8P6P

Mycoplasma pneumoniae small ribosomal subunit in chloramphenicol-treated cells


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 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 


Macromolecules

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2E [auth A]294Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75560 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3F [auth B]273Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P41205 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4G [auth C]205Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P46775 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5H [auth D]219Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50301 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6I [auth E]215Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75543 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7J [auth F]155Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75545 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8K [auth G]142Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50304 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9L [auth H]132Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75179 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10M [auth I]108Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75581 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11N [auth J]121Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50296 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12O [auth K]139Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75546 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13P [auth L]124Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50297 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZQ [auth M]61Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50305 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15R [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: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16S [auth O]94Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for A0A0H3DLS7 (Mycoplasmoides pneumoniae (strain ATCC 15531 / DSM 23978 / CIP 103766 / NBRC 14401 / NCTC 10119 / FH))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17T [auth P]85Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50309 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18U [auth Q]104Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75541 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19V [auth R]87Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75576 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20W [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: 24
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21X [auth T]60Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P57079 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31Z [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: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNAA [auth 3]2,907Mycoplasmoides pneumoniae M129
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Entity ID: 2
MoleculeChains LengthOrganismImage
16S ribosomal RNAB [auth 5]1,520Mycoplasmoides pneumoniae M129
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Entity ID: 3
MoleculeChains LengthOrganismImage
tRNA-Asp (P-site)C [auth 7]75Mycoplasmoides pneumoniae M129
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Entity ID: 4
MoleculeChains LengthOrganismImage
tRNA-Lys (A-site)D [auth 8]76Mycoplasmoides pneumoniae M129
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Entity ID: 25
MoleculeChains LengthOrganismImage
mRNA21Mycoplasmoides pneumoniae M129
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPD
Query on SPD

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AA [auth 5],
DA [auth 5]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
N2P
Query on N2P

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CA [auth 5]PENTANE-1,5-DIAMINE
C5 H14 N2
VHRGRCVQAFMJIZ-UHFFFAOYSA-N
PUT
Query on PUT

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BA [auth 5],
EA [auth 5]
1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
ZN
Query on ZN

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CE [auth M],
EE [auth Q]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth 5]
AC [auth 5]
AD [auth 5]
AE [auth K]
BB [auth 5]
AB [auth 5],
AC [auth 5],
AD [auth 5],
AE [auth K],
BB [auth 5],
BC [auth 5],
BD [auth 5],
BE [auth L],
CB [auth 5],
CC [auth 5],
CD [auth 5],
DB [auth 5],
DC [auth 5],
DD [auth 5],
DE [auth P],
EB [auth 5],
EC [auth 5],
ED [auth 5],
FA [auth 5],
FB [auth 5],
FC [auth 5],
FD [auth 5],
FE [auth Y],
GA [auth 5],
GB [auth 5],
GC [auth 5],
GD [auth 5],
HA [auth 5],
HB [auth 5],
HC [auth 5],
HD [auth 5],
IA [auth 5],
IB [auth 5],
IC [auth 5],
ID [auth 5],
JA [auth 5],
JB [auth 5],
JC [auth 5],
JD [auth 5],
KA [auth 5],
KB [auth 5],
KC [auth 5],
KD [auth 5],
LA [auth 5],
LB [auth 5],
LC [auth 5],
LD [auth 5],
MA [auth 5],
MB [auth 5],
MC [auth 5],
MD [auth 5],
NA [auth 5],
NB [auth 5],
NC [auth 5],
ND [auth 5],
OA [auth 5],
OB [auth 5],
OC [auth 5],
OD [auth 5],
PA [auth 5],
PB [auth 5],
PC [auth 5],
PD [auth 5],
QA [auth 5],
QB [auth 5],
QC [auth 5],
QD [auth 5],
RA [auth 5],
RB [auth 5],
RC [auth 5],
RD [auth 5],
SA [auth 5],
SB [auth 5],
SC [auth 5],
SD [auth 5],
TA [auth 5],
TB [auth 5],
TC [auth 5],
TD [auth 5],
UA [auth 5],
UB [auth 5],
UC [auth 5],
UD [auth 5],
VA [auth 5],
VB [auth 5],
VC [auth 5],
VD [auth 5],
WA [auth 5],
WB [auth 5],
WC [auth 5],
WD [auth 5],
XA [auth 5],
XB [auth 5],
XC [auth 5],
XD [auth 7],
YA [auth 5],
YB [auth 5],
YC [auth 5],
YD [auth 8],
ZA [auth 5],
ZB [auth 5],
ZC [auth 5],
ZD [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONWarp1.0.9
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

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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