6GC4 image
Deposition Date 2018-04-17
Release Date 2018-07-04
Last Version Date 2024-05-15
Entry Detail
PDB ID:
6GC4
Keywords:
Title:
50S ribosomal subunit assembly intermediate state 3
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
4.30 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:S (auth: 0)
Chain Length:56
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:T (auth: 2)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:B (auth: A)
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:W (auth: B)
Chain Length:119
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:C
Chain Length:271
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:D
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:E
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:V (auth: F)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:F (auth: G)
Chain Length:176
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:Y (auth: H)
Chain Length:50
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:G (auth: J)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:H (auth: K)
Chain Length:122
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:I (auth: L)
Chain Length:143
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:J (auth: N)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:U (auth: O)
Chain Length:116
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:K (auth: P)
Chain Length:114
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:L (auth: Q)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:M (auth: R)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:N (auth: S)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:O (auth: T)
Chain Length:93
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:P (auth: U)
Chain Length:102
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:A (auth: V)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:Z (auth: W)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:Q (auth: X)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:R (auth: Y)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:X (auth: Z)
Chain Length:58
Number of Molecules:1
Biological Source:Escherichia coli K-12
Ligand Molecules
Primary Citation
Structural Visualization of the Formation and Activation of the 50S Ribosomal Subunit during In Vitro Reconstitution.
Mol. Cell 70 881 893.e3 (2018)
PMID: 29883607 DOI: 10.1016/j.molcel.2018.05.003

Abstact

The assembly of ribosomal subunits is an essential prerequisite for protein biosynthesis in all domains of life. Although biochemical and biophysical approaches have advanced our understanding of ribosome assembly, our mechanistic comprehension of this process is still limited. Here, we perform an in vitro reconstitution of the Escherichia coli 50S ribosomal subunit. Late reconstitution products were subjected to high-resolution cryo-electron microscopy and multiparticle refinement analysis to reconstruct five distinct precursors of the 50S subunit with 4.3-3.8 Å resolution. These assembly intermediates define a progressive maturation pathway culminating in a late assembly particle, whose structure is more than 96% identical to a mature 50S subunit. Our structures monitor the formation and stabilization of structural elements in a nascent particle in unprecedented detail and identify the maturation of the rRNA-based peptidyl transferase center as the final critical step along the 50S assembly pathway.

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Primary Citation of related structures