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Cryo-EM structure of Staphylococcus aureus 70S ribosome (strain 15B196) in complex with MCX-190.

Analyse Cryo-EM structure of Staphylococcus aureus 70S ribosome (strain 15B196) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8Y38
Type: protein + RNA
Length: 9,896 residues
Chains: 50
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.58
Source: Staphylococcus aureus
Molecule: Large ribosomal subunit protein bL33B; Large ribosomal subunit protein bL34; Large…
UniProt: P66232, P66254, P66277, P66300, P60433, P60450, P61060, Q7A083, Q7A084, Q7A089, Q7A081, P0A0F7, Q7A080, Q7A087, Q7A085, Q8NX05, P66109, Q7A0Q2, Q7A079, Q7A078, P60736, Q7A1S4, P66134, P66154, P66174, P0A0G1, P66197, P66211, A0A2X2M020, P66554, P66564, P66580, P66596, P66617, P66631, P66647, P66335, P66358, A0A133PZQ5, P66389, P66413, Q7A116, P66441, Q8NVB4, P66469, A0A133PYC3, Q7A0R9
Ligands: A1D6G, MG
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · resolution 2.58 · 50 distinct chains · 28% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Large ribosomal subunit protein bL33B	protein	47	0% helix, 57% strand	P66232
2	Large ribosomal subunit protein bL34	protein	43	53% helix, 0% strand	P66254
3	Large ribosomal subunit protein bL35	protein	64	38% helix, 13% strand	P66277
4	Large ribosomal subunit protein bL36	protein	37	8% helix, 32% strand	P66300
A	23S ribosomal RNA	rna	2885	—	—
B	5S ribosomal RNA	rna	115	—	—
C	Large ribosomal subunit protein uL2	protein	274	6% helix, 26% strand	P60433
D	Large ribosomal subunit protein uL3	protein	215	11% helix, 36% strand	P60450
E	Large ribosomal subunit protein uL4	protein	206	31% helix, 14% strand	P61060
F	Large ribosomal subunit protein uL5	protein	175	33% helix, 11% strand	Q7A083
G	Large ribosomal subunit protein uL6	protein	175	22% helix, 30% strand	Q7A084
H	Large ribosomal subunit protein uL13	protein	145	27% helix, 16% strand	Q7A089
I	Large ribosomal subunit protein uL14	protein	122	7% helix, 34% strand	Q7A081
J	Large ribosomal subunit protein uL15	protein	146	17% helix, 10% strand	P0A0F7
K	Large ribosomal subunit protein uL16	protein	137	20% helix, 28% strand	Q7A080
L	Large ribosomal subunit protein bL17	protein	120	48% helix, 20% strand	Q7A087
M	Large ribosomal subunit protein uL18	protein	119	32% helix, 20% strand	Q7A085
N	Large ribosomal subunit protein bL19	protein	114	17% helix, 37% strand	Q8NX05
O	Large ribosomal subunit protein bL20	protein	116	76% helix, 0% strand	P66109
P	Large ribosomal subunit protein bL21	protein	102	0% helix, 59% strand	Q7A0Q2
Q	Large ribosomal subunit protein uL22	protein	112	38% helix, 35% strand	Q7A079
R	Large ribosomal subunit protein uL23	protein	89	21% helix, 35% strand	Q7A078
S	Large ribosomal subunit protein uL24	protein	103	3% helix, 41% strand	P60736
T	Large ribosomal subunit protein bL25	protein	94	21% helix, 49% strand	Q7A1S4
U	Large ribosomal subunit protein bL27	protein	82	0% helix, 37% strand	P66134
V	Large ribosomal subunit protein bL28	protein	58	0% helix, 45% strand	P66154
W	Large ribosomal subunit protein uL29	protein	67	78% helix, 0% strand	P66174
X	Large ribosomal subunit protein uL30	protein	58	36% helix, 24% strand	P0A0G1
Y	Large ribosomal subunit protein bL31B	protein	57	0% helix, 4% strand	P66197
Z	Large ribosomal subunit protein bL32	protein	48	21% helix, 13% strand	P66211
a	16S ribosomal RNA	rna	1479	—	—
b	Small ribosomal subunit protein uS2	protein	224	48% helix, 13% strand	A0A2X2M020
c	Small ribosomal subunit protein uS3	protein	202	31% helix, 28% strand	P66554
d	Small ribosomal subunit protein uS4	protein	199	38% helix, 5% strand	P66564
e	Small ribosomal subunit protein uS5	protein	156	30% helix, 35% strand	P66580
f	Small ribosomal subunit protein bS6	protein	95	27% helix, 38% strand	P66596
g	Small ribosomal subunit protein uS7	protein	155	57% helix, 9% strand	P66617
h	Small ribosomal subunit protein uS8	protein	131	28% helix, 34% strand	P66631
i	Small ribosomal subunit protein uS9	protein	127	32% helix, 19% strand	P66647
j	Small ribosomal subunit protein uS10	protein	97	21% helix, 41% strand	P66335
k	Small ribosomal subunit protein uS11	protein	114	25% helix, 23% strand	P66358
l	Small ribosomal subunit protein uS12	protein	135	7% helix, 31% strand	A0A133PZQ5
m	Small ribosomal subunit protein uS13	protein	116	44% helix, 3% strand	P66389
n	Small ribosomal subunit protein uS14B	protein	60	27% helix, 7% strand	P66413
o	Small ribosomal subunit protein uS15	protein	87	74% helix, 0% strand	Q7A116
p	Small ribosomal subunit protein bS16	protein	87	28% helix, 33% strand	P66441
q	Small ribosomal subunit protein uS17	protein	80	0% helix, 64% strand	Q8NVB4
r	Small ribosomal subunit protein bS18	protein	64	42% helix, 0% strand	P66469
s	Small ribosomal subunit protein uS19	protein	82	9% helix, 16% strand	A0A133PYC3
t	Small ribosomal subunit protein bS20	protein	81	84% helix, 0% strand	Q7A0R9

Ligands and binding sites

A1D6G · 7-[4-[3-[[(1~{S},2~{R},5~{R},6~{S},7~{S},8~{R},9~{R},11~{R},13~{R},14~{R})-8-[(2~{S},3~{R},4~{S},6~{R})-4-(dimethylamino)-6-methyl-3-oxidanyl-oxan-2-yl]oxy-2-ethyl-9-methoxy-1,5,7,9,11,13-hexamethyl-4,12,16-tris(oxidanylidene)-3,17-dioxa-15-azabicyclo[12.3.0]heptadecan-6-yl]oxycarbonylamino]propoxy]but-1-ynyl]-1-methyl-4-oxidanylidene-quinoline-3-carboxylic acid · ligand · chains A
MG · Magnesium ion · metal · 12 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	702	0.88	0.93	83	empty
2	1008	0.88	0.90	105	empty
3	804	0.87	0.91	82	empty
4	1146	0.86	0.88	106	empty
5	1071	0.86	0.88	102	empty

Interfaces

100 interfaces between chains.

A–C · 7218 Å² buried · 177 hydrogen bonds · protein-nucleic
A–D · 5278 Å² buried · 116 hydrogen bonds · protein-nucleic
A–J · 4535 Å² buried · 95 hydrogen bonds · protein-nucleic
A–E · 4510 Å² buried · 88 hydrogen bonds · protein-nucleic
A–O · 4170 Å² buried · 118 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 6 modified, 3 disulfide (nucleotide modification, disulfide).

Compared structures

P60433 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L2 (P60433) · a predicted model of the same protein · chain C against A, TM-score 0.99
P61060 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L4 (P61060) · a predicted model of the same protein · chain E against A, TM-score 0.99
Q7A116 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S15 (Q7A116) · a predicted model of the same protein · chain o against A, TM-score 0.98
P66631 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S8 (P66631) · a predicted model of the same protein · chain h against A, TM-score 0.98
P66580 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S5 (P66580) · a predicted model of the same protein · chain e against A, TM-score 0.98
Q7A089 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L13 (Q7A089) · a predicted model of the same protein · chain H against A, TM-score 0.98
Q7A081 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L14 (Q7A081) · a predicted model of the same protein · chain I against A, TM-score 0.98
P66109 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L20 (P66109) · a predicted model of the same protein · chain O against A, TM-score 0.98
P66564 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S4 (P66564) · a predicted model of the same protein · chain d against A, TM-score 0.98
Q7A087 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L17 (Q7A087) · a predicted model of the same protein · chain L against A, TM-score 0.98
Q7A080 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L16 (Q7A080) · a predicted model of the same protein · chain K against A, TM-score 0.98
P66554 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S3 (P66554) · a predicted model of the same protein · chain c against A, TM-score 0.98

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