8FL7 image
Entry Detail
PDB ID:
8FL7
EMDB ID:
Keywords:
Title:
Human nuclear pre-60S ribosomal subunit (State J2)
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2022-12-21
Release Date:
2023-07-12
Method Details:
Experimental Method:
Resolution:
2.55 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:polyribonucleotide
Description:5.8S rRNA
Chain IDs:B (auth: L1)
Chain Length:157
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:28S rRNA
Chain IDs:C (auth: L3)
Chain Length:5070
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:5S rRNA
Chain IDs:D (auth: L4)
Chain Length:121
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L11
Chain IDs:E (auth: L5)
Chain Length:178
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 L19
Chain IDs:M (auth: LD)
Chain Length:196
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L21
Chain IDs:N (auth: LE)
Chain Length:160
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L22
Chain IDs:O (auth: LF)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L23
Chain IDs:P (auth: LG)
Chain Length:140
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L23a
Chain IDs:Q (auth: LH)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L26
Chain IDs:R (auth: LI)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27
Chain IDs:S (auth: LJ)
Chain Length:136
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27a
Chain IDs:T (auth: LK)
Chain Length:148
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L28
Chain IDs:U (auth: LL)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L29
Chain IDs:V (auth: LM)
Chain Length:159
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L3
Chain IDs:W (auth: LN)
Chain Length:403
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L30
Chain IDs:X (auth: LO)
Chain Length:115
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L31
Chain IDs:Y (auth: LP)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L32
Chain IDs:Z (auth: LQ)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L34
Chain IDs:AA (auth: LR)
Chain Length:117
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L35
Chain IDs:BA (auth: LS)
Chain Length:123
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L35a
Chain IDs:CA (auth: LT)
Chain Length:110
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36
Chain IDs:DA (auth: LU)
Chain Length:105
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36a
Chain IDs:EA (auth: LV)
Chain Length:106
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L37
Chain IDs:FA (auth: LW)
Chain Length:97
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L37a
Chain IDs:GA (auth: LX)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L38
Chain IDs:HA (auth: LY)
Chain Length:70
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L39
Chain IDs:IA (auth: LZ)
Chain Length:51
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Nucleolar GTP-binding protein 2
Chain IDs:JA (auth: NC)
Chain Length:731
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein NSA2 homolog
Chain IDs:KA (auth: NF)
Chain Length:260
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Protein LLP homolog
Chain IDs:LA (auth: NK)
Chain Length:129
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ribosome biogenesis protein NOP53
Chain IDs:MA (auth: NL)
Chain Length:478
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Zinc finger protein 593
Chain IDs:NA (auth: NP)
Chain Length:134
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L4
Chain IDs:OA (auth: SA)
Chain Length:427
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L5
Chain IDs:PA (auth: SB)
Chain Length:297
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L6
Chain IDs:QA (auth: SC)
Chain Length:288
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L7
Chain IDs:RA (auth: SD)
Chain Length:248
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L7a
Chain IDs:SA (auth: SE)
Chain Length:266
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L8
Chain IDs:TA (auth: SF)
Chain Length:257
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L9
Chain IDs:UA (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:VA (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:WA (auth: SI)
Chain Length:255
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 6
Chain IDs:XA (auth: SK)
Chain Length:245
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Pescadillo homolog
Chain IDs:YA (auth: SM)
Chain Length:588
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:mRNA turnover protein 4 homolog
Chain IDs:ZA (auth: SQ)
Chain Length:239
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:GTP-binding protein 4
Chain IDs:AB (auth: SR)
Chain Length:634
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Probable ribosome biogenesis protein RLP24
Chain IDs:BB (auth: SV)
Chain Length:163
Number of Molecules:1
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
6MZ C A modified residue
A2M C A modified residue
HIC W HIS modified residue
OMC C C modified residue
OMG B G modified residue
OMU C U modified residue
PSU B U modified residue
UR3 C U 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