8FKW image
Deposition Date 2022-12-21
Release Date 2023-07-12
Last Version Date 2023-08-16
Entry Detail
PDB ID:
8FKW
Keywords:
RIBOSOME
Title:
Human nucleolar pre-60S ribosomal subunit (State D2)
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8FKW validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L12
Gene (Uniprot):RPL12
Chain IDs:A (auth: BA)
Chain Length:165
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P30050 Pfam ID:PF03946, PF00298
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10a
Gene (Uniprot):RPL10A
Chain IDs:B (auth: BB)
Chain Length:217
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62906 Pfam ID:PF00687
Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:C (auth: L1)
Chain Length:157
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:ITS2 rRNA
Chain IDs:D (auth: L2)
Chain Length:1167
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:28S rRNA
Chain IDs:E (auth: L3)
Chain Length:5070
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13
Gene (Uniprot):RPL13
Chain IDs:F (auth: L6)
Chain Length:211
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P26373 Pfam ID:PF01294
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13a
Gene (Uniprot):RPL13A
Chain IDs:G (auth: L7)
Chain Length:203
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P40429 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14
Gene (Uniprot):RPL14
Chain IDs:H (auth: L8)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P50914 Pfam ID:PF01929
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15
Gene (Uniprot):RPL15
Chain IDs:I (auth: L9)
Chain Length:204
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61313 Pfam ID:PF00827
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17
Gene (Uniprot):RPL17
Chain IDs:J (auth: LA)
Chain Length:184
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P18621 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18
Gene (Uniprot):RPL18
Chain IDs:K (auth: LB)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q07020 Pfam ID:PF17135
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18a
Gene (Uniprot):RPL18A
Chain IDs:L (auth: LC)
Chain Length:176
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q02543 Pfam ID:PF01775
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21
Gene (Uniprot):RPL21
Chain IDs:M (auth: LE)
Chain Length:160
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46778 Pfam ID:PF01157
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23
Gene (Uniprot):RPL23
Chain IDs:N (auth: LG)
Chain Length:140
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62829 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23a
Gene (Uniprot):RPL23A
Chain IDs:O (auth: LH)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62750 Pfam ID:PF03939, PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26
Gene (Uniprot):RPL26
Chain IDs:P (auth: LI)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61254 Pfam ID:PF16906, PF00467
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27a
Gene (Uniprot):RPL27A
Chain IDs:Q (auth: LK)
Chain Length:148
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46776 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:R (auth: LL)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46779 Pfam ID:PF01778
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:S (auth: LN)
Chain Length:403
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P39023 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31
Gene (Uniprot):RPL31
Chain IDs:T (auth: LP)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62899 Pfam ID:PF01198
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Gene (Uniprot):RPL32
Chain IDs:U (auth: LQ)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62910 Pfam ID:PF01655
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35
Gene (Uniprot):RPL35
Chain IDs:V (auth: LS)
Chain Length:123
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P42766 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35a
Gene (Uniprot):RPL35A
Chain IDs:W (auth: LT)
Chain Length:110
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P18077 Pfam ID:PF01247
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36
Gene (Uniprot):RPL36
Chain IDs:X (auth: LU)
Chain Length:105
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y3U8 Pfam ID:PF01158
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37
Gene (Uniprot):RPL37
Chain IDs:Y (auth: LW)
Chain Length:97
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61927 Pfam ID:PF01907
Polymer Type:polypeptide(L)
Molecule:Nucleolar complex protein 2 homolog
Chain IDs:Z (auth: NA)
Chain Length:749
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein-like 3
Gene (Uniprot):GNL3
Chain IDs:AA (auth: NB)
Chain Length:549
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BVP2 Pfam ID:PF08701, PF01926
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein NSA2 homolog
Gene (Uniprot):NSA2
Chain IDs:BA (auth: NF)
Chain Length:260
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O95478 Pfam ID:PF01201
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosome subunit biogenesis protein NIP7 homolog
Gene (Uniprot):NIP7
Chain IDs:CA (auth: NH)
Chain Length:180
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y221 Pfam ID:PF17833, PF03657
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ATP-dependent RNA helicase DDX54
Gene (Uniprot):DDX54
Chain IDs:DA (auth: NI)
Chain Length:881
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8TDD1 Pfam ID:PF00270, PF00271, PF08147
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein LLP homolog
Gene (Uniprot):LLPH
Chain IDs:EA (auth: NK)
Chain Length:129
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BRT6 Pfam ID:PF10169
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4
Gene (Uniprot):RPL4
Chain IDs:FA (auth: SA)
Chain Length:427
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P36578 Pfam ID:PF00573, PF14374
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Gene (Uniprot):RPL6
Chain IDs:GA (auth: SC)
Chain Length:288
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q02878 Pfam ID:PF03868, PF01159
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7
Gene (Uniprot):RPL7
Chain IDs:HA (auth: SD)
Chain Length:248
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P18124 Pfam ID:PF08079, PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7a
Gene (Uniprot):RPL7A
Chain IDs:IA (auth: SE)
Chain Length:266
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62424 Pfam ID:PF01248
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9
Gene (Uniprot):RPL9, RPL9P7, RPL9P8, RPL9P9
Chain IDs:JA (auth: SG)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P32969 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:MKI67 FHA domain-interacting nucleolar phosphoprotein
Gene (Uniprot):NIFK
Chain IDs:KA (auth: SH)
Chain Length:293
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BYG3 Pfam ID:PF00076, PF12196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-like 1
Gene (Uniprot):RPL7L1
Chain IDs:LA (auth: SI)
Chain Length:255
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q6DKI1 Pfam ID:PF08079, PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3
Gene (Uniprot):FTSJ3
Chain IDs:MA (auth: SJ)
Chain Length:847
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8IY81 Pfam ID:PF01728, PF11861, PF07780
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 6
Gene (Uniprot):EIF6
Chain IDs:NA (auth: SK)
Chain Length:245
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P56537 Pfam ID:PF01912
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal L1 domain-containing protein 1
Gene (Uniprot):RSL1D1
Chain IDs:OA (auth: SL)
Chain Length:490
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O76021 Pfam ID:PF00687
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pescadillo homolog
Gene (Uniprot):PES1
Chain IDs:PA (auth: SM)
Chain Length:588
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O00541 Pfam ID:PF06732, PF16589
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable rRNA-processing protein EBP2
Gene (Uniprot):EBNA1BP2
Chain IDs:QA (auth: SN)
Chain Length:306
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q99848 Pfam ID:PF05890
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein BRX1 homolog
Gene (Uniprot):BRIX1
Chain IDs:RA (auth: SO)
Chain Length:353
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8TDN6 Pfam ID:PF04427
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mRNA turnover protein 4 homolog
Gene (Uniprot):MRTO4
Chain IDs:SA (auth: SQ)
Chain Length:239
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9UKD2 Pfam ID:PF00466, PF17777
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:GTP-binding protein 4
Gene (Uniprot):GTPBP4
Chain IDs:TA (auth: SR)
Chain Length:634
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BZE4 Pfam ID:PF17835, PF06858, PF08155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein BOP1
Gene (Uniprot):BOP1
Chain IDs:UA (auth: SS)
Chain Length:746
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q14137 Pfam ID:PF08145, PF00400
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis regulatory protein homolog
Gene (Uniprot):RRS1
Chain IDs:VA (auth: ST)
Chain Length:365
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q15050 Pfam ID:PF04939
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar complex protein 3 homolog
Gene (Uniprot):NOC3L
Chain IDs:WA (auth: SU)
Chain Length:800
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8WTT2 Pfam ID:PF07540, PF03914
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable ribosome biogenesis protein RLP24
Gene (Uniprot):RSL24D1
Chain IDs:XA (auth: SV)
Chain Length:163
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9UHA3 Pfam ID:PF01246
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ATP-dependent RNA helicase DDX18
Gene (Uniprot):DDX18
Chain IDs:YA (auth: SW)
Chain Length:670
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NVP1 Pfam ID:PF00270, PF00271, PF13959
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase
Gene (Uniprot):NOP2
Chain IDs:ZA (auth: SY)
Chain Length:812
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46087 Pfam ID:PF22458, PF01189, PF08062
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 16
Gene (Uniprot):NOP16
Chain IDs:AB (auth: SZ)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y3C1 Pfam ID:PF09420
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
SEP UA SER modified residue
Ligand Molecules
ADP
GDP
K
MG
ZN
Primary Citation
Principles of human pre-60 S biogenesis.
Science 381 eadh3892 eadh3892 (2023)
PMID: 37410842 DOI: 10.1126/science.adh3892

Abstact

During the early stages of human large ribosomal subunit (60S) biogenesis, an ensemble of assembly factors establishes and fine-tunes the essential RNA functional centers of pre-60S particles by an unknown mechanism. Here, we report a series of cryo-electron microscopy structures of human nucleolar and nuclear pre-60S assembly intermediates at resolutions of 2.5 to 3.2 angstroms. These structures show how protein interaction hubs tether assembly factor complexes to nucleolar particles and how guanosine triphosphatases and adenosine triphosphatase couple irreversible nucleotide hydrolysis steps to the installation of functional centers. Nuclear stages highlight how a conserved RNA-processing complex, the rixosome, couples large-scale RNA conformational changes with pre-ribosomal RNA processing by the RNA degradation machinery. Our ensemble of human pre-60S particles provides a rich foundation with which to elucidate the molecular principles of ribosome formation.

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Protein

Chemical

Disease

Primary Citation of related structures
8FKW
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