ISDA

Deposition Date 2021-05-11

Release Date 2021-11-03

Last Version Date 2024-07-10

Entry Detail

PDB ID:

7OHQ

Keywords:

RIBOSOME

Title:

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

Biological Source:

Source Organism:

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

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.10 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: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

Polymer Type:polyribonucleotide
Molecule:ITS2
Chain IDs:E (auth: 6)
Chain Length:232
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

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 (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:G (auth: B)
Chain Length:647
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:H (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:I (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:J (auth: E)
Chain Length:130
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:K (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:L (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:M (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:N (auth: J)
Chain Length:88
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:Proteasome-interacting protein CIC1
Gene (Uniprot):CIC1
Chain IDs:O (auth: K)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P38779 Pfam ID:PF00687

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13-A
Gene (Uniprot):RPL13A
Chain IDs:P (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:Q (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:R (auth: N)
Chain Length:605
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:S (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:T (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:U (auth: Q)
Chain Length:455
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:V (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:W (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:X (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:Y (auth: U)
Chain Length:199
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:Z (auth: V)
Chain Length:137
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:AA (auth: W)
Chain Length:203
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:BA (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:CA (auth: Y)
Chain Length:245
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:DA (auth: Z)
Chain Length:106
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:EA (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:FA (auth: b)
Chain Length:647
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:GA (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:HA (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:IA (auth: e)
Chain Length:130
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:JA (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:KA (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:LA (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:MA (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:NA (auth: j)
Chain Length:88
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:OA (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:PA (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:QA (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:Pescadillo homolog
Gene (Uniprot):NOP7
Chain IDs:RA (auth: n)
Chain Length:605
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P53261 Pfam ID:PF06732, PF16589

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein 15
Gene (Uniprot):NOP15
Chain IDs:SA (auth: o)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P53927 Pfam ID:PF00076

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43-A
Gene (Uniprot):RPL43A
Chain IDs:TA (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 NOP53
Gene (Uniprot):NOP53
Chain IDs:UA (auth: q)
Chain Length:455
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q12080 Pfam ID:PF07767

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein NSA2
Gene (Uniprot):NSA2
Chain IDs:VA (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:WA (auth: s)
Chain Length:520
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P40010 Pfam ID:PF08701, PF01926

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein RLP7
Gene (Uniprot):RLP7
Chain IDs:XA (auth: t)
Chain Length:160
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P40693 Pfam ID:PF00327

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein RLP24
Gene (Uniprot):RLP24
Chain IDs:YA (auth: u)
Chain Length:199
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:ZA (auth: v)
Chain Length:137
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:AB (auth: w)
Chain Length:203
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:BB (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:CB (auth: y)
Chain Length:245
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:DB (auth: z)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P38202 Pfam ID:PF10338

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