4V7F image
Deposition Date 2013-12-10
Release Date 2014-07-09
Last Version Date 2024-02-28
Entry Detail
PDB ID:
4V7F
Keywords:
RIBOSOME
Title:
Arx1 pre-60S particle.
Biological Source:
Source Organism:
Saccharomyces cerevisiae (Taxon ID: 4932)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
8.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
4V7F validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:25S ribosomal RNA
Chain IDs:A (auth: 1)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:5.8S ribosomal RNA
Chain IDs:B (auth: 2)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:C (auth: 3)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L1
Gene (Uniprot):RPL1A
Chain IDs:D (auth: A)
Chain Length:217
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX43 Pfam ID:PF00687
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2
Gene (Uniprot):RPL2A
Chain IDs:E (auth: B)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX45 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:F (auth: C)
Chain Length:113
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P14126 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4
Gene (Uniprot):RPL4A
Chain IDs:G (auth: D)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P10664 Pfam ID:PF00573, PF14374
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11
Gene (Uniprot):RPL11A
Chain IDs:H (auth: E)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C0W9 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9
Gene (Uniprot):RPL9A
Chain IDs:I (auth: F)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05738 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Gene (Uniprot):RPL6A
Chain IDs:J (auth: G)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q02326 Pfam ID:PF01159
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8
Gene (Uniprot):RPL8A
Chain IDs:K (auth: H)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P17076 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L12
Gene (Uniprot):RPL12A
Chain IDs:L (auth: I)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX53 Pfam ID:PF03946, PF00298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16
Gene (Uniprot):RPL16A
Chain IDs:M (auth: J)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26784 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13
Gene (Uniprot):RPL13A
Chain IDs:N (auth: K)
Chain Length:92
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12690 Pfam ID:PF01294
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23
Gene (Uniprot):RPL23A
Chain IDs:O (auth: L)
Chain Length:593
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX41 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14
Gene (Uniprot):RPL14A
Chain IDs:P (auth: M)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36105 Pfam ID:PF00467, PF01929
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:Q (auth: N)
Chain Length:236
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P02406 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15
Gene (Uniprot):RPL15A
Chain IDs:R (auth: O)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05748 Pfam ID:PF00827
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Gene (Uniprot):RPL5
Chain IDs:S (auth: P)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26321 Pfam ID:PF17144, PF14204
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18
Gene (Uniprot):RPL18A
Chain IDs:T (auth: Q)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX49 Pfam ID:PF17135
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19
Gene (Uniprot):RPL19A
Chain IDs:U (auth: R)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX82 Pfam ID:PF01280
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L20
Gene (Uniprot):RPL20A
Chain IDs:V (auth: S)
Chain Length:172
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX23 Pfam ID:PF01775
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21
Gene (Uniprot):RPL21A
Chain IDs:W (auth: T)
Chain Length:160
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q02753 Pfam ID:PF01157
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17
Gene (Uniprot):RPL17A
Chain IDs:X (auth: U)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05740 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22
Gene (Uniprot):RPL22A
Chain IDs:Y (auth: V)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05749 Pfam ID:PF01776
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Gene (Uniprot):RPL25
Chain IDs:Z (auth: W)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04456 Pfam ID:PF03939, PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26
Gene (Uniprot):RPL26A
Chain IDs:AA (auth: X)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05743 Pfam ID:PF16906, PF00467
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27
Gene (Uniprot):RPL27A
Chain IDs:BA (auth: Y)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C2H6 Pfam ID:PF01777
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35
Gene (Uniprot):RPL35A
Chain IDs:CA (auth: Z)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX84 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7
Gene (Uniprot):RPL7A
Chain IDs:DA (auth: a)
Chain Length:217
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05737 Pfam ID:PF08079, PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:EA (auth: b)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P14120 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31
Gene (Uniprot):RPL31A
Chain IDs:FA (auth: c)
Chain Length:113
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C2H8 Pfam ID:PF01198
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Gene (Uniprot):RPL32
Chain IDs:GA (auth: d)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38061 Pfam ID:PF01655
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L33
Gene (Uniprot):RPL33A
Chain IDs:HA (auth: e)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05744 Pfam ID:PF01247
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34
Gene (Uniprot):RPL34A
Chain IDs:IA (auth: f)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P87262 Pfam ID:PF01199
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36
Gene (Uniprot):RPL36A
Chain IDs:JA (auth: g)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05745 Pfam ID:PF01158
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37
Gene (Uniprot):RPL37A
Chain IDs:KA (auth: h)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P49166 Pfam ID:PF01907
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Gene (Uniprot):RPL38
Chain IDs:LA (auth: i)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P49167 Pfam ID:PF01781
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):RPL39
Chain IDs:MA (auth: j)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04650 Pfam ID:PF00832
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43
Gene (Uniprot):RPL43A
Chain IDs:NA (auth: k)
Chain Length:92
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX25 Pfam ID:PF01780
Protein Blast
Polymer Type:polypeptide(L)
Molecule:metalloprotease ARX1
Gene (Uniprot):ARX1
Chain IDs:OA (auth: l)
Chain Length:593
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q03862
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 6
Gene (Uniprot):TIF6
Chain IDs:PA (auth: m)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12522 Pfam ID:PF01912
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mRNA turnover protein 4
Gene (Uniprot):MRT4
Chain IDs:QA (auth: n)
Chain Length:236
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P33201 Pfam ID:PF00466, PF17777
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar GTP-binding protein 1
Gene (Uniprot):NOG1
Chain IDs:RA (auth: o)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q02892 Pfam ID:PF17835, PF06858, PF08155
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein RLP24
Gene (Uniprot):RLP24
Chain IDs:SA (auth: p)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q07915 Pfam ID:PF01246
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome assembly protein 4
Gene (Uniprot):RSA4
Chain IDs:TA (auth: q)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P25382 Pfam ID:PF08154, PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein RLP7
Gene (Uniprot):RLP7
Chain IDs:UA (auth: r), VA (auth: s)
Chain Length:189
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P40693 Pfam ID:PF00327
Ligand Molecules
NA
Primary Citation
60S ribosome biogenesis requires rotation of the 5S ribonucleoprotein particle.
Nat Commun 5 3491 3491 (2014)
PMID: 24662372 DOI: 10.1038/ncomms4491

Abstact

During eukaryotic ribosome biogenesis, nascent ribosomal RNA (rRNA) forms pre-ribosomal particles containing ribosomal proteins and assembly factors. Subsequently, these immature rRNAs are processed and remodelled. Little is known about the premature assembly states of rRNAs and their structural rearrangement during ribosome biogenesis. Using cryo-EM we characterize a pre-60S particle, where the 5S rRNA and its associated ribosomal proteins L18 and L5 (5S ribonucleoprotein (RNP)) are rotated by almost 180° when compared with the mature subunit. Consequently, neighbouring 25S rRNA helices that protrude from the base of the central protuberance are deformed. This altered topology is stabilized by nearby assembly factors (Rsa4 and Nog1), which were identified by fitting their three-dimensional structures into the cryo-EM density. We suggest that the 5S RNP performs a semicircular movement during 60S biogenesis to adopt its final position, fulfilling a chaperone-like function in guiding the flanking 25S rRNA helices of the central protuberance to their final topology.

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Chemical

Disease

Primary Citation of related structures
4V7F
3J64
3J65
3J66