6LU8 image
Deposition Date 2020-01-26
Release Date 2020-08-26
Last Version Date 2025-09-17
Entry Detail
PDB ID:
6LU8
Keywords:
Title:
Cryo-EM structure of a human pre-60S ribosomal subunit - state A
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.13 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar GTP-binding protein 2
Gene (Uniprot):GNL2
Chain IDs:A (auth: 1)
Chain Length:731
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:28S rRNA
Chain IDs:B (auth: 2)
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 export protein NMD3
Gene (Uniprot):NMD3
Chain IDs:C (auth: 3)
Chain Length:503
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar GTP-binding protein 1
Gene (Uniprot):GTPBP4
Chain IDs:D (auth: 4)
Chain Length:634
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:E (auth: 5)
Chain Length:120
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:F (auth: 6)
Chain Length:245
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:G (auth: 7)
Chain Length:163
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:H (auth: 8)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Zinc finger protein 593
Gene (Uniprot):ZNF593
Chain IDs:I (auth: 9)
Chain Length:134
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10a
Gene (Uniprot):RPL10A
Chain IDs:J (auth: A)
Chain Length:217
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:K (auth: B)
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 L29
Gene (Uniprot):RPL29
Chain IDs:L (auth: C)
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 L4
Gene (Uniprot):RPL4
Chain IDs:M (auth: D)
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 L30
Gene (Uniprot):RPL30
Chain IDs:N (auth: E)
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 L34
Gene (Uniprot):RPL34
Chain IDs:O (auth: F)
Chain Length:117
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:P (auth: G)
Chain Length:266
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:Q (auth: H)
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 L9
Gene (Uniprot):RPL9, RPL9P7, RPL9P8, RPL9P9
Chain IDs:R (auth: I)
Chain Length:192
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:S (auth: K)
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 L27a
Gene (Uniprot):RPL27A
Chain IDs:T (auth: L)
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 L37
Gene (Uniprot):RPL37
Chain IDs:U (auth: M)
Chain Length:97
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:V (auth: N)
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 L38
Gene (Uniprot):RPL38
Chain IDs:W (auth: O)
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 L39
Gene (Uniprot):RPL39
Chain IDs:X (auth: P)
Chain Length:51
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:Y (auth: Q)
Chain Length:211
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Translation machinery-associated protein 16
Gene (Uniprot):TMA16
Chain IDs:Z (auth: R)
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:AA (auth: S)
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:BA (auth: U)
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 L13a
Gene (Uniprot):RPL13A
Chain IDs:CA (auth: V)
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 L36a
Gene (Uniprot):RPL36A
Chain IDs:DA (auth: W)
Chain Length:106
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37a
Gene (Uniprot):RPL37A
Chain IDs:EA (auth: X)
Chain Length:92
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:FA (auth: Y)
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:GA (auth: Z)
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 L19
Gene (Uniprot):RPL19
Chain IDs:HA (auth: a)
Chain Length:217
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:IA (auth: b)
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:JA (auth: c)
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 L22
Gene (Uniprot):RPL22
Chain IDs:KA (auth: d)
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 L23
Gene (Uniprot):RPL23
Chain IDs:LA (auth: e)
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:MA (auth: g)
Chain Length:266
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:NA (auth: h)
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 L27
Gene (Uniprot):RPL27
Chain IDs:OA (auth: i)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31
Gene (Uniprot):RPL31
Chain IDs:PA (auth: j)
Chain Length:125
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:QA (auth: k)
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 L28
Gene (Uniprot):RPL28
Chain IDs:RA (auth: l)
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 L8
Gene (Uniprot):RPL8
Chain IDs:SA (auth: m)
Chain Length:97
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:TA (auth: n)
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 L6
Gene (Uniprot):RPL6
Chain IDs:UA (auth: o)
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:VA (auth: p)
Chain Length:51
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Gene (Uniprot):RPL5
Chain IDs:WA (auth: r)
Chain Length:203
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein LLP homolog
Gene (Uniprot):LLPH
Chain IDs:XA (auth: z)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
OMU H U modified residue
Ligand Molecules
Primary Citation
Structural snapshots of human pre-60S ribosomal particles before and after nuclear export.
Nat Commun 11 3542 3542 (2020)
PMID: 32669547 DOI: 10.1038/s41467-020-17237-x

Abstact

Ribosome biogenesis is an elaborate and energetically expensive program that involve two hundred protein factors in eukaryotes. Nuclear export of pre-ribosomal particles is one central step which also serves as an internal structural checkpoint to ensure the proper completion of nuclear assembly events. Here we present four structures of human pre-60S particles isolated through a nuclear export factor NMD3, representing assembly stages immediately before and after nuclear export. These structures reveal locations of a dozen of human factors, including an uncharacterized factor TMA16 localized between the 5S RNA and the P0 stalk. Comparison of these structures shows a progressive maturation for the functional regions, such as peptidyl transferase centre and peptide exit tunnel, and illustrate a sequence of factor-assisted rRNA maturation events. These data facilitate our understanding of the global conservation of ribosome assembly in eukaryotes and species-specific features of human assembly factors.

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Primary Citation of related structures