8FKP image
Deposition Date 2022-12-21
Release Date 2023-07-12
Last Version Date 2024-05-01
Entry Detail
PDB ID:
8FKP
Keywords:
Title:
Human nucleolar pre-60S ribosomal subunit (State A1)
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
2.85 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:A (auth: L1)
Chain Length:157
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:ITS2 rRNA
Chain IDs:B (auth: L2)
Chain Length:1167
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:28S rRNA
Chain IDs:C (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:D (auth: L6)
Chain Length:211
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13a
Gene (Uniprot):RPL13A
Chain IDs:E (auth: L7)
Chain Length:203
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14
Gene (Uniprot):RPL14
Chain IDs:F (auth: L8)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15
Gene (Uniprot):RPL15
Chain IDs:G (auth: L9)
Chain Length:204
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17
Gene (Uniprot):RPL17
Chain IDs:H (auth: LA)
Chain Length:184
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18
Gene (Uniprot):RPL18
Chain IDs:I (auth: LB)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18a
Gene (Uniprot):RPL18A
Chain IDs:J (auth: LC)
Chain Length:176
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21
Gene (Uniprot):RPL21
Chain IDs:K (auth: LE)
Chain Length:160
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23
Gene (Uniprot):RPL23
Chain IDs:L (auth: LG)
Chain Length:140
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23a
Gene (Uniprot):RPL23A
Chain IDs:M (auth: LH)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26
Gene (Uniprot):RPL26
Chain IDs:N (auth: LI)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27a
Gene (Uniprot):RPL27A
Chain IDs:O (auth: LK)
Chain Length:148
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:P (auth: LN)
Chain Length:403
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Gene (Uniprot):RPL32
Chain IDs:Q (auth: LQ)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35
Gene (Uniprot):RPL35
Chain IDs:R (auth: LS)
Chain Length:123
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35a
Gene (Uniprot):RPL35A
Chain IDs:S (auth: LT)
Chain Length:110
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36
Gene (Uniprot):RPL36
Chain IDs:T (auth: LU)
Chain Length:105
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37
Gene (Uniprot):RPL37
Chain IDs:U (auth: LW)
Chain Length:97
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:V (auth: NB)
Chain Length:549
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Surfeit locus protein 6
Gene (Uniprot):SURF6
Chain IDs:W (auth: NE)
Chain Length:361
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RRP15-like protein
Gene (Uniprot):RRP15
Chain IDs:X (auth: NG)
Chain Length:282
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein MAK16 homolog
Gene (Uniprot):MAK16
Chain IDs:Y (auth: NM)
Chain Length:300
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Suppressor of SWI4 1 homolog
Gene (Uniprot):PPAN
Chain IDs:Z (auth: NN)
Chain Length:473
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal RNA processing protein 1 homolog A
Gene (Uniprot):RRP1
Chain IDs:AA (auth: NO)
Chain Length:461
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:WD repeat-containing protein 74
Gene (Uniprot):WDR74
Chain IDs:BA (auth: NQ)
Chain Length:385
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome production factor 1
Gene (Uniprot):RPF1
Chain IDs:CA (auth: NS)
Chain Length:349
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4
Gene (Uniprot):RPL4
Chain IDs:DA (auth: SA)
Chain Length:427
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Gene (Uniprot):RPL6
Chain IDs:EA (auth: SC)
Chain Length:288
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7
Gene (Uniprot):RPL7
Chain IDs:FA (auth: SD)
Chain Length:248
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7a
Gene (Uniprot):RPL7A
Chain IDs:GA (auth: SE)
Chain Length:266
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:MKI67 FHA domain-interacting nucleolar phosphoprotein
Gene (Uniprot):NIFK
Chain IDs:HA (auth: SH)
Chain Length:293
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-like 1
Gene (Uniprot):RPL7L1
Chain IDs:IA (auth: SI)
Chain Length:255
Number of Molecules:1
Biological Source:Homo sapiens
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:JA (auth: SJ)
Chain Length:847
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 6
Gene (Uniprot):EIF6
Chain IDs:KA (auth: SK)
Chain Length:245
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal L1 domain-containing protein 1
Gene (Uniprot):RSL1D1
Chain IDs:LA (auth: SL)
Chain Length:490
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pescadillo homolog
Gene (Uniprot):PES1
Chain IDs:MA (auth: SM)
Chain Length:588
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable rRNA-processing protein EBP2
Gene (Uniprot):EBNA1BP2
Chain IDs:NA (auth: SN)
Chain Length:306
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein BRX1 homolog
Gene (Uniprot):BRIX1
Chain IDs:OA (auth: SO)
Chain Length:353
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:GTP-binding protein 4
Gene (Uniprot):GTPBP4
Chain IDs:PA (auth: SR)
Chain Length:634
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein BOP1
Gene (Uniprot):BOP1
Chain IDs:QA (auth: SS)
Chain Length:746
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis regulatory protein homolog
Gene (Uniprot):RRS1
Chain IDs:RA (auth: ST)
Chain Length:365
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable ribosome biogenesis protein RLP24
Gene (Uniprot):RSL24D1
Chain IDs:SA (auth: SV)
Chain Length:163
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ATP-dependent RNA helicase DDX18
Gene (Uniprot):DDX18
Chain IDs:TA (auth: SW)
Chain Length:670
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 16
Gene (Uniprot):NOP16
Chain IDs:UA (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 Y MET modified residue
HIC P HIS modified residue
SEP QA 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