7OH3 image
Deposition Date 2021-05-08
Release Date 2021-11-03
Last Version Date 2024-07-10
Entry Detail
PDB ID:
7OH3
Keywords:
RIBOSOME
Title:
Nog1-TAP associated immature ribosomal particle population B from S. cerevisiae
Biological Source:
Source Organism:
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Taxon ID: 559292)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.40 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7OH3 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 (strain ATCC 204508 / 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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:rRNA-processing protein CGR1
Gene (Uniprot):CGR1
Chain IDs:D (auth: 5)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P53188 Pfam ID:PF03879
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2-A
Gene (Uniprot):RPL2A
Chain IDs:E (auth: A)
Chain Length:149
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:F (auth: B)
Chain Length:387
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:G (auth: C)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:H (auth: D)
Chain Length:113
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:I (auth: E)
Chain Length:176
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:J (auth: F)
Chain Length:244
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:K (auth: G)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:L (auth: H)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P05738 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
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 (strain ATCC 204508 / S288c)
UniProt ID:P0C0W9 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
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 (strain ATCC 204508 / S288c)
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:O (auth: M)
Chain Length:486
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:P (auth: N)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:Q (auth: O)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:R (auth: P)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:S (auth: Q)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:T (auth: R)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:U (auth: S)
Chain Length:520
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:V (auth: T)
Chain Length:160
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:W (auth: U)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:X (auth: V)
Chain Length:344
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:Y (auth: W)
Chain Length:236
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:Z (auth: X)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:AA (auth: Y)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:BA (auth: Z)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:CA (auth: a)
Chain Length:149
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:DA (auth: b)
Chain Length:387
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q02892 Pfam ID:PF17835, PF06858, PF08155
Structures with similar UniProt ID
Protein Blast
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 (strain ATCC 204508 / S288c)
UniProt ID:P14120 Pfam ID:PF01248
Structures with similar UniProt ID
Protein Blast
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 (strain ATCC 204508 / S288c)
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:GA (auth: e)
Chain Length:176
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:HA (auth: f)
Chain Length:244
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:IA (auth: g)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:JA (auth: h)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:KA (auth: i)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:LA (auth: j)
Chain Length:174
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:MA (auth: k)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:NA (auth: l)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:OA (auth: m)
Chain Length:486
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P53742 Pfam ID:PF08153, PF01926
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43-A
Gene (Uniprot):RPL43A
Chain IDs:PA (auth: p)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P0CX25 Pfam ID:PF01780
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein NSA2
Gene (Uniprot):NSA2
Chain IDs:QA (auth: r)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:RA (auth: s)
Chain Length:520
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P40010 Pfam ID:PF01926, PF08701
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein RLP24
Gene (Uniprot):RLP24
Chain IDs:SA (auth: u)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q07915 Pfam ID:PF01246
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein RPF2
Gene (Uniprot):RPF2
Chain IDs:TA (auth: v)
Chain Length:344
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P36160 Pfam ID:PF04427
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Regulator of ribosome biosynthesis
Gene (Uniprot):RRS1
Chain IDs:UA (auth: w)
Chain Length:236
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q08746 Pfam ID:PF04939
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome assembly protein 4
Gene (Uniprot):RSA4
Chain IDs:VA (auth: x)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:WA (auth: y)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:XA (auth: z)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P38202 Pfam ID:PF10338
Ligand Molecules
MG
ZN
Primary Citation
Analysis of subunit folding contribution of three yeast large ribosomal subunit proteins required for stabilisation and processing of intermediate nuclear rRNA precursors.
Plos One 16 e0252497 e0252497 (2021)
PMID: 34813592 DOI: 10.1371/journal.pone.0252497

Abstact

In yeast and human cells many of the ribosomal proteins (r-proteins) are required for the stabilisation and productive processing of rRNA precursors. Functional coupling of r-protein assembly with the stabilisation and maturation of subunit precursors potentially promotes the production of ribosomes with defined composition. To further decipher mechanisms of such an intrinsic quality control pathway we analysed here the contribution of three yeast large ribosomal subunit r-proteins rpL2 (uL2), rpL25 (uL23) and rpL34 (eL34) for intermediate nuclear subunit folding steps. Structure models obtained from single particle cryo-electron microscopy analyses provided evidence for specific and hierarchic effects on the stable positioning and remodelling of large ribosomal subunit domains. Based on these structural and previous biochemical data we discuss possible mechanisms of r-protein dependent hierarchic domain arrangement and the resulting impact on the stability of misassembled subunits.

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Protein

Chemical

Disease

Primary Citation of related structures
7OH3