6YLH image
Deposition Date 2020-04-07
Release Date 2020-07-29
Last Version Date 2025-10-01
Entry Detail
PDB ID:
6YLH
Keywords:
RIBOSOME
Title:
Rix1-Rea1 pre-60S particle - full composite structure
Biological Source:
Source Organism:
Saccharomyces cerevisiae (Taxon ID: 4932)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.10 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6YLH 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
Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:B (auth: 2)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:C (auth: 3)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable metalloprotease ARX1
Gene (Uniprot):ARX1
Chain IDs:D (auth: 4)
Chain Length:593
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q03862
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rRNA-processing protein CGR1
Gene (Uniprot):CGR1
Chain IDs:E (auth: 5)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P53188 Pfam ID:PF03879
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-rRNA-processing protein RIX1
Gene (Uniprot):RIX1
Chain IDs:GB (auth: 6), HB (auth: 7)
Chain Length:763
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38883 Pfam ID:PF08167
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2-A
Gene (Uniprot):RPL2A
Chain IDs:F (auth: A)
Chain Length:149
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX45 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:G (auth: B)
Chain Length:647
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P14126 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4-A
Gene (Uniprot):RPL4A
Chain IDs:H (auth: C)
Chain Length:175
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P10664 Pfam ID:PF00573, PF14374
Structures with similar UniProt ID
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
UniProt ID:P26321 Pfam ID:PF17144, PF14204
Structures with similar UniProt ID
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
UniProt ID:Q02326 Pfam ID:PF01159
Structures with similar UniProt ID
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
UniProt ID:P05737 Pfam ID:PF08079, PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8-A
Gene (Uniprot):RPL8A
Chain IDs:L (auth: G)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P17076 Pfam ID:PF01248
Structures with similar UniProt ID
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
UniProt ID:P05738 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Bud site selection protein 20
Gene (Uniprot):BUD20
Chain IDs:N (auth: I)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q08004 Pfam ID:PF12171
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11-A
Gene (Uniprot):RPL11A
Chain IDs:O (auth: J)
Chain Length:174
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C0W9 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-rRNA-processing protein IPI1
Chain IDs:P (auth: K)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38803 Pfam ID:PF12333
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13-A
Gene (Uniprot):RPL13A
Chain IDs:Q (auth: L)
Chain Length:51
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12690 Pfam ID:PF01294
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14-A
Gene (Uniprot):RPL14A
Chain IDs:R (auth: M)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36105 Pfam ID:PF00467, PF01929
Structures with similar UniProt ID
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
UniProt ID:P05748 Pfam ID:PF00827
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16-A
Gene (Uniprot):RPL16A
Chain IDs:T (auth: O)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26784 Pfam ID:PF00572
Structures with similar UniProt ID
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
UniProt ID:P05740 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18-A
Gene (Uniprot):RPL18A
Chain IDs:V (auth: Q)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX49 Pfam ID:PF17135
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19-A
Gene (Uniprot):RPL19A
Chain IDs:W (auth: R)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX82 Pfam ID:PF01280
Structures with similar UniProt ID
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
UniProt ID:P0CX23 Pfam ID:PF01775
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21-A
Gene (Uniprot):RPL21A
Chain IDs:Y (auth: T)
Chain Length:767
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q02753 Pfam ID:PF01157
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22-A
Gene (Uniprot):RPL22A
Chain IDs:Z (auth: U)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05749 Pfam ID:PF01776
Structures with similar UniProt ID
Protein Blast
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
UniProt ID:P0CX41 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome assembly factor MRT4
Gene (Uniprot):MRT4
Chain IDs:BA (auth: W)
Chain Length:555
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P33201 Pfam ID:PF00466, PF17777
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Gene (Uniprot):RPL25
Chain IDs:CA (auth: X)
Chain Length:515
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04456 Pfam ID:PF03939, PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26-A
Gene (Uniprot):RPL26A
Chain IDs:DA (auth: Y)
Chain Length:245
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05743 Pfam ID:PF16906, PF00467
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27-A
Gene (Uniprot):RPL27A
Chain IDs:EA (auth: Z)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C2H6 Pfam ID:PF01777
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:FA (auth: a)
Chain Length:149
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P02406 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar GTP-binding protein 1
Gene (Uniprot):NOG1
Chain IDs:GA (auth: b)
Chain Length:647
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q02892 Pfam ID:PF17835, PF06858, PF08155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein ALB1
Chain IDs:HA (auth: c)
Chain Length:175
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P47019 Pfam ID:PF09135
Structures with similar UniProt ID
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
UniProt ID:P0C2H8 Pfam ID:PF01198
Structures with similar UniProt ID
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
UniProt ID:P38061 Pfam ID:PF01655
Structures with similar UniProt ID
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
UniProt ID:P05744 Pfam ID:PF01247
Structures with similar UniProt ID
Protein Blast
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
UniProt ID:P87262 Pfam ID:PF01199
Structures with similar UniProt ID
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
UniProt ID:P0CX84 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36-A
Gene (Uniprot):RPL36A
Chain IDs:NA (auth: i)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05745 Pfam ID:PF01158
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37-A
Gene (Uniprot):RPL37A
Chain IDs:OA (auth: j)
Chain Length:174
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P49166 Pfam ID:PF01907
Structures with similar UniProt ID
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
UniProt ID:P49167 Pfam ID:PF01781
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):RPL39
Chain IDs:QA (auth: l)
Chain Length:51
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04650 Pfam ID:PF00832
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar GTP-binding protein 2
Gene (Uniprot):NOG2
Chain IDs:RA (auth: m)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P53742 Pfam ID:PF08153, PF01926
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:SA (auth: n)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P14120 Pfam ID:PF01248
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L1-A
Gene (Uniprot):RPL1A
Chain IDs:TA (auth: o)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX43 Pfam ID:PF00687
Structures with similar UniProt ID
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
UniProt ID:P0CX25 Pfam ID:PF01780
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L12-A
Gene (Uniprot):RPL12A
Chain IDs:VA (auth: q)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX53 Pfam ID:PF03946, PF00298
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein NSA2
Chain IDs:WA (auth: r)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P40078 Pfam ID:PF01201
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nuclear GTP-binding protein NUG1
Gene (Uniprot):NUG1
Chain IDs:XA (auth: s)
Chain Length:172
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P40010 Pfam ID:PF08701, PF01926
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein SDA1
Gene (Uniprot):SDA1
Chain IDs:YA (auth: t)
Chain Length:767
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P53313 Pfam ID:PF08158, PF05285, PF21638
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein RLP24
Gene (Uniprot):RLP24
Chain IDs:ZA (auth: u)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q07915 Pfam ID:PF01246
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Midasin
Gene (Uniprot):MDN1
Chain IDs:DB (auth: v)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12019 Pfam ID:PF07728, PF17867, PF17865, PF21108
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-rRNA-processing protein IPI3
Gene (Uniprot):IPI3
Chain IDs:EB (auth: w), FB (auth: 0)
Chain Length:555
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P53877 Pfam ID:PF00400
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome assembly protein 4
Gene (Uniprot):RSA4
Chain IDs:AB (auth: x)
Chain Length:515
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P25382 Pfam ID:PF08154, PF00400
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 6
Gene (Uniprot):TIF6
Chain IDs:BB (auth: y)
Chain Length:245
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12522 Pfam ID:PF01912
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:UPF0642 protein YBL028C
Gene (Uniprot):YBL0423
Chain IDs:CB (auth: z)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38202 Pfam ID:PF10338
Ligand Molecules
GTP
MG
ZN
Primary Citation
Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis.
Mol.Cell 79 615 628.e5 (2020)
PMID: 32668200 DOI: 10.1016/j.molcel.2020.06.032

Abstact

Ribosome assembly is driven by numerous assembly factors, including the Rix1 complex and the AAA ATPase Rea1. These two assembly factors catalyze 60S maturation at two distinct states, triggering poorly understood large-scale structural transitions that we analyzed by cryo-electron microscopy. Two nuclear pre-60S intermediates were discovered that represent previously unknown states after Rea1-mediated removal of the Ytm1-Erb1 complex and reveal how the L1 stalk develops from a pre-mature nucleolar to a mature-like nucleoplasmic state. A later pre-60S intermediate shows how the central protuberance arises, assisted by the nearby Rix1-Rea1 machinery, which was solved in its pre-ribosomal context to molecular resolution. This revealed a Rix12-Ipi32 tetramer anchored to the pre-60S via Ipi1, strategically positioned to monitor this decisive remodeling. These results are consistent with a general underlying principle that temporarily stabilized immature RNA domains are successively remodeled by assembly factors, thereby ensuring failsafe assembly progression.

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Disease

Primary Citation of related structures
6YLH
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