4WFA

The crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex with linezolid

• PDB DOI: https://doi.org/10.2210/pdb4WFA/pdb
• NAKB: 4WFA

• Classification: RIBOSOME
• Organism(s): Staphylococcus aureus subsp. aureus NCTC 8325, Staphylococcus aureus subsp. aureus USA300
• Mutation(s): No 


• Deposited: 2014-09-14 Released: 2015-10-21 
• Deposition Author(s): Eyal, Z., Matzov, D., Krupkin, M., Wekselman, I., Zimmerman, E., Rozenberg, H., Bashan, A., Yonath, A.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.39 Å
• R-Value Free: 0.243 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Starting Model: experimental

Literature

Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus.

Eyal, Z., Matzov, D., Krupkin, M., Wekselman, I., Paukner, S., Zimmerman, E., Rozenberg, H., Bashan, A., Yonath, A.

(2015) Proc Natl Acad Sci U S A 112: E5805-E5814

• PubMed: 26464510 
• DOI: https://doi.org/10.1073/pnas.1517952112
• Primary Citation of Related Structures:  
  4WCE, 4WF9, 4WFA, 4WFB


• PubMed Abstract: 
  

  The emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. Here we present the crystal structure of the large ribosomal subunit from Staphylococcus aureus, a versatile Gram-positive aggressive pathogen, and its complexes with the known antibiotics linezolid and telithromycin, as well as with a new, highly potent pleuromutilin derivative, BC-3205. These crystal structures shed light on specific structural motifs of the S. aureus ribosome and the binding modes of the aforementioned antibiotics. Moreover, by analyzing the ribosome structure and comparing it with those of nonpathogenic bacterial models, we identified some unique internal and peripheral structural motifs that may be potential candidates for improving known antibiotics and for use in the design of selective antibiotic drugs against S. aureus.

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Organizational Affiliation: 

Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 26-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1 

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

Macromolecule Content

• Total Structure Weight: 1,362.37 kDa 
• Atom Count: 81,465 
• Modelled Residue Count: 5,801 
• Deposited Residue Count: 6,252 
• Unique protein chains: 26
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	C [auth A]	277	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for P60430 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P60430  Go to UniProtKB:  P60430

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	D [auth B]	220	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for Q2FW06 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW06  Go to UniProtKB:  Q2FW06

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4	E [auth C]	207	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for Q2FW07 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW07  Go to UniProtKB:  Q2FW07

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5	F [auth D]	179	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for Q2FW18 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW18  Go to UniProtKB:  Q2FW18

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L6	G [auth E]	178	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for Q2FW21 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW21  Go to UniProtKB:  Q2FW21

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13	H [auth G]	145	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for Q2FW38 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW38  Go to UniProtKB:  Q2FW38

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	I [auth H]	122	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for Q2FW16 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW16  Go to UniProtKB:  Q2FW16

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15	J [auth I]	146	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for P0A0F8 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P0A0F8  Go to UniProtKB:  P0A0F8

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L16	K [auth J]	144	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for Q2FW13 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW13  Go to UniProtKB:  Q2FW13

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L17	L [auth K]	122	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for Q2FW33 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW33  Go to UniProtKB:  Q2FW33

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18	M [auth L]	119	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for Q2FW22 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW22  Go to UniProtKB:  Q2FW22

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19	N [auth M]	116	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for Q2FZ42 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FZ42  Go to UniProtKB:  Q2FZ42

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L20	O [auth N]	118	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for Q2FXQ1 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FXQ1  Go to UniProtKB:  Q2FXQ1

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L21	P [auth O]	102	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for Q2FXS8 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FXS8  Go to UniProtKB:  Q2FXS8

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22	Q [auth P]	117	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for Q2FW11 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW11  Go to UniProtKB:  Q2FW11

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L23	R [auth Q]	91	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for Q2FW08 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW08  Go to UniProtKB:  Q2FW08

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24	S [auth R]	105	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for Q2FW17 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW17  Go to UniProtKB:  Q2FW17

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L25	T [auth S]	217	Staphylococcus aureus subsp. aureus USA300	Mutation(s): 0
UniProt
Find proteins for Q2FJE0 (Staphylococcus aureus (strain USA300)) Explore Q2FJE0  Go to UniProtKB:  Q2FJE0

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L27	U [auth T]	94	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for Q2FXT0 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FXT0  Go to UniProtKB:  Q2FXT0

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L28	V [auth U]	62	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for Q2FZ60 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FZ60  Go to UniProtKB:  Q2FZ60

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L29	W [auth V]	69	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for Q2FW14 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW14  Go to UniProtKB:  Q2FW14

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L30	X [auth W]	59	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for P0A0G2 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P0A0G2  Go to UniProtKB:  P0A0G2

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32	Y [auth Z]	58	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for Q2FZF1 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FZF1  Go to UniProtKB:  Q2FZF1

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L34	Z [auth 2]	45	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for Q2FUQ0 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FUQ0  Go to UniProtKB:  Q2FUQ0

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L35	AA [auth 3]	66	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for Q2FXQ0 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FXQ0  Go to UniProtKB:  Q2FXQ0

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L36	BA [auth 4]	37	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0
UniProt
Find proteins for Q2FW29 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW29  Go to UniProtKB:  Q2FW29

Entity ID: 1
Molecule	Chains	Length	Organism	Image
23S rRNA	A [auth X]	2,923	Staphylococcus aureus subsp. aureus NCTC 8325

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5S rRNA	B [auth Y]	114	Staphylococcus aureus subsp. aureus NCTC 8325

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZLD	CA [auth X]	N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide C16 H20 F N3 O4 TYZROVQLWOKYKF-ZDUSSCGKSA-N
EPE	IQ [auth X], JQ [auth X], KQ [auth X], LQ [auth X]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
SPD	MQ [auth X], NQ [auth X], OQ [auth X], PQ [auth X], QQ [auth X], RQ [auth X], SQ [auth X], TQ [auth X], UR [auth J]	SPERMIDINE C7 H19 N3 ATHGHQPFGPMSJY-UHFFFAOYSA-N
MPD	DA [auth X], EA [auth X], FA [auth X], GA [auth X], HA [auth X], IA [auth X], JA [auth X], KA [auth X], LA [auth X]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
MN	AD [auth X], AE [auth X], AF [auth X], AG [auth X], AH [auth X], AJ [auth X], AK [auth X], BD [auth X], BE [auth X], BF [auth X], BG [auth X], BH [auth X], BJ [auth X], BK [auth X], BQ [auth X], BR [auth X], BS [auth Z], CD [auth X], CE [auth X], CF [auth X], CG [auth X], CH [auth X], CJ [auth X], CK [auth X], CQ [auth X], CR [auth X], DD [auth X], DE [auth X], DF [auth X], DG [auth X], DH [auth X], DJ [auth X], DK [auth X], ED [auth X], EE [auth X], EF [auth X], EG [auth X], EH [auth X], EJ [auth X], EK [auth X], FD [auth X], FE [auth X], FF [auth X], FG [auth X], FH [auth X], FJ [auth X], FK [auth X], FR [auth Y], GD [auth X], GE [auth X], GF [auth X], GG [auth X], GH [auth X], GJ [auth X], GK [auth X], GR [auth Y], HD [auth X], HE [auth X], HF [auth X], HG [auth X], HH [auth X], HI [auth X], HJ [auth X], HK [auth X], HQ [auth X], ID [auth X], IE [auth X], IF [auth X], IG [auth X], IH [auth X], II [auth X], IK [auth X], JD [auth X], JE [auth X], JF [auth X], JG [auth X], JH [auth X], JI [auth X], JK [auth X], KD [auth X], KE [auth X], KF [auth X], KG [auth X], KH [auth X], KI [auth X], KK [auth X], KO [auth X], LD [auth X], LE [auth X], LF [auth X], LG [auth X], LH [auth X], LI [auth X], LK [auth X], LO [auth X], MD [auth X], ME [auth X], MF [auth X], MG [auth X], MH [auth X], MI [auth X], MK [auth X], NC [auth X], ND [auth X], NE [auth X], NF [auth X], NG [auth X], NH [auth X], NI [auth X], OC [auth X], OD [auth X], OE [auth X], OF [auth X], OG [auth X], OH [auth X], OI [auth X], PC [auth X], PD [auth X], PE [auth X], PF [auth X], PG [auth X], PH [auth X], PI [auth X], QC [auth X], QD [auth X], QE [auth X], QF [auth X], QG [auth X], QH [auth X], QI [auth X], RC [auth X], RD [auth X], RE [auth X], RF [auth X], RG [auth X], RH [auth X], RI [auth X], SC [auth X], SD [auth X], SE [auth X], SF [auth X], SG [auth X], SH [auth X], SI [auth X], TC [auth X], TD [auth X], TE [auth X], TF [auth X], TG [auth X], TH [auth X], TI [auth X], UC [auth X], UD [auth X], UE [auth X], UF [auth X], UG [auth X], UH [auth X], UI [auth X], VC [auth X], VD [auth X], VE [auth X], VF [auth X], VG [auth X], VH [auth X], VI [auth X], WC [auth X], WD [auth X], WE [auth X], WF [auth X], WG [auth X], WH [auth X], WI [auth X], WR [auth M], XC [auth X], XD [auth X], XE [auth X], XF [auth X], XG [auth X], XH [auth X], XI [auth X], YC [auth X], YD [auth X], YE [auth X], YF [auth X], YG [auth X], YH [auth X], YI [auth X], YQ [auth X], ZC [auth X], ZD [auth X], ZE [auth X], ZF [auth X], ZG [auth X], ZI [auth X], ZJ [auth X]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
EOH	MR [auth Y], UQ [auth X], VQ [auth X], WQ [auth X], XQ [auth X]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N
MG	AB [auth X], AC [auth X], AI [auth X], AL [auth X], AM [auth X], AN [auth X], AO [auth X], AP [auth X], AQ [auth X], AR [auth X], AS [auth W], BB [auth X], BC [auth X], BI [auth X], BL [auth X], BM [auth X], BN [auth X], BO [auth X], BP [auth X], CB [auth X], CC [auth X], CI [auth X], CL [auth X], CM [auth X], CN [auth X], CO [auth X], CP [auth X], CS [auth Z], DB [auth X], DC [auth X], DI [auth X], DL [auth X], DM [auth X], DN [auth X], DO [auth X], DP [auth X], DQ [auth X], DR [auth X], DS [auth Z], EB [auth X], EC [auth X], EI [auth X], EL [auth X], EM [auth X], EN [auth X], EP [auth X], EQ [auth X], ER [auth Y], FB [auth X], FC [auth X], FI [auth X], FL [auth X], FM [auth X], FN [auth X], FO [auth X], FP [auth X], FQ [auth X], GB [auth X], GC [auth X], GI [auth X], GL [auth X], GM [auth X], GN [auth X], GO [auth X], GP [auth X], GQ [auth X], HB [auth X], HC [auth X], HL [auth X], HM [auth X], HN [auth X], HO [auth X], HP [auth X], HR [auth Y], IB [auth X], IC [auth X], IJ [auth X], IL [auth X], IM [auth X], IN [auth X], IO [auth X], IP [auth X], IR [auth Y], JB [auth X], JC [auth X], JJ [auth X], JL [auth X], JM [auth X], JN [auth X], JO [auth X], JP [auth X], JR [auth Y], KB [auth X], KC [auth X], KJ [auth X], KL [auth X], KM [auth X], KN [auth X], KP [auth X], KR [auth Y], LB [auth X], LC [auth X], LJ [auth X], LL [auth X], LM [auth X], LN [auth X], LP [auth X], LR [auth Y], MA [auth X], MB [auth X], MC [auth X], MJ [auth X], ML [auth X], MM [auth X], MN [auth X], MO [auth X], MP [auth X], NA [auth X], NB [auth X], NJ [auth X], NK [auth X], NL [auth X], NM [auth X], NN [auth X], NO [auth X], NP [auth X], NR [auth A], OA [auth X], OB [auth X], OJ [auth X], OK [auth X], OL [auth X], OM [auth X], ON [auth X], OO [auth X], OP [auth X], OR [auth A], PA [auth X], PB [auth X], PJ [auth X], PK [auth X], PL [auth X], PM [auth X], PN [auth X], PO [auth X], PP [auth X], PR [auth B], QA [auth X], QB [auth X], QJ [auth X], QK [auth X], QL [auth X], QM [auth X], QN [auth X], QO [auth X], QP [auth X], QR [auth C], RA [auth X], RB [auth X], RJ [auth X], RK [auth X], RL [auth X], RM [auth X], RN [auth X], RO [auth X], RP [auth X], RR [auth G], SA [auth X], SB [auth X], SJ [auth X], SK [auth X], SL [auth X], SM [auth X], SN [auth X], SO [auth X], SP [auth X], SR [auth G], TA [auth X], TB [auth X], TJ [auth X], TK [auth X], TL [auth X], TM [auth X], TN [auth X], TO [auth X], TP [auth X], TR [auth I], UA [auth X], UB [auth X], UJ [auth X], UK [auth X], UL [auth X], UM [auth X], UN [auth X], UO [auth X], UP [auth X], VA [auth X], VB [auth X], VJ [auth X], VK [auth X], VL [auth X], VM [auth X], VN [auth X], VO [auth X], VP [auth X], VR [auth K], WA [auth X], WB [auth X], WJ [auth X], WK [auth X], WL [auth X], WM [auth X], WN [auth X], WO [auth X], WP [auth X], XA [auth X], XB [auth X], XJ [auth X], XK [auth X], XL [auth X], XM [auth X], XN [auth X], XO [auth X], XP [auth X], XR [auth N], YA [auth X], YB [auth X], YJ [auth X], YK [auth X], YL [auth X], YM [auth X], YN [auth X], YO [auth X], YP [auth X], YR [auth O], ZA [auth X], ZB [auth X], ZH [auth X], ZK [auth X], ZL [auth X], ZM [auth X], ZN [auth X], ZO [auth X], ZP [auth X], ZQ [auth X], ZR [auth O]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	EO [auth X]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.39 Å
• R-Value Free: 0.243 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 279.922	α = 90
b = 279.922	β = 90
c = 870.586	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-21 
Deposition Author(s): Eyal, Z., Matzov, D., Krupkin, M., Wekselman, I., Zimmerman, E., Rozenberg, H., Bashan, A., Yonath, A.E.

Revision History  

• Version 1.0: 2015-10-21
  Type: Initial release
  
• Version 1.1: 2015-10-28
  Changes: Database references
• Version 1.2: 2015-11-04
  Changes: Database references
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description