7Y41

Mycobacterium smegmatis 50S ribosomal subunit from Log Phase of growth

• PDB DOI: https://doi.org/10.2210/pdb7Y41/pdb
• EM Map EMD-33599: EMDB EMDataResource
• NAKB: 7Y41

• Classification: RIBOSOME
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Mutation(s): No 


• Deposited: 2022-06-13 Released: 2023-05-03 
• Deposition Author(s): Sengupta, J., Baid, P.
• Funding Organization(s): Science and Engineering Research Board (SERB), Council of Scientific & Industrial Research (CSIR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structures reveal a unique conformational dynamics of the Mycobacterium 23S rRNA helices

Sengupta, J., Baid, P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 1,479.79 kDa 
• Atom Count: 97,056 
• Modelled Residue Count: 6,766 
• Deposited Residue Count: 7,078 
• Unique protein chains: 31
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal subunit bL37	A [auth 3]	24	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QTP4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QTP4  Go to UniProtKB:  A0QTP4

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	D [auth C]	278	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSD4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSD4  Go to UniProtKB:  A0QSD4

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	E [auth D]	217	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSD1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSD1  Go to UniProtKB:  A0QSD1

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4	F [auth E]	215	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSD2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSD2  Go to UniProtKB:  A0QSD2

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5	G [auth F]	187	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSG1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSG1  Go to UniProtKB:  A0QSG1

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L6	H [auth G]	179	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSG4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSG4  Go to UniProtKB:  A0QSG4

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L10	I	175	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QS62 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QS62  Go to UniProtKB:  A0QS62

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L11	J	142	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QS45 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QS45  Go to UniProtKB:  A0QS45

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13	K	147	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSP8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSP8  Go to UniProtKB:  A0QSP8

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	L	122	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSF9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSF9  Go to UniProtKB:  A0QSF9

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15	M	147	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSG8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSG8  Go to UniProtKB:  A0QSG8

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L16	N	138	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSD8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSD8  Go to UniProtKB:  A0QSD8

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L17	O	199	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSL9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSL9  Go to UniProtKB:  A0QSL9

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18	P	127	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSG5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSG5  Go to UniProtKB:  A0QSG5

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19	Q	113	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QV42 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QV42  Go to UniProtKB:  A0QV42

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L20	R	129	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QYU6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QYU6  Go to UniProtKB:  A0QYU6

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L21	S	103	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0R151 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R151  Go to UniProtKB:  A0R151

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22	T	153	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSD6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSD6  Go to UniProtKB:  A0QSD6

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L23	U	100	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSD3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSD3  Go to UniProtKB:  A0QSD3

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24	V	105	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSG0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSG0  Go to UniProtKB:  A0QSG0

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L25	W	215	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0R3D2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R3D2  Go to UniProtKB:  A0R3D2

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L27	X	88	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0R150 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R150  Go to UniProtKB:  A0R150

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L28	Y	64	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QV03 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QV03  Go to UniProtKB:  A0QV03

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L29	Z	77	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSD9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSD9  Go to UniProtKB:  A0QSD9

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L30	AA [auth a]	61	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSG7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSG7  Go to UniProtKB:  A0QSG7

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32	BA [auth b]	57	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0R3I9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R3I9  Go to UniProtKB:  A0R3I9

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L33 1	CA [auth c]	55	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QS39 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QS39  Go to UniProtKB:  A0QS39

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L34	DA [auth d]	47	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0R7K0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R7K0  Go to UniProtKB:  A0R7K0

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L35	EA [auth e]	64	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QYU7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QYU7  Go to UniProtKB:  A0QYU7

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L36	FA [auth f]	37	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSL4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSL4  Go to UniProtKB:  A0QSL4

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L31	GA [auth g]	75	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0R215 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R215  Go to UniProtKB:  A0R215

Entity ID: 2
Molecule	Chains	Length	Organism	Image
23S ribosomal RNA	B [auth A]	3,120	Mycolicibacterium smegmatis MC2 155

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5S ribosomal RNA	C [auth B]	118	Mycolicibacterium smegmatis MC2 155

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	AQ [auth f], BQ [auth g], XP [auth Y], YP [auth c]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	AB [auth A], AC [auth A], AD [auth A], AE [auth A], AF [auth A], AG [auth A], AH [auth A], AI [auth A], AJ [auth A], AK [auth A], AL [auth A], AM [auth A], AN [auth A], AO [auth A], AP [auth A], BB [auth A], BC [auth A], BD [auth A], BE [auth A], BF [auth A], BG [auth A], BH [auth A], BI [auth A], BJ [auth A], BK [auth A], BL [auth A], BM [auth A], BN [auth A], BO [auth A], BP [auth A], CB [auth A], CC [auth A], CD [auth A], CE [auth A], CF [auth A], CG [auth A], CH [auth A], CI [auth A], CJ [auth A], CK [auth A], CL [auth A], CM [auth A], CN [auth A], CO [auth A], CP [auth A], DB [auth A], DC [auth A], DD [auth A], DE [auth A], DF [auth A], DG [auth A], DH [auth A], DI [auth A], DJ [auth A], DK [auth A], DL [auth A], DM [auth A], DN [auth A], DO [auth A], DP [auth B], EB [auth A], EC [auth A], ED [auth A], EE [auth A], EF [auth A], EG [auth A], EH [auth A], EI [auth A], EJ [auth A], EK [auth A], EL [auth A], EM [auth A], EN [auth A], EO [auth A], EP [auth B], FB [auth A], FC [auth A], FD [auth A], FE [auth A], FF [auth A], FG [auth A], FH [auth A], FI [auth A], FJ [auth A], FK [auth A], FL [auth A], FM [auth A], FN [auth A], FO [auth A], FP [auth B], GB [auth A], GC [auth A], GD [auth A], GE [auth A], GF [auth A], GG [auth A], GH [auth A], GI [auth A], GJ [auth A], GK [auth A], GL [auth A], GM [auth A], GN [auth A], GO [auth A], GP [auth B], HA [auth A], HB [auth A], HC [auth A], HD [auth A], HE [auth A], HF [auth A], HG [auth A], HH [auth A], HI [auth A], HJ [auth A], HK [auth A], HL [auth A], HM [auth A], HN [auth A], HO [auth A], HP [auth B], IA [auth A], IB [auth A], IC [auth A], ID [auth A], IE [auth A], IF [auth A], IG [auth A], IH [auth A], II [auth A], IJ [auth A], IK [auth A], IL [auth A], IM [auth A], IN [auth A], IO [auth A], IP [auth B], JA [auth A], JB [auth A], JC [auth A], JD [auth A], JE [auth A], JF [auth A], JG [auth A], JH [auth A], JI [auth A], JJ [auth A], JK [auth A], JL [auth A], JM [auth A], JN [auth A], JO [auth A], JP [auth B], KA [auth A], KB [auth A], KC [auth A], KD [auth A], KE [auth A], KF [auth A], KG [auth A], KH [auth A], KI [auth A], KJ [auth A], KK [auth A], KL [auth A], KM [auth A], KN [auth A], KO [auth A], KP [auth B], LA [auth A], LB [auth A], LC [auth A], LD [auth A], LE [auth A], LF [auth A], LG [auth A], LH [auth A], LI [auth A], LJ [auth A], LK [auth A], LL [auth A], LM [auth A], LN [auth A], LO [auth A], LP [auth B], MA [auth A], MB [auth A], MC [auth A], MD [auth A], ME [auth A], MF [auth A], MG [auth A], MH [auth A], MI [auth A], MJ [auth A], MK [auth A], ML [auth A], MM [auth A], MN [auth A], MO [auth A], MP [auth C], NA [auth A], NB [auth A], NC [auth A], ND [auth A], NE [auth A], NF [auth A], NG [auth A], NH [auth A], NI [auth A], NJ [auth A], NK [auth A], NL [auth A], NM [auth A], NN [auth A], NO [auth A], NP [auth C], OA [auth A], OB [auth A], OC [auth A], OD [auth A], OE [auth A], OF [auth A], OG [auth A], OH [auth A], OI [auth A], OJ [auth A], OK [auth A], OL [auth A], OM [auth A], ON [auth A], OO [auth A], OP [auth C], PA [auth A], PB [auth A], PC [auth A], PD [auth A], PE [auth A], PF [auth A], PG [auth A], PH [auth A], PI [auth A], PJ [auth A], PK [auth A], PL [auth A], PM [auth A], PN [auth A], PO [auth A], PP [auth C], QA [auth A], QB [auth A], QC [auth A], QD [auth A], QE [auth A], QF [auth A], QG [auth A], QH [auth A], QI [auth A], QJ [auth A], QK [auth A], QL [auth A], QM [auth A], QN [auth A], QO [auth A], QP [auth C], RA [auth A], RB [auth A], RC [auth A], RD [auth A], RE [auth A], RF [auth A], RG [auth A], RH [auth A], RI [auth A], RJ [auth A], RK [auth A], RL [auth A], RM [auth A], RN [auth A], RO [auth A], RP [auth E], SA [auth A], SB [auth A], SC [auth A], SD [auth A], SE [auth A], SF [auth A], SG [auth A], SH [auth A], SI [auth A], SJ [auth A], SK [auth A], SL [auth A], SM [auth A], SN [auth A], SO [auth A], SP [auth F], TA [auth A], TB [auth A], TC [auth A], TD [auth A], TE [auth A], TF [auth A], TG [auth A], TH [auth A], TI [auth A], TJ [auth A], TK [auth A], TL [auth A], TM [auth A], TN [auth A], TO [auth A], TP [auth M], UA [auth A], UB [auth A], UC [auth A], UD [auth A], UE [auth A], UF [auth A], UG [auth A], UH [auth A], UI [auth A], UJ [auth A], UK [auth A], UL [auth A], UM [auth A], UN [auth A], UO [auth A], UP [auth N], VA [auth A], VB [auth A], VC [auth A], VD [auth A], VE [auth A], VF [auth A], VG [auth A], VH [auth A], VI [auth A], VJ [auth A], VK [auth A], VL [auth A], VM [auth A], VN [auth A], VO [auth A], VP [auth N], WA [auth A], WB [auth A], WC [auth A], WD [auth A], WE [auth A], WF [auth A], WG [auth A], WH [auth A], WI [auth A], WJ [auth A], WK [auth A], WL [auth A], WM [auth A], WN [auth A], WO [auth A], WP [auth T], XA [auth A], XB [auth A], XC [auth A], XD [auth A], XE [auth A], XF [auth A], XG [auth A], XH [auth A], XI [auth A], XJ [auth A], XK [auth A], XL [auth A], XM [auth A], XN [auth A], XO [auth A], YA [auth A], YB [auth A], YC [auth A], YD [auth A], YE [auth A], YF [auth A], YG [auth A], YH [auth A], YI [auth A], YJ [auth A], YK [auth A], YL [auth A], YM [auth A], YN [auth A], YO [auth A], ZA [auth A], ZB [auth A], ZC [auth A], ZD [auth A], ZE [auth A], ZF [auth A], ZG [auth A], ZH [auth A], ZI [auth A], ZJ [auth A], ZK [auth A], ZL [auth A], ZM [auth A], ZN [auth A], ZO [auth A], ZP [auth e]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-03 
Deposition Author(s): Sengupta, J., Baid, P.

---

Funding Organization	Location	Grant Number
Science and Engineering Research Board (SERB)	India	CRG/2019/001788
Council of Scientific & Industrial Research (CSIR)	India	MLP-139

Revision History  

• Version 1.0: 2023-05-03
  Type: Initial release