ISDA

Deposition Date 2020-03-12

Release Date 2020-08-26

Last Version Date 2024-10-16

Entry Detail

PDB ID:

6M62

Keywords:

RIBOSOME

Title:

Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state.

Biological Source:

Source Organism:

Saccharomyces cerevisiae S288C (Taxon ID: 559292)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.20 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:RDN25-1 rRNA
Chain IDs:A (auth: 1)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

Polymer Type:polyribonucleotide
Molecule:RDN58-1 rRNA
Chain IDs:B (auth: 2)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

Polymer Type:polyribonucleotide
Molecule:RDN5-2 rRNA
Chain IDs:C (auth: 3)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C

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 S288C

UniProt ID:Q03862

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 S288c

UniProt ID:P53188 Pfam ID:PF03879

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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2-A
Gene (Uniprot):RPL2A
Chain IDs:G (auth: A)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P0CX45 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:H (auth: B)
Chain Length:647
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P14126 Pfam ID:PF00297

Protein Blast

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

UniProt ID:P10664 Pfam ID:PF00573, PF14374

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Gene (Uniprot):RPL5
Chain IDs:J (auth: D)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P26321 Pfam ID:PF17144, PF14204

Protein Blast

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

UniProt ID:Q02326 Pfam ID:PF01159

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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8-A
Gene (Uniprot):RPL8A
Chain IDs:M (auth: G)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P17076 Pfam ID:PF01248

Protein Blast

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

UniProt ID:P05738 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Bud site selection protein 20
Gene (Uniprot):BUD20
Chain IDs:O (auth: I)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:Q08004 Pfam ID:PF12171

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11-A
Gene (Uniprot):RPL11A
Chain IDs:P (auth: J)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P0C0W9 Pfam ID:PF00281, PF00673

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Proteasome-interacting protein CIC1
Gene (Uniprot):CIC1
Chain IDs:Q (auth: K)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P38779 Pfam ID:PF00687

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13-A
Gene (Uniprot):RPL13A
Chain IDs:R (auth: L)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:Q12690 Pfam ID:PF01294

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14-A
Gene (Uniprot):RPL14A
Chain IDs:S (auth: M)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:T (auth: N)
Chain Length:605
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P05748 Pfam ID:PF00827

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16-A
Gene (Uniprot):RPL16A
Chain IDs:U (auth: O)
Chain Length:220
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P26784 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17-A
Gene (Uniprot):RPL17A
Chain IDs:V (auth: P)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P05740 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18-A
Gene (Uniprot):RPL18A
Chain IDs:W (auth: Q)
Chain Length:455
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P0CX49 Pfam ID:PF17135

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19-A
Gene (Uniprot):RPL19A
Chain IDs:X (auth: R)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P0CX82 Pfam ID:PF01280

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L20-A
Gene (Uniprot):RPL20A
Chain IDs:Y (auth: S)
Chain Length:520
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P0CX23 Pfam ID:PF01775

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21-A
Gene (Uniprot):RPL21A
Chain IDs:Z (auth: T)
Chain Length:160
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:Q02753 Pfam ID:PF01157

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22-A
Gene (Uniprot):RPL22A
Chain IDs:AA (auth: U)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P05749 Pfam ID:PF01776

Protein Blast

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

UniProt ID:P0CX41 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome assembly factor MRT4
Gene (Uniprot):MRT4
Chain IDs:CA (auth: W)
Chain Length:203
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P33201 Pfam ID:PF00466, PF17777

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Gene (Uniprot):RPL25
Chain IDs:DA (auth: X)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:EA (auth: Y)
Chain Length:245
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:FA (auth: Z)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P0C2H6 Pfam ID:PF01777

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:GA (auth: a)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P02406 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Nucleolar GTP-binding protein 1
Gene (Uniprot):NOG1
Chain IDs:HA (auth: b)
Chain Length:647
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae 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:IA (auth: c)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P14120 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31-A
Gene (Uniprot):RPL31A
Chain IDs:JA (auth: d)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P0C2H8 Pfam ID:PF01198

Protein Blast

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

UniProt ID:P38061 Pfam ID:PF01655

Protein Blast

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

UniProt ID:P05744 Pfam ID:PF01247

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34-A
Gene (Uniprot):RPL34A
Chain IDs:MA (auth: g)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P87262 Pfam ID:PF01199

Protein Blast

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

UniProt ID:P0CX84 Pfam ID:PF00831

Protein Blast

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

UniProt ID:P05745 Pfam ID:PF01158

Protein Blast

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

UniProt ID:P49166 Pfam ID:PF01907

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Gene (Uniprot):RPL38
Chain IDs:QA (auth: k)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P49167 Pfam ID:PF01781

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):RPL39
Chain IDs:RA (auth: l)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P04650 Pfam ID:PF00832

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Nucleolar GTP-binding protein 2
Gene (Uniprot):NOG2
Chain IDs:SA (auth: m)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P53742 Pfam ID:PF08153, PF01926

Protein Blast

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

UniProt ID:P53261 Pfam ID:PF06732, PF16589

Protein Blast

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

UniProt ID:P53927 Pfam ID:PF00076

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43-A
Gene (Uniprot):RPL43A
Chain IDs:VA (auth: p)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P0CX25 Pfam ID:PF01780

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein NOP53
Gene (Uniprot):NOP53
Chain IDs:WA (auth: q)
Chain Length:455
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:Q12080 Pfam ID:PF07767

Protein Blast

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

UniProt ID:P40078 Pfam ID:PF01201

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Nuclear GTP-binding protein NUG1
Gene (Uniprot):NUG1
Chain IDs:YA (auth: s)
Chain Length:520
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P40010 Pfam ID:PF08701, PF01926

Protein Blast

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

UniProt ID:P40693 Pfam ID:PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein RLP24
Gene (Uniprot):RLP24
Chain IDs:AB (auth: u)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:Q07915 Pfam ID:PF01246

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein RPF2
Gene (Uniprot):RPF2
Chain IDs:BB (auth: v)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P36160 Pfam ID:PF04427

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Regulator of ribosome biosynthesis
Gene (Uniprot):RRS1
Chain IDs:CB (auth: w)
Chain Length:203
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:Q08746 Pfam ID:PF04939

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome assembly protein 4
Gene (Uniprot):RSA4
Chain IDs:DB (auth: x)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P25382 Pfam ID:PF08154, PF00400

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 6
Gene (Uniprot):TIF6
Chain IDs:EB (auth: y)
Chain Length:245
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:Q12522 Pfam ID:PF01912

Protein Blast

Polymer Type:polypeptide(L)
Molecule:UPF0642 protein YBL028C
Gene (Uniprot):YBL0423
Chain IDs:FB (auth: z)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c

UniProt ID:P38202 Pfam ID:PF10338

Ligand Molecules

GTP

Primary Citation

Coupling of 5S RNP rotation with maturation of functional centers during large ribosomal subunit assembly.

Micic, J, Li, Y, Wu, S, Wilson, D, Tutuncuoglu, B, Gao, N, Woolford Jr, J.L.Show

Nat Commun 11 3751 3751 (2020)

PMID: 32719344 DOI: 10.1038/s41467-020-17534-5

Abstact

The protein composition and structure of assembling 60S ribosomal subunits undergo numerous changes as pre-ribosomes transition from the nucleolus to the nucleoplasm. This includes stable anchoring of the Rpf2 subcomplex containing 5S rRNA, rpL5, rpL11, Rpf2 and Rrs1, which initially docks onto the flexible domain V of rRNA at earlier stages of assembly. In this work, we tested the function of the C-terminal domain (CTD) of Rpf2 during these anchoring steps, by truncating this extension and assaying effects on middle stages of subunit maturation. The rpf2Δ255-344 mutation affects proper folding of rRNA helices H68-70 during anchoring of the Rpf2 subcomplex. In addition, several assembly factors (AFs) are absent from pre-ribosomes or in altered conformations. Consequently, major remodeling events fail to occur: rotation of the 5S RNP, maturation of the peptidyl transferase center (PTC) and the nascent polypeptide exit tunnel (NPET), and export of assembling subunits to the cytoplasm.

Legend

Protein

Chemical

Disease

Primary Citation of related structures