8P7Y

Mycoplasma pneumoniae 70S ribosome with second S4 protein on large subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into context-dependent inhibitory mechanisms of chloramphenicol in cells.

Xue, L.Spahn, C.M.T.Schacherl, M.Mahamid, J.

(2024) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-024-01441-0
  • Primary Citation of Related Structures:  
    8P6P, 8P7X, 8P7Y, 8P8B, 8P8V, 8P8W

  • PubMed Abstract: 

    Ribosome-targeting antibiotics represent an important class of antimicrobial drugs. Chloramphenicol (Cm) is a well-studied ribosomal peptidyl transferase center (PTC) binder and growing evidence suggests that its inhibitory action depends on the sequence of the nascent peptide. How such selective inhibition on the molecular scale manifests on the cellular level remains unclear. Here, we use cryo-electron tomography to analyze the impact of Cm inside the bacterium Mycoplasma pneumoniae. By resolving the Cm-bound ribosomes to 3.0 Å, we elucidate Cm's coordination with natural nascent peptides and transfer RNAs in the PTC. We find that Cm leads to the accumulation of a number of translation elongation states, indicating ongoing futile accommodation cycles, and to extensive ribosome collisions. We, thus, suggest that, beyond its direct inhibition of protein synthesis, the action of Cm may involve the activation of cellular stress responses. This work exemplifies how in-cell structural biology can expand the understanding of mechanisms of action for extensively studied antibiotics.


  • Organizational Affiliation

    Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. liangxue@ibp.ac.cn.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34A [auth 0]48Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35B [auth 1]59Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75447 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36C [auth 2]37Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P52864 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2J [auth A]294Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3K [auth B]273Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4DA [auth U],
L [auth C]
205Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5M [auth D]219Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6N [auth E]215Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7O [auth F]155Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8P [auth G]142Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9Q [auth H]132Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10R [auth I]108Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11S [auth J]121Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12T [auth K]139Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13U [auth L]124Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZV [auth M]61Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15W [auth N]86Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75173 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16X [auth O]94Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Y [auth P]85Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18Z [auth Q]104Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19AA [auth R]87Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20BA [auth S]87Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75237 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21CA [auth T]60Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Trigger factorEA [auth X]444Mycoplasmoides pneumoniae M129Mutation(s): 0 
EC: 5.2.1.8
UniProt
Find proteins for P75454 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent chainGA [auth Z]36Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2HA [auth a]287Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3IA [auth b]287Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4JA [auth c]212Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5KA [auth d]180Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6LA [auth e]184Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9MA [auth f]149Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10NA [auth g]161Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11OA [auth h]137Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13PA [auth i]146Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14QA [auth j]122Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15RA [auth k]151Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16SA [auth l]139Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17TA [auth m]124Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18UA [auth n]116Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19VA [auth o]119Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20WA [auth p]127Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21XA [auth q]100Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22YA [auth r]159Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23ZA [auth s]237Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24AB [auth t]111Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27BB [auth u]104Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75458 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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UniProt GroupP75458
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28CB [auth v]65Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75171 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29DB [auth w]111Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50310 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31EB [auth x]97Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P78020 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32FB [auth y]57Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75238 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33 1GB [auth z]53Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P78015 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLM (Subject of Investigation/LOI)
Query on CLM

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IB [auth 3]CHLORAMPHENICOL
C11 H12 Cl2 N2 O5
WIIZWVCIJKGZOK-RKDXNWHRSA-N
SPM
Query on SPM

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CK [auth 3],
FP [auth b],
QK [auth 3],
YK [auth 3]
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
LYS
Query on LYS

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WO [auth 8]LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
SPD
Query on SPD

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BL [auth 5]
DK [auth 3]
DL [auth 5]
EK [auth 3]
FK [auth 3]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
N2P
Query on N2P

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CL [auth 5],
SK [auth 3],
TK [auth 3],
WK [auth 3]
PENTANE-1,5-DIAMINE
C5 H14 N2
VHRGRCVQAFMJIZ-UHFFFAOYSA-N
PUT
Query on PUT

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AK [auth 3]
BK [auth 3]
EL [auth 5]
GK [auth 3]
RK [auth 3]
1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
ZN
Query on ZN

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AP [auth Q]
HB [auth 2]
HP [auth x]
KP [auth y]
LP [auth z]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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JB [auth 3]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AC [auth 3]
AD [auth 3]
AE [auth 3]
AF [auth 3]
AG [auth 3]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chan Zuckerberg InitiativeUnited StatesVisual Proteomics Imaging
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-20
    Type: Initial release
  • Version 1.1: 2024-12-25
    Changes: Database references