8P8B

Mycoplasma pneumoniae large ribosomal subunit in chloramphenicol-treated cells

• PDB DOI: https://doi.org/10.2210/pdb8P8B/pdb
• EM Map EMD-17134: EMDB EMDataResource

• Classification: TRANSLATION
• Organism(s): Mycoplasmoides pneumoniae M129
• Mutation(s): No 


• Deposited: 2023-05-31 Released: 2024-11-20 
• Deposition Author(s): Schacherl, M., Xue, L., Spahn, C.M.T., Mahamid, J.
• Funding Organization(s): Chan Zuckerberg Initiative, German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: CELL 
• Reconstruction Method: SUBTOMOGRAM AVERAGING 

Starting Models: experimental

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 31-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 2,044.19 kDa 
• Atom Count: 97,182 
• Modelled Residue Count: 6,773 
• Deposited Residue Count: 9,130 
• Unique protein chains: 31
• Unique nucleic acid chains: 7

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L34	A [auth 0]	48	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P78006 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P78006  Go to UniProtKB:  P78006

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L35	B [auth 1]	59	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75447 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75447  Go to UniProtKB:  P75447

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L36	C [auth 2]	37	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P52864 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P52864  Go to UniProtKB:  P52864

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Trigger factor	J [auth X]	444	Mycoplasmoides pneumoniae M129	Mutation(s): 0  EC: 5.2.1.8
UniProt
Find proteins for P75454 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75454  Go to UniProtKB:  P75454

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
nascent peptide	L [auth Z]	36	Mycoplasmoides pneumoniae M129	Mutation(s): 0

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	M [auth a]	287	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75577 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75577  Go to UniProtKB:  P75577

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	N [auth b]	287	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75580 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75580  Go to UniProtKB:  P75580

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4	O [auth c]	212	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75579 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75579  Go to UniProtKB:  P75579

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5	P [auth d]	180	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for Q50306 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q50306  Go to UniProtKB:  Q50306

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L6	Q [auth e]	184	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for Q50303 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q50303  Go to UniProtKB:  Q50303

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L9	R [auth f]	149	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75540 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75540  Go to UniProtKB:  P75540

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L10	S [auth g]	161	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75240 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75240  Go to UniProtKB:  P75240

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L11	T [auth h]	137	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75550 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75550  Go to UniProtKB:  P75550

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13	U [auth i]	146	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75178 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75178  Go to UniProtKB:  P75178

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	V [auth j]	122	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for Q50308 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q50308  Go to UniProtKB:  Q50308

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15	W [auth k]	151	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for Q50300 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q50300  Go to UniProtKB:  Q50300

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L16	X [auth l]	139	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P41204 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P41204  Go to UniProtKB:  P41204

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L17	Y [auth m]	124	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for Q59547 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q59547  Go to UniProtKB:  Q59547

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18	Z [auth n]	116	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for Q50302 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q50302  Go to UniProtKB:  Q50302

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19	AA [auth o]	119	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75133 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75133  Go to UniProtKB:  P75133

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L20	BA [auth p]	127	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P78023 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P78023  Go to UniProtKB:  P78023

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L21	CA [auth q]	100	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P78026 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P78026  Go to UniProtKB:  P78026

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22	DA [auth r]	159	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75575 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75575  Go to UniProtKB:  P75575

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L23	EA [auth s]	237	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75578 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75578  Go to UniProtKB:  P75578

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24	FA [auth t]	111	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for Q50307 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q50307  Go to UniProtKB:  Q50307

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L27	GA [auth u]	104	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75458 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75458  Go to UniProtKB:  P75458

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L28	HA [auth v]	65	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75171 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75171  Go to UniProtKB:  P75171

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L29	IA [auth w]	111	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for Q50310 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q50310  Go to UniProtKB:  Q50310

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L31	JA [auth x]	97	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P78020 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P78020  Go to UniProtKB:  P78020

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32	KA [auth y]	57	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75238 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75238  Go to UniProtKB:  P75238

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L33 1	LA [auth z]	53	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P78015 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P78015  Go to UniProtKB:  P78015

Entity ID: 4
Molecule	Chains	Length	Organism	Image
23S ribosomal RNA	D [auth 3]	2,907	Mycoplasmoides pneumoniae M129

Entity ID: 5
Molecule	Chains	Length	Organism	Image
5S ribosomal RNA	E [auth 4]	108	Mycoplasmoides pneumoniae M129

Entity ID: 6
Molecule	Chains	Length	Organism	Image
16S ribosomal RNA	F [auth 5]	1,520	Mycoplasmoides pneumoniae M129

Entity ID: 7
Molecule	Chains	Length	Organism	Image
tRNA-Ala (E-site)	G [auth 6]	76	Mycoplasmoides pneumoniae M129

Entity ID: 8
Molecule	Chains	Length	Organism	Image
tRNA-Asp (P-site)	H [auth 7]	75	Mycoplasmoides pneumoniae M129

Entity ID: 9
Molecule	Chains	Length	Organism	Image
tRNA-Lys (A-site)	I [auth 8]	76	Mycoplasmoides pneumoniae M129

Entity ID: 11
Molecule	Chains	Length	Organism	Image
mRNA	K [auth Y]	9	Mycoplasmoides pneumoniae M129

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLM (Subject of Investigation/LOI)	NA [auth 3]	CHLORAMPHENICOL C11 H12 Cl2 N2 O5 WIIZWVCIJKGZOK-RKDXNWHRSA-N
SPM	BK [auth 3], FJ [auth 3], LK [auth b], TJ [auth 3]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N
LYS	IK [auth 8]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O
SPD	AK [auth 3], CK [auth 3], GJ [auth 3], HJ [auth 3], IJ [auth 3], KJ [auth 3], LJ [auth 3], MJ [auth 3], NJ [auth 3], OJ [auth 3], PJ [auth 3], QJ [auth 3], RJ [auth 3], SJ [auth 3], XJ [auth 3], YJ [auth 3]	SPERMIDINE C7 H19 N3 ATHGHQPFGPMSJY-UHFFFAOYSA-N
N2P	VJ [auth 3], WJ [auth 3], ZJ [auth 3]	PENTANE-1,5-DIAMINE C5 H14 N2 VHRGRCVQAFMJIZ-UHFFFAOYSA-N
PUT	AJ [auth 3], BJ [auth 3], CJ [auth 3], DJ [auth 3], EJ [auth 3], JJ [auth 3], UJ [auth 3]	1,4-DIAMINOBUTANE C4 H12 N2 KIDHWZJUCRJVML-UHFFFAOYSA-N
ZN	MA [auth 2], NK [auth x], QK [auth y], RK [auth z]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	OA [auth 3]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	AB [auth 3], AC [auth 3], AD [auth 3], AE [auth 3], AF [auth 3], AG [auth 3], AH [auth 3], AI [auth 3], BB [auth 3], BC [auth 3], BD [auth 3], BE [auth 3], BF [auth 3], BG [auth 3], BH [auth 3], BI [auth 3], CB [auth 3], CC [auth 3], CD [auth 3], CE [auth 3], CF [auth 3], CG [auth 3], CH [auth 3], CI [auth 3], DB [auth 3], DC [auth 3], DD [auth 3], DE [auth 3], DF [auth 3], DG [auth 3], DH [auth 3], DI [auth 3], DK [auth 4], EB [auth 3], EC [auth 3], ED [auth 3], EE [auth 3], EF [auth 3], EG [auth 3], EH [auth 3], EI [auth 3], EK [auth 6], FB [auth 3], FC [auth 3], FD [auth 3], FE [auth 3], FF [auth 3], FG [auth 3], FH [auth 3], FI [auth 3], FK [auth 7], GB [auth 3], GC [auth 3], GD [auth 3], GE [auth 3], GF [auth 3], GG [auth 3], GH [auth 3], GI [auth 3], GK [auth 8], HB [auth 3], HC [auth 3], HD [auth 3], HE [auth 3], HF [auth 3], HG [auth 3], HH [auth 3], HI [auth 3], HK [auth 8], IB [auth 3], IC [auth 3], ID [auth 3], IE [auth 3], IF [auth 3], IG [auth 3], IH [auth 3], II [auth 3], JB [auth 3], JC [auth 3], JD [auth 3], JE [auth 3], JF [auth 3], JG [auth 3], JH [auth 3], JI [auth 3], JK [auth b], KB [auth 3], KC [auth 3], KD [auth 3], KE [auth 3], KF [auth 3], KG [auth 3], KH [auth 3], KI [auth 3], KK [auth b], LB [auth 3], LC [auth 3], LD [auth 3], LE [auth 3], LF [auth 3], LG [auth 3], LH [auth 3], LI [auth 3], MB [auth 3], MC [auth 3], MD [auth 3], ME [auth 3], MF [auth 3], MG [auth 3], MH [auth 3], MI [auth 3], MK [auth i], NB [auth 3], NC [auth 3], ND [auth 3], NE [auth 3], NF [auth 3], NG [auth 3], NH [auth 3], NI [auth 3], OB [auth 3], OC [auth 3], OD [auth 3], OE [auth 3], OF [auth 3], OG [auth 3], OH [auth 3], OI [auth 3], OK [auth y], PA [auth 3], PB [auth 3], PC [auth 3], PD [auth 3], PE [auth 3], PF [auth 3], PG [auth 3], PH [auth 3], PI [auth 3], PK [auth y], QA [auth 3], QB [auth 3], QC [auth 3], QD [auth 3], QE [auth 3], QF [auth 3], QG [auth 3], QH [auth 3], QI [auth 3], RA [auth 3], RB [auth 3], RC [auth 3], RD [auth 3], RE [auth 3], RF [auth 3], RG [auth 3], RH [auth 3], RI [auth 3], SA [auth 3], SB [auth 3], SC [auth 3], SD [auth 3], SE [auth 3], SF [auth 3], SG [auth 3], SH [auth 3], SI [auth 3], TA [auth 3], TB [auth 3], TC [auth 3], TD [auth 3], TE [auth 3], TF [auth 3], TG [auth 3], TH [auth 3], TI [auth 3], UA [auth 3], UB [auth 3], UC [auth 3], UD [auth 3], UE [auth 3], UF [auth 3], UG [auth 3], UH [auth 3], UI [auth 3], VA [auth 3], VB [auth 3], VC [auth 3], VD [auth 3], VE [auth 3], VF [auth 3], VG [auth 3], VH [auth 3], VI [auth 3], WA [auth 3], WB [auth 3], WC [auth 3], WD [auth 3], WE [auth 3], WF [auth 3], WG [auth 3], WH [auth 3], WI [auth 3], XA [auth 3], XB [auth 3], XC [auth 3], XD [auth 3], XE [auth 3], XF [auth 3], XG [auth 3], XH [auth 3], XI [auth 3], YA [auth 3], YB [auth 3], YC [auth 3], YD [auth 3], YE [auth 3], YF [auth 3], YG [auth 3], YH [auth 3], YI [auth 3], ZA [auth 3], ZB [auth 3], ZC [auth 3], ZD [auth 3], ZE [auth 3], ZF [auth 3], ZG [auth 3], ZH [auth 3], ZI [auth 3]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: CELL 
• Reconstruction Method: SUBTOMOGRAM AVERAGING 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	Warp	1.0.9
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-20 
Deposition Author(s): Schacherl, M., Xue, L., Spahn, C.M.T., Mahamid, J.

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Funding Organization	Location	Grant Number
Chan Zuckerberg Initiative	United States	Visual Proteomics Imaging
German Research Foundation (DFG)	Germany	--

Revision History  

• Version 1.0: 2024-11-20
  Type: Initial release