8ESQ image
Deposition Date 2022-10-14
Release Date 2022-11-30
Last Version Date 2024-06-19
Entry Detail
PDB ID:
8ESQ
Keywords:
RIBOSOME
Title:
Ytm1 associated nascent 60S ribosome State 2
Biological Source:
Source Organism:
Schizosaccharomyces pombe (Taxon ID: 4896)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.80 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8ESQ validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:RNA (2231-MER)
Chain IDs:B (auth: 1)
Chain Length:3497
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Polymer Type:polyribonucleotide
Molecule:RNA (150-MER)
Chain IDs:C (auth: 2)
Chain Length:165
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein mak16
Gene (Uniprot):mak16
Chain IDs:D (auth: 3)
Chain Length:302
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:Q9UTE6 Pfam ID:PF01778, PF04874
Polymer Type:polyribonucleotide
Molecule:RNA (81-MER)
Chain IDs:E (auth: 6)
Chain Length:300
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Noc2
Gene (Uniprot):SPAC1142.04
Chain IDs:A (auth: 7)
Chain Length:707
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:Q9P7G0 Pfam ID:PF03715
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):rpl39
Chain IDs:F (auth: 8)
Chain Length:51
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:P05767 Pfam ID:PF00832
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein brx1
Gene (Uniprot):brx1
Chain IDs:G (auth: A)
Chain Length:148
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:Q9HGL6 Pfam ID:PF04427
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3-A
Gene (Uniprot):rpl301
Chain IDs:H (auth: B)
Chain Length:642
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:P40372 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4-B
Gene (Uniprot):rpl401
Chain IDs:I (auth: C)
Chain Length:117
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:Q9P784 Pfam ID:PF00573, PF14374
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ATP-dependent RNA helicase has1
Gene (Uniprot):has1
Chain IDs:J (auth: D)
Chain Length:113
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:Q09916 Pfam ID:PF00270, PF00271, PF13959
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Gene (Uniprot):rpl6
Chain IDs:K (auth: E)
Chain Length:127
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:P79071 Pfam ID:PF01159
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-B
Gene (Uniprot):rpl702
Chain IDs:L (auth: F)
Chain Length:250
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:P25457 Pfam ID:PF08079, PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8
Gene (Uniprot):rpl8
Chain IDs:M (auth: G)
Chain Length:259
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:O13672 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9-A
Gene (Uniprot):rpl901
Chain IDs:N (auth: H)
Chain Length:190
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:Q10232 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar complex-associated protein 3
Gene (Uniprot):noc3
Chain IDs:O (auth: I)
Chain Length:747
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:O94288 Pfam ID:PF07540, PF03914
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable rRNA-processing protein ebp2
Gene (Uniprot):ebp2
Chain IDs:P (auth: J)
Chain Length:91
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:O13802 Pfam ID:PF05890
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Putative ribosome biogenesis protein C8F11.04
Gene (Uniprot):SPAC8F11.04
Chain IDs:Q (auth: K)
Chain Length:74
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:Q9UT32 Pfam ID:PF00687
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13
Gene (Uniprot):rpl13
Chain IDs:R (auth: L)
Chain Length:180
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:O74175 Pfam ID:PF01294
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14
Gene (Uniprot):rpl14
Chain IDs:S (auth: M)
Chain Length:740
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:O94238 Pfam ID:PF00467, PF01929
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15-A
Gene (Uniprot):rpl15
Chain IDs:T (auth: N)
Chain Length:201
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:O74895 Pfam ID:PF00827
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16-B
Gene (Uniprot):rpl1601
Chain IDs:U (auth: O)
Chain Length:197
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:O42991 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17-A
Gene (Uniprot):rpl1701
Chain IDs:V (auth: P)
Chain Length:187
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:O14339 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18-A
Gene (Uniprot):rpl1801
Chain IDs:W (auth: Q)
Chain Length:608
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:Q10192 Pfam ID:PF17135
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19-A
Gene (Uniprot):rpl1901
Chain IDs:X (auth: R)
Chain Length:193
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:P05734 Pfam ID:PF01280
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L20-A
Gene (Uniprot):rpl2001
Chain IDs:Y (auth: S)
Chain Length:176
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:P0CT68 Pfam ID:PF01775
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21-A
Gene (Uniprot):rpl2101
Chain IDs:FB (auth: T)
Chain Length:249
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:Q9UUC1 Pfam ID:PF01157
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22
Gene (Uniprot):rpl22
Chain IDs:Z (auth: U)
Chain Length:192
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:Q09668 Pfam ID:PF01776
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23-A
Gene (Uniprot):rpl2301
Chain IDs:AA (auth: V)
Chain Length:139
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:P0CT60 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome assembly factor mrt4
Gene (Uniprot):mrt4
Chain IDs:BA (auth: W)
Chain Length:241
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:Q9USZ6 Pfam ID:PF00466, PF17777
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25-A
Gene (Uniprot):rpl2501
Chain IDs:CA (auth: X)
Chain Length:306
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:Q10330 Pfam ID:PF03939, PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26
Gene (Uniprot):rpl26
Chain IDs:DA (auth: Y)
Chain Length:244
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:P78946 Pfam ID:PF16906, PF00467
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27-A
Gene (Uniprot):rpl2701
Chain IDs:EA (auth: Z)
Chain Length:136
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:O14388 Pfam ID:PF00467, PF01777
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28-A
Gene (Uniprot):rpl2802
Chain IDs:FA (auth: a)
Chain Length:148
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:P36585 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable nucleolar GTP-binding protein 1
Gene (Uniprot):nog1
Chain IDs:GA (auth: b)
Chain Length:642
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:O94659 Pfam ID:PF17835, PF06858, PF08155
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30-2
Gene (Uniprot):rpl3002
Chain IDs:HA (auth: c)
Chain Length:117
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:Q9UTP0 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31
Gene (Uniprot):rpl31
Chain IDs:IA (auth: d)
Chain Length:113
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:Q9URX6 Pfam ID:PF01198
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32-A
Gene (Uniprot):rpl3202
Chain IDs:JA (auth: e)
Chain Length:127
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:P79015 Pfam ID:PF01655
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L33-B
Gene (Uniprot):rpl35a
Chain IDs:KA (auth: f)
Chain Length:250
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:Q9USG6 Pfam ID:PF01247
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34-A
Gene (Uniprot):rpl3401
Chain IDs:LA (auth: g)
Chain Length:259
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:O42846 Pfam ID:PF01199
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35
Gene (Uniprot):rpl35
Chain IDs:MA (auth: h)
Chain Length:190
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:O74904 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36-B
Gene (Uniprot):rpl3602
Chain IDs:NA (auth: i)
Chain Length:747
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:O94658 Pfam ID:PF01158
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37-B
Gene (Uniprot):rpl3702
Chain IDs:OA (auth: j)
Chain Length:91
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:P05733 Pfam ID:PF01907
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38-1
Gene (Uniprot):rpl3801
Chain IDs:PA (auth: k)
Chain Length:74
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:Q9USR7 Pfam ID:PF01781
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosome subunit biogenesis protein nip7
Gene (Uniprot):nip7
Chain IDs:QA (auth: l)
Chain Length:180
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:Q1MTQ9 Pfam ID:PF17833, PF03657
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein erb1
Gene (Uniprot):erb1
Chain IDs:RA (auth: m)
Chain Length:740
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:O74399 Pfam ID:PF08145, PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pescadillo homolog
Gene (Uniprot):ppp1
Chain IDs:SA (auth: n)
Chain Length:201
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:O60164 Pfam ID:PF06732
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized RNA-binding protein C1827.05c
Gene (Uniprot):SPCC1827.05c
Chain IDs:TA (auth: o)
Chain Length:197
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:O74978 Pfam ID:PF00076
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein ytm1
Gene (Uniprot):ytm1
Chain IDs:UA (auth: p)
Chain Length:187
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:Q9URY0 Pfam ID:PF08154, PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:25S rRNA (cytosine-C(5))-methyltransferase nop2
Gene (Uniprot):nop2
Chain IDs:VA (auth: q)
Chain Length:608
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:O94268 Pfam ID:PF22458, PF01189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein nsa2
Gene (Uniprot):nsa2
Chain IDs:WA (auth: r)
Chain Length:193
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:Q9UU79 Pfam ID:PF01201
Protein Blast
Polymer Type:polypeptide(L)
Molecule:GTPase grn1
Gene (Uniprot):grn1
Chain IDs:XA (auth: s)
Chain Length:176
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:O74791 Pfam ID:PF08701, PF01926
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-A
Gene (Uniprot):rlp7
Chain IDs:YA (auth: t)
Chain Length:249
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:P17937 Pfam ID:PF08079, PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein rlp24
Gene (Uniprot):rlp24
Chain IDs:ZA (auth: u)
Chain Length:192
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:Q10353 Pfam ID:PF01246
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 16
Gene (Uniprot):nop16
Chain IDs:AB (auth: v)
Chain Length:139
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:Q9Y7Z1 Pfam ID:PF09420
Protein Blast
Polymer Type:polypeptide(L)
Molecule:AdoMet-dependent rRNA methyltransferase spb1
Gene (Uniprot):spb1
Chain IDs:BB (auth: w)
Chain Length:241
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:O42832 Pfam ID:PF01728, PF11861, PF07780
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Brix domain-containing protein C4F8.04
Gene (Uniprot):SPAC4F8.04
Chain IDs:CB (auth: x)
Chain Length:306
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:O14180 Pfam ID:PF04427
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 6
Gene (Uniprot):tif6
Chain IDs:DB (auth: y)
Chain Length:244
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:O94476 Pfam ID:PF01912
Protein Blast
Polymer Type:polypeptide(L)
Molecule:UPF0642 protein C32H8.05
Gene (Uniprot):SPBC32H8.05
Chain IDs:EB (auth: z)
Chain Length:136
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
UniProt ID:Q96WW3 Pfam ID:PF10338
Ligand Molecules
ZN
Primary Citation
Chromatin localization of nucleophosmin organizes ribosome biogenesis.
Mol.Cell 82 4443 ? (2022)
PMID: 36423630 DOI: 10.1016/j.molcel.2022.10.033

Abstact

Ribosome biogenesis takes place in the nucleolus, a nuclear membrane-less organelle. Although well studied, it remains unknown how nascent ribosomal subunits separate from the central chromatin compartment and move to the outer granular component, where maturation occurs. We find that the Schizosaccharomyces pombe nucleophosmin-like protein Fkbp39 localizes to rDNA sites encoding the 60S subunit rRNA, and this localization contributes to its specific association with nascent 60S subunits. Fkbp39 dissociates from chromatin to bind nascent 60S subunits, causing the latter to partition away from chromatin and from nascent 40S subunits through liquid-liquid phase separation. In vivo, Fkbp39 binding directs the translocation of nascent 60S subunits toward the nucleophosmin-rich granular component. This process increases the efficiency of 60S subunit assembly, facilitating the incorporation of 60S RNA domain III. Thus, chromatin localization determines the specificity of nucleophosmin in sorting nascent ribosomal subunits and coordinates their movement into specialized assembly compartments within the nucleolus.

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Protein

Chemical

Disease

Primary Citation of related structures
8ESQ