ISDA

Deposition Date 2021-05-11

Release Date 2021-11-10

Last Version Date 2024-07-10

Entry Detail

PDB ID:

7OHR

Keywords:

RIBOSOME

Title:

Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae

Biological Source:

Source Organism:

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Taxon ID: 559292)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

4.72 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download 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:ITS2
Chain IDs:C (auth: 6)
Chain Length:232
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein BRX1
Gene (Uniprot):BRX1
Chain IDs:D (auth: A)
Chain Length:291
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q08235 Pfam ID:PF04427

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:E (auth: B)
Chain Length:387
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P14126 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4-A
Gene (Uniprot):RPL4A
Chain IDs:F (auth: C)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P10664 Pfam ID:PF00573, PF14374

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ATP-dependent RNA helicase HAS1
Gene (Uniprot):HAS1
Chain IDs:G (auth: D)
Chain Length:113
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q03532 Pfam ID:PF00270, PF00271, PF13959

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6-A
Gene (Uniprot):RPL6A
Chain IDs:H (auth: E)
Chain Length:176
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q02326 Pfam ID:PF01159

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-A
Gene (Uniprot):RPL7A
Chain IDs:I (auth: F)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / 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:J (auth: G)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P17076 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9-A
Gene (Uniprot):RPL9A
Chain IDs:K (auth: H)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05738 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Nucleolar complex-associated protein 3
Gene (Uniprot):NOC3
Chain IDs:L (auth: I)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q07896 Pfam ID:PF07540, PF03914

Protein Blast

Polymer Type:polypeptide(L)
Molecule:rRNA-processing protein EBP2
Gene (Uniprot):EBP2
Chain IDs:M (auth: J)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P36049 Pfam ID:PF05890

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Proteasome-interacting protein CIC1
Gene (Uniprot):CIC1
Chain IDs:N (auth: K)
Chain Length:376
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P38779 Pfam ID:PF00687

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 (strain ATCC 204508 / 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:807
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / 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:605
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / 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:220
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / 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:460
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / 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 (strain ATCC 204508 / 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:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / 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 (strain ATCC 204508 / S288c)

UniProt ID:P0CX23 Pfam ID:PF01775

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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23-A
Gene (Uniprot):RPL23A
Chain IDs:X (auth: V)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX41 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome assembly factor MRT4
Gene (Uniprot):MRT4
Chain IDs:Y (auth: W)
Chain Length:841
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P33201 Pfam ID:PF00466, PF17777

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

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

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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Nucleolar GTP-binding protein 1
Gene (Uniprot):NOG1
Chain IDs:CA (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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:DA (auth: c)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P14120 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31-A
Gene (Uniprot):RPL31A
Chain IDs:EA (auth: d)
Chain Length:113
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0C2H8 Pfam ID:PF01198

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Gene (Uniprot):RPL32
Chain IDs:FA (auth: e)
Chain Length:176
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P38061 Pfam ID:PF01655

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L33-A
Gene (Uniprot):RPL33A
Chain IDs:GA (auth: f)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05744 Pfam ID:PF01247

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34-A
Gene (Uniprot):RPL34A
Chain IDs:HA (auth: g)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P87262 Pfam ID:PF01199

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35-A
Gene (Uniprot):RPL35A
Chain IDs:IA (auth: h)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX84 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36-A
Gene (Uniprot):RPL36A
Chain IDs:JA (auth: i)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05745 Pfam ID:PF01158

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37-A
Gene (Uniprot):RPL37A
Chain IDs:KA (auth: j)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P49166 Pfam ID:PF01907

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Gene (Uniprot):RPL38
Chain IDs:LA (auth: k)
Chain Length:376
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P49167 Pfam ID:PF01781

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosome subunit biogenesis protein NIP7
Gene (Uniprot):NIP7
Chain IDs:MA (auth: l)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q08962 Pfam ID:PF17833, PF03657

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein ERB1
Gene (Uniprot):ERB1
Chain IDs:NA (auth: m)
Chain Length:807
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q04660 Pfam ID:PF08145, PF00400

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Pescadillo homolog
Gene (Uniprot):NOP7
Chain IDs:OA (auth: n)
Chain Length:605
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P53261 Pfam ID:PF06732, PF16589

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein 15
Gene (Uniprot):NOP15
Chain IDs:PA (auth: o)
Chain Length:220
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P53927 Pfam ID:PF00076

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein YTM1
Gene (Uniprot):YTM1
Chain IDs:QA (auth: p)
Chain Length:460
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q12024 Pfam ID:PF08154, PF00400

Protein Blast

Polymer Type:polypeptide(L)
Molecule:25S rRNA (cytosine(2870)-C(5))-methyltransferase
Gene (Uniprot):NOP2
Chain IDs:RA (auth: q)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P40991 Pfam ID:PF01189 EC:2.1.1.310

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein NSA2
Gene (Uniprot):NSA2
Chain IDs:SA (auth: r)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / 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 (strain ATCC 204508 / S288c)

UniProt ID:P40010 Pfam ID:PF08701, PF01926

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein RLP7
Gene (Uniprot):RLP7
Chain IDs:UA (auth: t)
Chain Length:322
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P40693 Pfam ID:PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein RLP24
Gene (Uniprot):RLP24
Chain IDs:VA (auth: u)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q07915 Pfam ID:PF01246

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 16
Gene (Uniprot):NOP16
Chain IDs:WA (auth: v)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P40007 Pfam ID:PF09420

Protein Blast

Polymer Type:polypeptide(L)
Molecule:27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
Gene (Uniprot):SPB1
Chain IDs:XA (auth: w)
Chain Length:841
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P25582 Pfam ID:PF01728, PF11861, PF07780 EC:2.1.1.167

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 (strain ATCC 204508 / S288c)

UniProt ID:Q12522 Pfam ID:PF01912

Ligand Molecules

Primary Citation

Analysis of subunit folding contribution of three yeast large ribosomal subunit proteins required for stabilisation and processing of intermediate nuclear rRNA precursors.

Poll, G, Pilsl, M, Griesenbeck, J, Tschochner, H, Milkereit, P.Show

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