ISDA: 8FL2

Deposition Date 2022-12-21

Release Date 2023-07-12

Last Version Date 2026-07-01

Entry Detail

PDB ID:

8FL2

Keywords:

RIBOSOME

Title:

Human nuclear pre-60S ribosomal subunit (State I1)

Biological Source:

Source Organism(s):

Homo sapiens (Taxon ID: 9606)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.67 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L12
Gene (Uniprot):RPL12
Chain IDs:A (auth: BA)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P30050 Pfam ID:PF03946, PF00298

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10a
Gene (Uniprot):RPL10A
Chain IDs:B (auth: BB)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62906 Pfam ID:PF00687

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal biogenesis protein
Gene (Uniprot):LAS1L
Chain IDs:C (auth: BD)
Chain Length:0
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:0
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polyribonucleotide
Molecule:ITS2 rRNA
Chain IDs:E (auth: L2)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polyribonucleotide
Molecule:28S rRNA
Chain IDs:F (auth: L3)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:G (auth: L4)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11
Gene (Uniprot):RPL11
Chain IDs:H (auth: L5)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62913 Pfam ID:PF00281, PF00673

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13
Gene (Uniprot):RPL13
Chain IDs:I (auth: L6)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P26373 Pfam ID:PF01294

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13a
Gene (Uniprot):RPL13A
Chain IDs:J (auth: L7)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P40429 Pfam ID:PF00572

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14
Gene (Uniprot):RPL14
Chain IDs:K (auth: L8)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P50914 Pfam ID:PF01929

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15
Gene (Uniprot):RPL15
Chain IDs:L (auth: L9)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61313 Pfam ID:PF00827

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17
Gene (Uniprot):RPL17
Chain IDs:M (auth: LA)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P18621 Pfam ID:PF00237

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18
Gene (Uniprot):RPL18
Chain IDs:N (auth: LB)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q07020 Pfam ID:PF17135

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18a
Gene (Uniprot):RPL18A
Chain IDs:O (auth: LC)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q02543 Pfam ID:PF01775

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19
Gene (Uniprot):RPL19
Chain IDs:P (auth: LD)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P84098 Pfam ID:PF01280, PF25476

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21
Gene (Uniprot):RPL21
Chain IDs:Q (auth: LE)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46778 Pfam ID:PF01157

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22
Gene (Uniprot):RPL22
Chain IDs:R (auth: LF)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P35268 Pfam ID:PF01776

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23
Gene (Uniprot):RPL23
Chain IDs:S (auth: LG)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62829 Pfam ID:PF00238

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23a
Gene (Uniprot):RPL23A
Chain IDs:T (auth: LH)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62750 Pfam ID:PF03939, PF00276

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26
Gene (Uniprot):RPL26
Chain IDs:U (auth: LI)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61254 Pfam ID:PF16906, PF00467

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27
Gene (Uniprot):RPL27
Chain IDs:V (auth: LJ)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61353 Pfam ID:PF00467, PF01777

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27a
Gene (Uniprot):RPL27A
Chain IDs:W (auth: LK)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46776 Pfam ID:PF00828

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:X (auth: LL)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46779 Pfam ID:PF01778

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:Y (auth: LN)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P39023 Pfam ID:PF00297

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:Z (auth: LO)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62888 Pfam ID:PF01248

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31
Gene (Uniprot):RPL31
Chain IDs:AA (auth: LP)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62899 Pfam ID:PF01198

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Gene (Uniprot):RPL32
Chain IDs:BA (auth: LQ)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62910 Pfam ID:PF01655

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34
Gene (Uniprot):RPL34
Chain IDs:CA (auth: LR)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P49207 Pfam ID:PF01199

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35
Gene (Uniprot):RPL35
Chain IDs:DA (auth: LS)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P42766 Pfam ID:PF00831

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35a
Gene (Uniprot):RPL35A
Chain IDs:EA (auth: LT)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P18077 Pfam ID:PF01247

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36
Gene (Uniprot):RPL36
Chain IDs:FA (auth: LU)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9Y3U8 Pfam ID:PF01158

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37
Gene (Uniprot):RPL37
Chain IDs:GA (auth: LW)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61927 Pfam ID:PF01907

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37a
Gene (Uniprot):RPL37A
Chain IDs:HA (auth: LX)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61513 Pfam ID:PF01780

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Gene (Uniprot):RPL38
Chain IDs:IA (auth: LY)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P63173 Pfam ID:PF01781

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):RPL39
Chain IDs:JA (auth: LZ)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62891 Pfam ID:PF00832

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding pr
Gene (Uniprot):GNL3
Chain IDs:KA (auth: NB)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BVP2 Pfam ID:PF08701, PF01926

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Nucleolar GTP-binding protein
Gene (Uniprot):GNL2
Chain IDs:LA (auth: NC)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q13823 Pfam ID:PF08153, PF01926

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein N
Gene (Uniprot):NSA2
Chain IDs:MA (auth: NF)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O95478 Pfam ID:PF01201

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Notchless protein homolog 1
Gene (Uniprot):NLE1
Chain IDs:NA (auth: NJ)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NVX2 Pfam ID:PF08154, PF00400

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Protein LLP homolog
Gene (Uniprot):LLPH
Chain IDs:OA (auth: NK)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BRT6 Pfam ID:PF10169

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein N
Gene (Uniprot):NOP53
Chain IDs:PA (auth: NL)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NZM5 Pfam ID:PF07767

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Zinc finger protein 593
Gene (Uniprot):ZNF593
Chain IDs:QA (auth: NP)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O00488 Pfam ID:PF12171

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Protein SDA1 homolog
Gene (Uniprot):SDAD1
Chain IDs:RA (auth: NT)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NVU7 Pfam ID:PF08158, PF05285, PF21638

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Testis-expressed protein 10
Gene (Uniprot):TEX10
Chain IDs:SA (auth: NU)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NXF1 Pfam ID:PF12333, PF25781

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:WD repeat-containing protein
Gene (Uniprot):WDR18
Chain IDs:TA (auth: NV), UA (auth: NW)
Chain Length:0
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:Q9BV38 Pfam ID:PF00400, PF14077

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Proline-, glutamic acid- and
Gene (Uniprot):PELP1
Chain IDs:VA (auth: NX), WA (auth: NY)
Chain Length:0
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:Q8IZL8 Pfam ID:PF08167, PF08166

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Coiled-coil domain-containing
Gene (Uniprot):CCDC86
Chain IDs:XA (auth: NZ)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9H6F5 Pfam ID:PF03879

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4
Gene (Uniprot):RPL4
Chain IDs:YA (auth: SA)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P36578 Pfam ID:PF00573, PF14374

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Gene (Uniprot):RPL5
Chain IDs:ZA (auth: SB)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P46777 Pfam ID:PF17144, PF14204

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Gene (Uniprot):RPL6
Chain IDs:AB (auth: SC)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q02878 Pfam ID:PF03868, PF01159

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7
Gene (Uniprot):RPL7
Chain IDs:BB (auth: SD)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P18124 Pfam ID:PF08079, PF00327

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7a
Gene (Uniprot):RPL7A
Chain IDs:CB (auth: SE)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62424 Pfam ID:PF01248

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8
Gene (Uniprot):RPL8
Chain IDs:DB (auth: SF)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62917 Pfam ID:PF00181, PF03947

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9
Gene (Uniprot):RPL9, RPL9P7, RPL9P8, RPL9P9
Chain IDs:EB (auth: SG)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P32969 Pfam ID:PF00347

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:MKI67 FHA domain-interacting
Gene (Uniprot):NIFK
Chain IDs:FB (auth: SH)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BYG3 Pfam ID:PF00076, PF12196

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-like
Gene (Uniprot):RPL7L1
Chain IDs:GB (auth: SI)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q6DKI1 Pfam ID:PF08079, PF00327

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initia
Gene (Uniprot):EIF6
Chain IDs:HB (auth: SK)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P56537 Pfam ID:PF01912

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal L1 domain-containin
Gene (Uniprot):RSL1D1
Chain IDs:IB (auth: SL)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O76021 Pfam ID:PF00687

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Pescadillo homolog
Gene (Uniprot):PES1
Chain IDs:JB (auth: SM)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O00541 Pfam ID:PF06732, PF16589

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:mRNA turnover protein 4 homol
Gene (Uniprot):MRTO4
Chain IDs:KB (auth: SQ)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9UKD2 Pfam ID:PF00466, PF17777

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:GTP-binding protein 4
Gene (Uniprot):GTPBP4
Chain IDs:LB (auth: SR)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BZE4 Pfam ID:PF17835, PF06858, PF08155

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Probable ribosome biogenesis
Gene (Uniprot):RSL24D1
Chain IDs:MB (auth: SV)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9UHA3 Pfam ID:PF01246

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
1MA	F	A	modified residue
5MC	F	C	modified residue
6MZ	F	A	modified residue
A2M	F	A	modified residue
HIC	Y	HIS	modified residue
OMC	F	C	modified residue
OMG	D	G	modified residue
OMU	F	U	modified residue
PSU	D	U	modified residue
UR3	F	U	modified residue

Ligand Molecules

GDP

GTP

Primary Citation

Principles of human pre-60 S biogenesis.

Vanden Broeck, A, Klinge, S.Show

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures

Abstact

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