9SKD image
Deposition Date 2025-09-02
Release Date 2026-09-23
Last Version Date 2026-10-07
Entry Detail
PDB ID:
9SKD
Keywords:
Title:
Model of M. pneumoniae 50S membrane complex
Biological Source:
Source Organism(s):
Method Details:
Experimental Method:
Resolution:
7.70 Å
Aggregation State:
CELL
Reconstruction Method:
SUBTOMOGRAM AVERAGING
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmH
Chain IDs:A (auth: 0)
Chain Length:47
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:B (auth: 1)
Chain Length:59
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:C (auth: 2)
Chain Length:37
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:D (auth: 3)
Chain Length:2878
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:E (auth: 4)
Chain Length:105
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polyribonucleotide
Molecule:tRNA-Phe
Chain IDs:F (auth: 8)
Chain Length:51
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:SecDF
Gene (Uniprot):F11_orf887, MP442
Chain IDs:G (auth: 9)
Chain Length:944
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Gene (Uniprot):rplJ
Chain IDs:H (auth: A)
Chain Length:161
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplL
Chain IDs:I (auth: B), J (auth: C), K (auth: D), L (auth: E)
Chain Length:29
Number of Molecules:4
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplB
Chain IDs:M (auth: a)
Chain Length:285
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplC
Chain IDs:N (auth: b)
Chain Length:229
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplD
Chain IDs:O (auth: c)
Chain Length:210
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplE
Chain IDs:P (auth: d)
Chain Length:175
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplF
Chain IDs:Q (auth: e)
Chain Length:176
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplI
Chain IDs:R (auth: f)
Chain Length:145
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplK
Chain IDs:S (auth: h)
Chain Length:128
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplM
Chain IDs:T (auth: i)
Chain Length:144
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:U (auth: j)
Chain Length:122
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplO
Chain IDs:V (auth: k)
Chain Length:148
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplP
Chain IDs:W (auth: l)
Chain Length:136
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplQ
Chain IDs:X (auth: m)
Chain Length:119
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplR
Chain IDs:Y (auth: n)
Chain Length:116
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplS
Chain IDs:Z (auth: o)
Chain Length:115
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplT
Chain IDs:AA (auth: p)
Chain Length:114
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplU
Chain IDs:BA (auth: q)
Chain Length:99
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplV
Chain IDs:CA (auth: r)
Chain Length:139
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplW
Chain IDs:DA (auth: s)
Chain Length:92
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:EA (auth: t)
Chain Length:111
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmA
Chain IDs:FA (auth: u)
Chain Length:86
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmB
Chain IDs:GA (auth: v)
Chain Length:63
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmC
Chain IDs:HA (auth: w)
Chain Length:108
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmE
Chain IDs:IA (auth: x)
Chain Length:44
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmF
Chain IDs:JA (auth: y)
Chain Length:56
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmG1
Chain IDs:KA (auth: z)
Chain Length:50
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Ligand Molecules
Primary Citation
Single-cell visual proteomics of a minimal bacterium reveals structural coordination of gene expression machineries.
Cell ? ? ? (2026)
PMID: 42790420 DOI: 10.1016/j.cell.2026.08.054

Abstact

Translation is a central process in gene expression. Its regulation is complex, depends on factors that include cell state and the subcellular environment, and is subject to modulation via crosstalk to processes such as transcription or translocation. Here, we used cryo-electron tomography of native and antibiotic-perturbed Mycoplasma pneumoniae cells to resolve 140 maps that recapitulate bacterial translation during the initiation, elongation, and recycling phases. We visualized multiple transcription-translation complexes, allowing us to propose a threading-based translation reinitiation mechanism and to provide structural evidence for a long-hypothesized supercomplex that coordinates transcription, translation, and membrane attachment. We resolved abundant membrane-associated large ribosomal subunits and suggest that dissociation from membranes depends on the conditional initiation of new translation, consistent with a potentially conserved mechanism in mammalian cells. This work visualizes the multilayered control of bacterial translation and demonstrates the power of in-cell structural biology to investigate regulatory circuits in gene expression.

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Chemical

Disease

Primary Citation of related structures
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