MolNFT v2 · #222907 · protein + RNA

Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) and MsmegEF-Tu(GDP) (Composite structure 6)

8V9L · 16S Ribosomal RNA: “Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130…”. Electron microscopy at 3.0, 2 ligands (GDP, ZN), 20 pockets (best druggability 0.88). MolNFT v2…

PDB: 8V9L
Type: protein + RNA
Length: 11,629 residues
Chains: 59
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.0
Source: Mycolicibacterium smegmatis MC2 155
Molecule: 16S Ribosomal RNA; 30S Ribosomal Protein S2; 30S ribosomal protein S3; 30S ribosomal…
UniProt: A0QVB8, A0QSD7, A0QSL7, A0QSG6, A0A2U9Q0X2, A0QS97, A0QSG3, A0QSP9, A0QSD0, A0QSL6, A0QS96, A0QSL5, A0QSG2, A0QVQ3, A0QV37, A0QSE0, A0R7F7, A0QSD5, A0R102, A0QS98, A0QRI6, A0QSD4, A0QSD1, A0QSD2, A0QSG1, A0QSG4, A0R7F6, A0QS62, A0QS45, A0QSP8, A0QSF9, A0QSG8, A0QSD8, A0QSL9, I7FGD9, A0QV42, A0QYU6, A0R151, A0QSD6, A0QSD3, A0QSG0, A0R3D2, A0R150, I7FJ52, A0QSD9, A0QSG7, A0R215, A0R3I9, A0QS39, A0R7K0, A0QYU7, A0QSL4, A0QTP4
Ligands: GDP, ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · resolution 3.0 · 59 distinct chains · 30% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
a	16S Ribosomal RNA	rna	1511	—	—
b	30S Ribosomal Protein S2	protein	228	47% helix, 12% strand	A0QVB8
c	30S ribosomal protein S3	protein	208	34% helix, 32% strand	A0QSD7
d	30S ribosomal protein S4	protein	200	42% helix, 9% strand	A0QSL7
e	Small ribosomal subunit protein uS5	protein	180	38% helix, 33% strand	A0QSG6
f	30S ribosomal protein S6	protein	96	30% helix, 44% strand	A0A2U9Q0X2
g	30S ribosomal protein S7	protein	155	54% helix, 10% strand	A0QS97
h	Small ribosomal subunit protein uS8	protein	131	27% helix, 31% strand	A0QSG3
i	30S ribosomal protein S9	protein	126	34% helix, 21% strand	A0QSP9
j	30S ribosomal protein S10	protein	99	25% helix, 40% strand	A0QSD0
k	30S ribosomal protein S11	protein	115	28% helix, 30% strand	A0QSL6
l	30S ribosomal protein S12	protein	122	10% helix, 28% strand	A0QS96
m	30S ribosomal protein S13	protein	116	52% helix, 2% strand	A0QSL5
n	Small ribosomal subunit protein uS14B	protein	60	32% helix, 8% strand	A0QSG2
o	Small ribosomal subunit protein uS15	protein	88	76% helix, 0% strand	A0QVQ3
p	30S ribosomal protein S16	protein	113	34% helix, 26% strand	A0QV37
q	30S ribosomal protein S17	protein	94	0% helix, 54% strand	A0QSE0
r	Small ribosomal subunit protein bS18B	protein	65	40% helix, 3% strand	A0R7F7
s	30S ribosomal protein S19	protein	82	27% helix, 17% strand	A0QSD5
t	30S ribosomal protein S20	protein	85	87% helix, 0% strand	A0R102
u	30S Ribosomal Protein S22	protein	32	88% helix, 0% strand	—
v	poly-U mRNA	rna	4	—	—
x	Elongation factor Tu	protein	387	23% helix, 34% strand	A0QS98
y	pe/E deacylated phenylanaline-tRNA	rna	74	—	—
z	Ribosome hibernation factor Balon (MSMEG_1130)	protein	375	39% helix, 22% strand	A0QRI6
A	23S Ribosomal RNA	rna	3073	—	—
B	5S Ribosomal RNA	rna	118	—	—
C	50S ribosomal protein L2	protein	275	8% helix, 24% strand	A0QSD4
D	50S ribosomal protein L3	protein	214	10% helix, 38% strand	A0QSD1
E	Large ribosomal subunit protein uL4	protein	209	33% helix, 14% strand	A0QSD2
F	Large ribosomal subunit protein uL5	protein	182	35% helix, 18% strand	A0QSG1
G	50S ribosomal protein L6	protein	176	18% helix, 36% strand	A0QSG4
H	50S ribosomal protein L9	protein	151	30% helix, 23% strand	A0R7F6
I	50S ribosomal protein L10	protein	126	47% helix, 21% strand	A0QS62
J	50S ribosomal protein L11	protein	133	39% helix, 17% strand	A0QS45
L	Large ribosomal subunit protein uL13	protein	146	32% helix, 13% strand	A0QSP8
M	50S ribosomal protein L14	protein	122	7% helix, 38% strand	A0QSF9
N	50S ribosomal protein L15	protein	145	17% helix, 15% strand	A0QSG8
O	Large ribosomal subunit protein uL16	protein	136	20% helix, 28% strand	A0QSD8
P	50S ribosomal protein L17	protein	118	47% helix, 14% strand	A0QSL9
Q	Large ribosomal subunit protein uL18	protein	126	39% helix, 20% strand	I7FGD9
R	50S ribosomal protein L19	protein	113	12% helix, 42% strand	A0QV42
S	Large ribosomal subunit protein bL20	protein	124	72% helix, 0% strand	A0QYU6
T	Large ribosomal subunit protein bL21	protein	100	0% helix, 60% strand	A0R151
U	Large ribosomal subunit protein uL22	protein	114	35% helix, 36% strand	A0QSD6
V	Large ribosomal subunit protein uL23	protein	97	22% helix, 34% strand	A0QSD3
W	50S ribosomal protein L24	protein	97	3% helix, 53% strand	A0QSG0
X	50S ribosomal protein L25	protein	192	15% helix, 41% strand	A0R3D2
Y	50S ribosomal protein L27	protein	79	0% helix, 39% strand	A0R150
Z	Large ribosomal subunit protein bL28	protein	63	8% helix, 38% strand	I7FJ52
1	50S ribosomal protein L29	protein	64	78% helix, 0% strand	A0QSD9
2	50S ribosomal protein L30	protein	59	29% helix, 27% strand	A0QSG7
3	Large ribosomal subunit protein bL31	protein	59	19% helix, 22% strand	A0R215
4	50S ribosomal protein L32	protein	54	28% helix, 22% strand	A0R3I9
5	Large ribosomal subunit protein bL33A	protein	49	0% helix, 51% strand	A0QS39
6	50S ribosomal protein L34	protein	46	48% helix, 0% strand	A0R7K0
7	50S ribosomal protein L35	protein	63	27% helix, 16% strand	A0QYU7
8	50S ribosomal protein L36	protein	37	8% helix, 43% strand	A0QSL4
9	50S Ribosomal Protein L27	protein	23	30% helix, 0% strand	A0QTP4

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · chains x
ZN · Zinc ion · metal · 2 copies · chains Z, 5

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	1008	0.88	0.91	97	empty
2	1120	0.88	0.90	112	empty
3	872	0.87	0.90	95	empty
4	866	0.86	0.89	91	empty
5	1056	0.85	0.87	101	empty

Interfaces

132 interfaces between chains.

A–C · 6977 Å² buried · 132 hydrogen bonds · protein-nucleic
A–D · 4818 Å² buried · 74 hydrogen bonds · protein-nucleic
A–N · 4418 Å² buried · 90 hydrogen bonds · protein-nucleic
A–S · 4320 Å² buried · 91 hydrogen bonds · protein-nucleic
A–E · 4192 Å² buried · 80 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

A0QSG6 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S5 (A0QSG6) · a predicted model of the same protein · chain e against A, TM-score 0.99
A0QSF9 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L14 (A0QSF9) · a predicted model of the same protein · chain M against A, TM-score 0.98
A0R151 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L21 (A0R151) · a predicted model of the same protein · chain T against A, TM-score 0.96
A0QSG4 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L6 (A0QSG4) · a predicted model of the same protein · chain G against A, TM-score 0.96
A0QSE0 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S17 (A0QSE0) · a predicted model of the same protein · chain q against A, TM-score 0.95
A0QS97 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S7 (A0QS97) · a predicted model of the same protein · chain g against A, TM-score 0.95
A0QSP8 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L13 (A0QSP8) · a predicted model of the same protein · chain L against A, TM-score 0.95
A0QYU7 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L35 (A0QYU7) · a predicted model of the same protein · chain 7 against A, TM-score 0.94
A0R3I9 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L32 (A0R3I9) · a predicted model of the same protein · chain 4 against A, TM-score 0.91
A0QSD5 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S19 (A0QSD5) · a predicted model of the same protein · chain s against A, TM-score 0.90
A0QS98 · AlphaFold monomer V2.0 prediction for elongation factor tu (A0QS98) · a predicted model of the same protein · chain x against A, TM-score 0.58

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