8FL3 image
Deposition Date 2022-12-21
Release Date 2023-07-12
Last Version Date 2023-07-19
Entry Detail
PDB ID:
8FL3
Keywords:
RIBOSOME
Title:
Human nuclear pre-60S ribosomal subunit (State I2)
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.53 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8FL3 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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal biogenesis protein LAS1L
Gene (Uniprot):LAS1L
Chain IDs:C (auth: BD)
Chain Length:734
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y4W2 Pfam ID:PF04031
Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:D (auth: L1)
Chain Length:157
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
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:F (auth: L4)
Chain Length:121
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11
Gene (Uniprot):RPL11
Chain IDs:G (auth: L5)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62913 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13
Gene (Uniprot):RPL13
Chain IDs:H (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:I (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:J (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:K (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:L (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:M (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:N (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 L19
Gene (Uniprot):RPL19
Chain IDs:O (auth: LD)
Chain Length:196
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P84098 Pfam ID:PF01280
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21
Gene (Uniprot):RPL21
Chain IDs:P (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 L22
Gene (Uniprot):RPL22
Chain IDs:Q (auth: LF)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P35268 Pfam ID:PF01776
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23
Gene (Uniprot):RPL23
Chain IDs:R (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:S (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:T (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 L27
Gene (Uniprot):RPL27
Chain IDs:U (auth: LJ)
Chain Length:136
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61353 Pfam ID:PF00467, PF01777
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27a
Gene (Uniprot):RPL27A
Chain IDs:V (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:W (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:X (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 L30
Gene (Uniprot):RPL30
Chain IDs:Y (auth: LO)
Chain Length:115
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62888 Pfam ID:PF01248
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31
Gene (Uniprot):RPL31
Chain IDs:Z (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:AA (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 L34
Gene (Uniprot):RPL34
Chain IDs:BA (auth: LR)
Chain Length:117
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P49207 Pfam ID:PF01199
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35
Gene (Uniprot):RPL35
Chain IDs:CA (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:DA (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:EA (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:FA (auth: LW)
Chain Length:97
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61927 Pfam ID:PF01907
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37a
Gene (Uniprot):RPL37A
Chain IDs:GA (auth: LX)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61513 Pfam ID:PF01780
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Gene (Uniprot):RPL38
Chain IDs:HA (auth: LY)
Chain Length:70
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P63173 Pfam ID:PF01781
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):RPL39
Chain IDs:IA (auth: LZ)
Chain Length:51
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62891 Pfam ID:PF00832
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein-like 3
Gene (Uniprot):GNL3
Chain IDs:JA (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:Nucleolar GTP-binding protein 2
Gene (Uniprot):GNL2
Chain IDs:KA (auth: NC)
Chain Length:731
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13823 Pfam ID:PF08153, PF01926
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein NSA2 homolog
Gene (Uniprot):NSA2
Chain IDs:LA (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:Notchless protein homolog 1
Gene (Uniprot):NLE1
Chain IDs:MA (auth: NJ)
Chain Length:485
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NVX2 Pfam ID:PF08154, PF00400
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein LLP homolog
Gene (Uniprot):LLPH
Chain IDs:NA (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:Ribosome biogenesis protein NOP53
Gene (Uniprot):NOP53
Chain IDs:OA (auth: NL)
Chain Length:478
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NZM5 Pfam ID:PF07767
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Zinc finger protein 593
Gene (Uniprot):ZNF593
Chain IDs:PA (auth: NP)
Chain Length:134
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O00488 Pfam ID:PF12171
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein SDA1 homolog
Gene (Uniprot):SDAD1
Chain IDs:QA (auth: NT)
Chain Length:687
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NVU7 Pfam ID:PF08158, PF05285, PF21638
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Testis-expressed protein 10
Gene (Uniprot):TEX10
Chain IDs:RA (auth: NU)
Chain Length:929
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NXF1 Pfam ID:PF12333
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:WD repeat-containing protein 18
Gene (Uniprot):WDR18
Chain IDs:SA (auth: NV), TA (auth: NW)
Chain Length:432
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:Q9BV38 Pfam ID:PF00400, PF14077
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proline-, glutamic acid- and leucine-rich protein 1
Gene (Uniprot):PELP1
Chain IDs:UA (auth: NX), VA (auth: NY)
Chain Length:1130
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:Q8IZL8 Pfam ID:PF08167, PF08166
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Coiled-coil domain-containing protein 86
Gene (Uniprot):CCDC86
Chain IDs:WA (auth: NZ)
Chain Length:360
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H6F5 Pfam ID:PF03879
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4
Gene (Uniprot):RPL4
Chain IDs:XA (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 L5
Gene (Uniprot):RPL5
Chain IDs:YA (auth: SB)
Chain Length:297
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46777 Pfam ID:PF17144, PF14204
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Gene (Uniprot):RPL6
Chain IDs:ZA (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:AB (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:BB (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 L8
Gene (Uniprot):RPL8
Chain IDs:CB (auth: SF)
Chain Length:257
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62917 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9
Gene (Uniprot):RPL9, RPL9P7, RPL9P8, RPL9P9
Chain IDs:DB (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:EB (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:FB (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:Eukaryotic translation initiation factor 6
Gene (Uniprot):EIF6
Chain IDs:GB (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:Pescadillo homolog
Gene (Uniprot):PES1
Chain IDs:HB (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:mRNA turnover protein 4 homolog
Gene (Uniprot):MRTO4
Chain IDs:IB (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:JB (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:Probable ribosome biogenesis protein RLP24
Gene (Uniprot):RSL24D1
Chain IDs:KB (auth: SV)
Chain Length:163
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9UHA3 Pfam ID:PF01246
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
1MA E A modified residue
5MC E C modified residue
6MZ E A modified residue
A2M E A modified residue
HIC X HIS modified residue
OMC E C modified residue
OMG D G modified residue
OMU E U modified residue
PSU D U modified residue
UR3 E U modified residue
Ligand Molecules
GDP
GTP
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
8FL3