8FKV image
Entry Detail
PDB ID:
8FKV
EMDB ID:
Keywords:
Title:
Human nucleolar pre-60S ribosomal subunit (State D1)
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2022-12-21
Release Date:
2023-07-12
Method Details:
Experimental Method:
Resolution:
2.47 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L12
Chain IDs:A (auth: BA)
Chain Length:165
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L10a
Chain IDs:B (auth: BB)
Chain Length:217
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:5.8S rRNA
Chain IDs:C (auth: L1)
Chain Length:157
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:ITS2 rRNA
Chain IDs:D (auth: L2)
Chain Length:1167
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:28S rRNA
Chain IDs:E (auth: L3)
Chain Length:5070
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L13
Chain IDs:F (auth: L6)
Chain Length:211
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L13a
Chain IDs:G (auth: L7)
Chain Length:203
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L14
Chain IDs:H (auth: L8)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L15
Chain IDs:I (auth: L9)
Chain Length:204
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L17
Chain IDs:J (auth: LA)
Chain Length:184
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L18
Chain IDs:K (auth: LB)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L18a
Chain IDs:L (auth: LC)
Chain Length:176
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L21
Chain IDs:M (auth: LE)
Chain Length:160
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L23
Chain IDs:N (auth: LG)
Chain Length:140
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L23a
Chain IDs:O (auth: LH)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L26
Chain IDs:P (auth: LI)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27a
Chain IDs:Q (auth: LK)
Chain Length:148
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L3
Chain IDs:R (auth: LN)
Chain Length:403
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L31
Chain IDs:S (auth: LP)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L32
Chain IDs:T (auth: LQ)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L35
Chain IDs:U (auth: LS)
Chain Length:123
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L35a
Chain IDs:V (auth: LT)
Chain Length:110
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36
Chain IDs:W (auth: LU)
Chain Length:105
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L37
Chain IDs:X (auth: LW)
Chain Length:97
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Nucleolar complex protein 2 homolog
Chain IDs:Y (auth: NA)
Chain Length:749
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Guanine nucleotide-binding protein-like 3
Chain IDs:Z (auth: NB)
Chain Length:549
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein NSA2 homolog
Chain IDs:AA (auth: NF)
Chain Length:260
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosome subunit biogenesis protein NIP7 homolog
Chain IDs:BA (auth: NH)
Chain Length:180
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:ATP-dependent RNA helicase DDX54
Chain IDs:CA (auth: NI)
Chain Length:881
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Protein LLP homolog
Chain IDs:DA (auth: NK)
Chain Length:129
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Protein MAK16 homolog
Chain IDs:EA (auth: NM)
Chain Length:300
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ribosomal RNA processing protein 1 homolog A
Chain IDs:FA (auth: NO)
Chain Length:461
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:WD repeat-containing protein 74
Chain IDs:GA (auth: NQ)
Chain Length:385
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ribosome production factor 1
Chain IDs:HA (auth: NS)
Chain Length:349
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L4
Chain IDs:IA (auth: SA)
Chain Length:427
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L6
Chain IDs:JA (auth: SC)
Chain Length:288
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L7
Chain IDs:KA (auth: SD)
Chain Length:248
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L7a
Chain IDs:LA (auth: SE)
Chain Length:266
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L9
Chain IDs:MA (auth: SG)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:MKI67 FHA domain-interacting nucleolar phosphoprotein
Chain IDs:NA (auth: SH)
Chain Length:293
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L7-like 1
Chain IDs:OA (auth: SI)
Chain Length:255
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3
Chain IDs:PA (auth: SJ)
Chain Length:847
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 6
Chain IDs:QA (auth: SK)
Chain Length:245
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ribosomal L1 domain-containing protein 1
Chain IDs:RA (auth: SL)
Chain Length:490
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Pescadillo homolog
Chain IDs:SA (auth: SM)
Chain Length:588
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Probable rRNA-processing protein EBP2
Chain IDs:TA (auth: SN)
Chain Length:306
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein BRX1 homolog
Chain IDs:UA (auth: SO)
Chain Length:353
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:mRNA turnover protein 4 homolog
Chain IDs:VA (auth: SQ)
Chain Length:239
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:GTP-binding protein 4
Chain IDs:WA (auth: SR)
Chain Length:634
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein BOP1
Chain IDs:XA (auth: SS)
Chain Length:746
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis regulatory protein homolog
Chain IDs:YA (auth: ST)
Chain Length:365
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Nucleolar complex protein 3 homolog
Chain IDs:ZA (auth: SU)
Chain Length:800
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Probable ribosome biogenesis protein RLP24
Chain IDs:AB (auth: SV)
Chain Length:163
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:ATP-dependent RNA helicase DDX18
Chain IDs:BB (auth: SW)
Chain Length:670
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase
Chain IDs:CB (auth: SY)
Chain Length:812
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Nucleolar protein 16
Chain IDs:DB (auth: SZ)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
AME EA MET modified residue
SEP XA SER modified residue
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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Primary Citation of related structures