8V87 image
Deposition Date 2023-12-04
Release Date 2024-05-01
Last Version Date 2024-05-01
Entry Detail
PDB ID:
8V87
Keywords:
Title:
60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map)
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.66 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:25S ribosomal RNA
Chain IDs:A (auth: 1)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polyribonucleotide
Molecule:5.8S ribosomal RNA
Chain IDs:B (auth: 2)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:ATP-dependent RNA helicase DBP10
Gene (Uniprot):DBP10
Chain IDs:C (auth: 3)
Chain Length:995
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polyribonucleotide
Molecule:ITS2 RNA
Chain IDs:D (auth: 6)
Chain Length:232
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:60S ribosomal subunit assembly/export protein LOC1
Gene (Uniprot):LOC1
Chain IDs:E (auth: 7)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Nucleolar complex protein 2
Gene (Uniprot):NOC2
Chain IDs:F (auth: 8)
Chain Length:710
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein BRX1
Gene (Uniprot):BRX1
Chain IDs:G (auth: A)
Chain Length:291
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:H (auth: B)
Chain Length:387
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4-A
Gene (Uniprot):RPL4A
Chain IDs:I (auth: C)
Chain Length:362
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:ATP-dependent RNA helicase HAS1
Gene (Uniprot):HAS1
Chain IDs:J (auth: D)
Chain Length:113
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6-A
Gene (Uniprot):RPL6A
Chain IDs:K (auth: E)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-A
Gene (Uniprot):RPL7A
Chain IDs:L (auth: F)
Chain Length:244
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL8A
Gene (Uniprot):RPL8A
Chain IDs:M (auth: G)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL6A
Gene (Uniprot):RPL9A
Chain IDs:N (auth: H)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Nucleolar complex-associated protein 3
Gene (Uniprot):NOC3
Chain IDs:O (auth: I)
Chain Length:663
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:rRNA-processing protein EBP2
Gene (Uniprot):EBP2
Chain IDs:P (auth: J)
Chain Length:427
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Proteasome-interacting protein CIC1
Gene (Uniprot):CIC1
Chain IDs:Q (auth: K)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13-A
Gene (Uniprot):RPL13A
Chain IDs:R (auth: L)
Chain Length:181
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14-A
Gene (Uniprot):RPL14A
Chain IDs:S (auth: M)
Chain Length:807
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL15A
Gene (Uniprot):RPL15A
Chain IDs:T (auth: N)
Chain Length:605
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13A
Gene (Uniprot):RPL16A
Chain IDs:U (auth: O)
Chain Length:220
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17-A
Gene (Uniprot):RPL17A
Chain IDs:V (auth: P)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18-A
Gene (Uniprot):RPL18A
Chain IDs:W (auth: Q)
Chain Length:618
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19-A
Gene (Uniprot):RPL19A
Chain IDs:X (auth: R)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL20A
Gene (Uniprot):RPL20A
Chain IDs:Y (auth: S)
Chain Length:520
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
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 BY4741
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23-A
Gene (Uniprot):RPL23A
Chain IDs:AA (auth: V)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Ribosome assembly factor MRT4
Gene (Uniprot):MRT4
Chain IDs:BA (auth: W)
Chain Length:841
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Gene (Uniprot):RPL25
Chain IDs:CA (auth: X)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
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 BY4741
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 BY4741
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL1A
Gene (Uniprot):RPL1A
Chain IDs:FA (auth: a)
Chain Length:291
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
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 BY4741
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 BY4741
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31-A
Gene (Uniprot):RPL31A
Chain IDs:IA (auth: d)
Chain Length:113
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
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 BY4741
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 BY4741
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34-A
Gene (Uniprot):RPL34A
Chain IDs:LA (auth: g)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35-A
Gene (Uniprot):RPL35A
Chain IDs:MA (auth: h)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36-A
Gene (Uniprot):RPL36A
Chain IDs:NA (auth: i)
Chain Length:663
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37-A
Gene (Uniprot):RPL37A
Chain IDs:OA (auth: j)
Chain Length:427
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
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 BY4741
Polymer Type:polypeptide(L)
Molecule:60S ribosome subunit biogenesis protein NIP7
Gene (Uniprot):NIP7
Chain IDs:QA (auth: l)
Chain Length:181
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein ERB1
Gene (Uniprot):ERB1
Chain IDs:RA (auth: m)
Chain Length:807
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Pescadillo homolog
Gene (Uniprot):NOP7
Chain IDs:SA (auth: n)
Chain Length:605
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein 15
Gene (Uniprot):NOP15
Chain IDs:TA (auth: o)
Chain Length:220
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:YTM1 isoform 1
Chain IDs:UA (auth: p)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:25S rRNA (cytosine(2870)-C(5))-methyltransferase
Gene (Uniprot):NOP2
Chain IDs:VA (auth: q)
Chain Length:618
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
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 BY4741
Polymer Type:polypeptide(L)
Molecule:Nuclear GTP-binding protein NUG1
Gene (Uniprot):NUG1
Chain IDs:XA (auth: s)
Chain Length:520
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein RLP7
Gene (Uniprot):RLP7
Chain IDs:YA (auth: t)
Chain Length:322
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein RLP24
Gene (Uniprot):RLP24
Chain IDs:ZA (auth: u)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 16
Gene (Uniprot):NOP16
Chain IDs:AB (auth: v)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
Polymer Type:polypeptide(L)
Molecule:27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
Gene (Uniprot):SPB1
Chain IDs:BB (auth: w)
Chain Length:841
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae BY4741
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 BY4741
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 BY4741
Primary Citation
The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis.
Nat Commun 15 3296 3296 (2024)
PMID: 38632236 DOI: 10.1038/s41467-024-47616-7

Abstact

DEAD-box ATPases play crucial roles in guiding rRNA restructuring events during the biogenesis of large (60S) ribosomal subunits, but their precise molecular functions are currently unknown. In this study, we present cryo-EM reconstructions of nucleolar pre-60S intermediates that reveal an unexpected, alternate secondary structure within the nascent peptidyl-transferase-center (PTC). Our analysis of three sequential nucleolar pre-60S intermediates reveals that the DEAD-box ATPase Dbp10/DDX54 remodels this alternate base pairing and enables the formation of the rRNA junction that anchors the mature form of the universally conserved PTC A-loop. Post-catalysis, Dbp10 captures rRNA helix H61, initiating the concerted exchange of biogenesis factors during late nucleolar 60S maturation. Our findings show that Dbp10 activity is essential for the formation of the ribosome active site and reveal how this function is integrated with subsequent assembly steps to drive the biogenesis of the large ribosomal subunit.

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Primary Citation of related structures