ISDA

Deposition Date 2018-11-29

Release Date 2019-03-13

Last Version Date 2024-11-20

Entry Detail

PDB ID:

6N8K

Keywords:

RIBOSOME

Title:

Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit

Biological Source:

Source Organism:

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

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.60 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA
Chain IDs:TA (auth: 1)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:UA (auth: 2)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:VA (auth: 3)
Chain Length:158
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:C (auth: A)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:E (auth: B)
Chain Length:387
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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 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:PA (auth: D)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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 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:L (auth: F)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:N (auth: G)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:Q (auth: H)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

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:P (auth: I)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

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:QA (auth: J)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:V (auth: L)
Chain Length:51
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:X (auth: M)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:Z (auth: N)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:BA (auth: O)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:CA (auth: P)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:DA (auth: Q)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:EA (auth: R)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:FA (auth: S)
Chain Length:217
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:GA (auth: T)
Chain Length:160
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:HA (auth: U)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:IA (auth: V)
Chain Length:518
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:JA (auth: W)
Chain Length:236
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:KA (auth: X)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:LA (auth: Y)
Chain Length:245
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:NA (auth: Z)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:D (auth: a)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:F (auth: b)
Chain Length:387
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:H (auth: c)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:I (auth: d)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:K (auth: e)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:M (auth: f)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:O (auth: g)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:R (auth: h)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:S (auth: i)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:T (auth: j)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:U (auth: k)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:W (auth: l)
Chain Length:51
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

UniProt ID:P04650 Pfam ID:PF00832

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Gene (Uniprot):RPL29
Chain IDs:SA (auth: o)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

UniProt ID:P05747 Pfam ID:PF01779

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43-A
Gene (Uniprot):RPL43A
Chain IDs:Y (auth: p)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

UniProt ID:P0CX25 Pfam ID:PF01780

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L42-A
Gene (Uniprot):RPL42A
Chain IDs:RA (auth: q)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

UniProt ID:P0CX27 Pfam ID:PF00935

Polymer Type:polypeptide(L)
Molecule:Ribosomal Protein uL1
Chain IDs:A (auth: s)
Chain Length:217
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein RLP24
Gene (Uniprot):RLP24
Chain IDs:AA (auth: u)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

UniProt ID:Q07915 Pfam ID:PF01246

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal export protein NMD3
Gene (Uniprot):NMD3
Chain IDs:B (auth: v)
Chain Length:518
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

UniProt ID:P38861 Pfam ID:PF04981, PF21193, PF21192

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 6
Gene (Uniprot):TIF6
Chain IDs:MA (auth: y)
Chain Length:245
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:OA (auth: z)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

UniProt ID:P38202 Pfam ID:PF10338

Ligand Molecules

GTP

Primary Citation

Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome.

Zhou, Y, Musalgaonkar, S, Johnson, A.W, Taylor, D.W.Show

Nat Commun 10 958 958 (2019)

PMID: 30814529 DOI: 10.1038/s41467-019-08880-0

Abstact

The catalytic activity of the ribosome is mediated by RNA, yet proteins are essential for the function of the peptidyl transferase center (PTC). In eukaryotes, final assembly of the PTC occurs in the cytoplasm by insertion of the ribosomal protein Rpl10 (uL16). We determine structures of six intermediates in late nuclear and cytoplasmic maturation of the large subunit that reveal a tightly-choreographed sequence of protein and RNA rearrangements controlling the insertion of Rpl10. We also determine the structure of the biogenesis factor Yvh1 and show how it promotes assembly of the P stalk, a critical element for recruitment of GTPases that drive translation. Together, our structures provide a blueprint for final assembly of a functional ribosome.

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Protein

Chemical

Disease

Primary Citation of related structures