4V8T image
Deposition Date 2012-08-07
Release Date 2014-07-09
Last Version Date 2024-05-08
Entry Detail
PDB ID:
4V8T
Keywords:
RIBOSOME
Title:
Cryo-EM Structure of the 60S Ribosomal Subunit in Complex with Arx1 and Rei1
Biological Source:
Source Organism:
Saccharomyces cerevisiae S288C (Taxon ID: 559292)
Host Organism:
Escherichia coli BL21(DE3)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
8.10 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
4V8T validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:ES27 OF THE 25S RRNA
Chain IDs:UA (auth: 1)
Chain Length:114
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE
Polymer Type:polyribonucleotide
Molecule:25S RIBOSOMAL RNA
Chain IDs:VA (auth: 5)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polyribonucleotide
Molecule:5S RIBOSOMAL RNA
Chain IDs:WA (auth: 7)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polyribonucleotide
Molecule:5.8S RIBOSOMAL RNA
Chain IDs:XA (auth: 8)
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:A
Chain Length:149
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:B
Chain Length:59
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: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:D
Chain Length:113
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:E
Chain Length:176
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:F
Chain Length:244
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: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:H
Chain Length:191
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:60S ribosomal protein L10
Gene (Uniprot):RPL10
Chain IDs:I
Chain Length:221
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P41805 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11-A
Gene (Uniprot):RPL11A
Chain IDs:J
Chain Length:174
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0C0W9 Pfam ID:PF00281, PF00673
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L12
Chain IDs:K
Chain Length:155
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13-A
Gene (Uniprot):RPL13A
Chain IDs: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: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: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:Large ribosomal subunit protein uL13A
Gene (Uniprot):RPL16A
Chain IDs:O
Chain Length:106
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: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: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:R
Chain Length:153
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:S
Chain Length:46
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: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:U
Chain Length:121
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:V
Chain Length:137
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:60S ribosomal protein L24-A
Gene (Uniprot):RPL24A
Chain IDs:W
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P04449 Pfam ID:PF01246
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Gene (Uniprot):RPL25
Chain IDs: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:Y
Chain Length:127
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:Z
Chain Length:136
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:AA (auth: a)
Chain Length:149
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:60S ribosomal protein L29
Gene (Uniprot):RPL29
Chain IDs:BA (auth: b)
Chain Length:59
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 L30
Gene (Uniprot):RPL30
Chain IDs:CA (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:DA (auth: d)
Chain Length:113
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:EA (auth: e)
Chain Length:176
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:FA (auth: f)
Chain Length:244
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:GA (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:HA (auth: h)
Chain Length:191
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:IA (auth: i)
Chain Length:221
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:JA (auth: j)
Chain Length:174
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:KA (auth: k)
Chain Length:155
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:LA (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:Ubiquitin-60S ribosomal protein L40
Gene (Uniprot):RPL40A
Chain IDs:MA (auth: m)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CH08 Pfam ID:PF00240, PF01020
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41-A
Gene (Uniprot):RPL41A
Chain IDs:NA (auth: n)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX86 Pfam ID:PF05162
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L42-A
Gene (Uniprot):RPL42A
Chain IDs:OA (auth: o)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P0CX27 Pfam ID:PF00935
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 S288C
UniProt ID:P0CX25 Pfam ID:PF01780
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL10
Gene (Uniprot):RPP0
Chain IDs:QA (auth: q)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P05317 Pfam ID:PF00466, PF17777, PF00428
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN P1 ALPHA,Large ribosomal subunit protein P1A
Gene (Uniprot):RPP1A
Chain IDs:RA (auth: r)
Chain Length:153
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE, Saccharomyces cerevisiae S288C
UniProt ID:P05318 Pfam ID:PF00428
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN P2 BETA
Chain IDs:SA (auth: s)
Chain Length:46
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable metalloprotease ARX1
Gene (Uniprot):ARX1
Chain IDs:TA (auth: t)
Chain Length:160
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:Q03862
Ligand Molecules
ZN
Primary Citation
Cryo-Em Structures of Arx1 and Maturation Factors Rei1 and Jjj1 Bound to the 60S Ribosomal Subunit
Nat.Struct.Mol.Biol. 19 1228 ? (2012)
PMID: 23142985 DOI: 10.1038/NSMB.2425

Abstact

Eukaryotic ribosome biogenesis requires many protein factors that facilitate the assembly, nuclear export and final maturation of 40S and 60S particles. We have biochemically characterized ribosomal complexes of the yeast 60S-biogenesis factor Arx1 and late-maturation factors Rei1 and Jjj1 and determined their cryo-EM structures. Arx1 was visualized bound to the 60S subunit together with Rei1, at 8.1-Å resolution, to reveal the molecular details of Arx1 binding whereby Arx1 arrests the eukaryotic-specific rRNA expansion segment 27 near the polypeptide tunnel exit. Rei1 and Jjj1, which have been implicated in Arx1 recycling, bind in the vicinity of Arx1 and form a network of interactions. We suggest that, in addition to the role of Arx1 during pre-60S nuclear export, the binding of Arx1 conformationally locks the pre-60S subunit and inhibits the premature association of nascent chain-processing factors to the polypeptide tunnel exit.

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Primary Citation of related structures
4V8T
4B6A
4B6B
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