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- PDB-9sk8: Model of M. pneumoniae 30S IF1/2/3 tRNA -

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Basic information

Entry
Database: PDB / ID: 9sk8
TitleModel of M. pneumoniae 30S IF1/2/3 tRNA
Components
  • (Small ribosomal subunit protein ...) x 20
  • (Translation initiation factor IF- ...) x 3
  • 16S ribosomal RNA
  • Initiator fMet-tRNAfMet
KeywordsTRANSLATION / 30S / ribosome
Function / homology
Function and homology information


ribosome disassembly / translation initiation factor activity / ribosomal small subunit assembly / ribosome binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding ...ribosome disassembly / translation initiation factor activity / ribosomal small subunit assembly / ribosome binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribonucleoprotein complex / structural constituent of ribosome / ribosome / translation / mRNA binding / GTPase activity / GTP binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Translation initiation factor 3, conserved site / Initiation factor 3 signature. / Translation initiation factor 3, C-terminal / Translation initiation factor IF-3, C-terminal domain / Translation initiation factor IF-1 / Translation initiation factor 3 / Translation initiation factor 3, N-terminal / Translation initiation factor 3 (IF-3), N-terminal domain superfamily / Translation initiation factor 3 (IF-3), C-terminal domain superfamily / Translation initiation factor IF-3, N-terminal domain ...Translation initiation factor 3, conserved site / Initiation factor 3 signature. / Translation initiation factor 3, C-terminal / Translation initiation factor IF-3, C-terminal domain / Translation initiation factor IF-1 / Translation initiation factor 3 / Translation initiation factor 3, N-terminal / Translation initiation factor 3 (IF-3), N-terminal domain superfamily / Translation initiation factor 3 (IF-3), C-terminal domain superfamily / Translation initiation factor IF-3, N-terminal domain / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / : / Elongation factor G domain 2 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / Ribosomal protein S14, type Z / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S21 / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S14/S29 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S2 signature 2. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / : / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / KH domain / Small GTP-binding protein domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S10 / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / K homology domain superfamily, prokaryotic type / Ribosomal protein S2, conserved site / : / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S5 / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein bS21 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS10 / Translation initiation factor IF-2 / Translation initiation factor IF-3 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Translation initiation factor IF-1 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17
Similarity search - Component
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 6.6 Å
AuthorsDobbs, J.M. / Mahamid, J.
Funding support United States, Denmark, 2items
OrganizationGrant numberCountry
Chan Zuckerberg Initiative2021-234620 United States
Independent Research Fund Denmark - Medical Sciences0106-00010A Denmark
CitationJournal: Cell / Year: 2026
Title: Single-cell visual proteomics of a minimal bacterium reveals structural coordination of gene expression machineries.
Authors: Joseph M Dobbs / Rasmus K Jensen / Julia Mahamid /
Abstract: 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 ...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.
History
DepositionSep 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
5: 16S ribosomal RNA
6: Initiator fMet-tRNAfMet
A: Small ribosomal subunit protein uS2
B: Small ribosomal subunit protein uS3
C: Small ribosomal subunit protein uS4
D: Small ribosomal subunit protein uS5
E: Small ribosomal subunit protein bS6
F: Small ribosomal subunit protein uS7
G: Small ribosomal subunit protein uS8
H: Small ribosomal subunit protein uS9
I: Small ribosomal subunit protein uS10
J: Small ribosomal subunit protein uS11
K: Small ribosomal subunit protein uS12
L: Small ribosomal subunit protein uS13
M: Small ribosomal subunit protein uS14
N: Small ribosomal subunit protein uS15
O: Small ribosomal subunit protein bS16
P: Small ribosomal subunit protein uS17
Q: Small ribosomal subunit protein bS18
R: Small ribosomal subunit protein uS19
S: Small ribosomal subunit protein bS20
T: Small ribosomal subunit protein bS21
U: Translation initiation factor IF-3
V: Translation initiation factor IF-1
W: Translation initiation factor IF-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)876,94027
Polymers876,80925
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 2 types, 2 molecules 56

#1: RNA chain 16S ribosomal RNA


Mass: 482405.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: GenBank: 26117688
#2: RNA chain Initiator fMet-tRNAfMet


Mass: 22591.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: GenBank: 3042778399

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Small ribosomal subunit protein ... , 20 types, 20 molecules ABCDEFGHIJKLMNOPQRST

#3: Protein Small ribosomal subunit protein uS2 / 30S ribosomal protein S2


Mass: 28427.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75560
#4: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 24162.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P41205
#5: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23589.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P46775
#6: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 16715.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50301
#7: Protein Small ribosomal subunit protein bS6 / 30S ribosomal protein S6


Mass: 19352.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75543
#8: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 17765.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75545
#9: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 15771.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50304
#10: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 14603.050 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75179
#11: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10


Mass: 11524.757 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75581
#12: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 11877.700 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50296
#13: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 15319.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75546
#14: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 13520.724 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50297
#15: Protein Small ribosomal subunit protein uS14 / 30S ribosomal protein S14 type Z


Mass: 6770.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50305
#16: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 9576.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75173
#17: Protein Small ribosomal subunit protein bS16


Mass: 10064.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: A0A0H3DLS7
#18: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 9599.267 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50309
#19: Protein Small ribosomal subunit protein bS18 / 30S ribosomal protein S18


Mass: 7631.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75541
#20: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 9682.159 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75576
#21: Protein Small ribosomal subunit protein bS20 / 30S ribosomal protein S20


Mass: 8977.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75237
#22: Protein Small ribosomal subunit protein bS21 / 30S ribosomal protein S21


Mass: 6724.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P57079

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Translation initiation factor IF- ... , 3 types, 3 molecules UVW

#23: Protein Translation initiation factor IF-3


Mass: 18684.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P78024
#24: Protein Translation initiation factor IF-1


Mass: 7479.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50298
#25: Protein Translation initiation factor IF-2


Mass: 63990.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75590

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Non-polymers , 1 types, 2 molecules

#26: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Mycoplasma cell / Type: CELL / Entity ID: #1-#25 / Source: NATURAL
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 2500 nm
Image recordingElectron dose: 3.2 e/Å2 / Avg electron dose per subtomogram: 120 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1Warpvolume selection
12M3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6094 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 254 / Num. of volumes extracted: 323168
Atomic model buildingProtocol: RIGID BODY FIT / Details: Rigid body fit in ChimeraX

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