8P7Y image
Deposition Date 2023-05-31
Release Date 2024-11-20
Last Version Date 2025-03-12
Entry Detail
PDB ID:
8P7Y
Keywords:
TRANSLATION
Title:
Mycoplasma pneumoniae 70S ribosome with second S4 protein on large subunit
Biological Source:
Source Organism:
Mycoplasmoides pneumoniae M129 (Taxon ID: 272634)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.70 Å
Aggregation State:
CELL
Reconstruction Method:
SUBTOMOGRAM AVERAGING
8P7Y validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:A (auth: 0)
Chain Length:48
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P78006 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
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
UniProt ID:P75447 Pfam ID:PF01632
Structures with similar UniProt ID
Protein Blast
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
UniProt ID:P52864 Pfam ID:PF00444
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:D (auth: 3)
Chain Length:2907
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:E (auth: 4)
Chain Length:108
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:F (auth: 5)
Chain Length:1520
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polyribonucleotide
Molecule:tRNA-Ala (E-site)
Chain IDs:G (auth: 6)
Chain Length:76
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polyribonucleotide
Molecule:tRNA-Asp (P-site)
Chain IDs:H (auth: 7)
Chain Length:75
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polyribonucleotide
Molecule:tRNA-Lys (A-site)
Chain IDs:I (auth: 8)
Chain Length:76
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:J (auth: A)
Chain Length:294
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75560 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:K (auth: B)
Chain Length:273
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P41205 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:L (auth: C), DA (auth: U)
Chain Length:205
Number of Molecules:2
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P46775 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:M (auth: D)
Chain Length:219
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:Q50301 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:N (auth: E)
Chain Length:215
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75543 Pfam ID:PF01250
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:O (auth: F)
Chain Length:155
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75545 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:P (auth: G)
Chain Length:161
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:Q50304 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:Q (auth: H)
Chain Length:132
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75179 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:R (auth: I)
Chain Length:146
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75581 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:S (auth: J)
Chain Length:121
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:Q50296 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:T (auth: K)
Chain Length:151
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75546 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:U (auth: L)
Chain Length:124
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:Q50297 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Gene (Uniprot):rpsZ
Chain IDs:V (auth: M)
Chain Length:61
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:Q50305 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:W (auth: N)
Chain Length:116
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75173 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Chain IDs:X (auth: O)
Chain Length:94
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75131
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:Y (auth: P)
Chain Length:127
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:Q50309 Pfam ID:PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:Z (auth: Q)
Chain Length:100
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75541 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:AA (auth: R)
Chain Length:87
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75576 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:BA (auth: S)
Chain Length:237
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75237 Pfam ID:PF01649
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Gene (Uniprot):rpsU
Chain IDs:CA (auth: T)
Chain Length:111
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P57079
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Trigger factor
Gene (Uniprot):tig
Chain IDs:EA (auth: X)
Chain Length:97
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75454 Pfam ID:PF05697, PF00254, PF05698
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:FA (auth: Y)
Chain Length:21
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Polymer Type:polypeptide(L)
Molecule:Nascent chain
Chain IDs:GA (auth: Z)
Chain Length:36
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:HA (auth: a)
Chain Length:294
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75577 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:IA (auth: b)
Chain Length:273
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75580 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:JA (auth: c)
Chain Length:205
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75579 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:KA (auth: d)
Chain Length:219
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:Q50306 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:LA (auth: e)
Chain Length:215
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:Q50303 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:MA (auth: f)
Chain Length:155
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75540 Pfam ID:PF01281, PF03948
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Gene (Uniprot):rplJ
Chain IDs:NA (auth: g)
Chain Length:161
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75240 Pfam ID:PF00466
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:OA (auth: h)
Chain Length:132
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75550 Pfam ID:PF03946, PF00298
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:PA (auth: i)
Chain Length:146
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75178 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:QA (auth: j)
Chain Length:121
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:Q50308 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:RA (auth: k)
Chain Length:151
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:Q50300 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:SA (auth: l)
Chain Length:124
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P41204 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:TA (auth: m)
Chain Length:61
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:Q59547 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:UA (auth: n)
Chain Length:116
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:Q50302 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:VA (auth: o)
Chain Length:94
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75133 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:WA (auth: p)
Chain Length:127
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P78023 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:XA (auth: q)
Chain Length:100
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P78026 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:YA (auth: r)
Chain Length:87
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75575 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:ZA (auth: s)
Chain Length:237
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75578 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:AB (auth: t)
Chain Length:111
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:Q50307 Pfam ID:PF00467, PF17136
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:BB (auth: u)
Chain Length:205
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75458 Pfam ID:PF01016
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:CB (auth: v)
Chain Length:65
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75171 Pfam ID:PF00830
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:DB (auth: w)
Chain Length:111
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:Q50310 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:EB (auth: x)
Chain Length:97
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P78020 Pfam ID:PF01197
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:FB (auth: y)
Chain Length:21
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P75238 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33 1
Gene (Uniprot):rpmG1
Chain IDs:GB (auth: z)
Chain Length:36
Number of Molecules:1
Biological Source:Mycoplasmoides pneumoniae M129
UniProt ID:P78015 Pfam ID:PF00471
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
1MG D G modified residue
2MA D A modified residue
5MC F C modified residue
7MG F G modified residue
B8T F C modified residue
MA6 F A modified residue
OMG D G modified residue
Ligand Molecules
CLM
K
LYS
MG
N2P
PUT
SPD
SPM
ZN
Primary Citation
Structural insights into context-dependent inhibitory mechanisms of chloramphenicol in cells.
Nat.Struct.Mol.Biol. 32 257 267 (2025)
PMID: 39668257 DOI: 10.1038/s41594-024-01441-0

Abstact

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.

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Protein

Chemical

Disease

Primary Citation of related structures
8P7Y
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