Length:362
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:I (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:J (auth: E)
Chain Length:130
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:K (auth: F)
Chain Length:244
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:L (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:M (auth: H)
Chain Length:191
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:N (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:O (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 L28
Gene (Uniprot):RPL28
Chain IDs:P (auth: K)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P02406 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13-A
Gene (Uniprot):RPL13A
Chain IDs:Q (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:R (auth: M)
Chain Length:780
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:S (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:T (auth: O)
Chain Length:59
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:U (auth: P)
Chain Length:184
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:V (auth: Q)
Chain Length:106
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:W (auth: R)
Chain Length:189
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:X (auth: S)
Chain Length:172
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:Y (auth: T)
Chain Length:780
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:Z (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:AA (auth: V)
Chain Length:518
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:BA (auth: W)
Chain Length:236
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:CA (auth: X)
Chain Length:780
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:DA (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:EA (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 L12-A
Gene (Uniprot):RPL12A
Chain IDs:FA (auth: a)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX53 Pfam ID:PF03946, PF00298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar GTP-binding protein 1
Gene (Uniprot):NOG1
Chain IDs:GA (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:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:HA (auth: c)
Chain Length:362
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 L31-A
Gene (Uniprot):RPL31A
Chain IDs:IA (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:JA (auth: e)
Chain Length:130
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:KA (auth: f)
Chain Length:244
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:LA (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:MA (auth: h)
Chain Length:191
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:NA (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:OA (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:PA (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:QA (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:60S ribosomal protein L29
Gene (Uniprot):RPL29
Chain IDs:TA (auth: o)
Chain Length:59
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05747 Pfam ID:PF01779
Polymer Type:polypeptide(L)
Molecule:Unknown protein
Chain IDs:FB (auth: oC)
Chain Length:170
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C ATCC 204508 / S288c
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43-A
Gene (Uniprot):RPL43A
Chain IDs:UA (auth: p)
Chain Length:184
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 L42-A
Gene (Uniprot):RPL42A
Chain IDs:VA (auth: q)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX27 Pfam ID:PF00935
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein NSA2
Gene (Uniprot):NSA2
Chain IDs:WA (auth: r)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P40078 Pfam ID:PF01201
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein RLP24
Gene (Uniprot):RLP24
Chain IDs:YA (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:60S ribosomal export protein NMD3
Gene (Uniprot):NMD3
Chain IDs:ZA (auth: v)
Chain Length:518
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P38861 Pfam ID:PF04981, PF21193, PF21192
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 6
Gene (Uniprot):TIF6
Chain IDs:CB (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:DB (auth: z)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P38202 Pfam ID:PF10338
Ligand Molecules
AGS
MG
Primary Citation
Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1.
Nat.Struct.Mol.Biol. 29 942 953 (2022)
PMID: 36097293 DOI: 10.1038/s41594-022-00832-5

Abstact

The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation. The molecular mechanism of release remained elusive. Here, we report a series of cryo-EM structures that captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion segment ES27 form a joint docking platform that positions Drg1 for efficient extraction of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction by a hand-over-hand translocation mechanism. Our results uncover substrate recognition and processing by Drg1 step by step and provide a comprehensive mechanistic picture of the conserved modus operandi of AAA-ATPases.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
7Z34