Research workbench

Time-resolved cryo-EM study of the 70S recycling by the HflX:3rd Intermediate

Analyse Time-resolved cryo-EM study of the 70S recycling by the HflX:3rd Intermediate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8G38
Type: protein + RNA
Length: 10,475 residues
Chains: 52
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.2
Source: Escherichia coli
Molecule: 50S ribosomal protein L32; 50S ribosomal protein L33; 50S ribosomal protein L34; 50S…
UniProt: A0A828UBL8, A0A891SPC3, B7MGC4, E9XJC8, A0A0E2L017, A0A1X3JB59, P60438, A1AGK6, D6IEK6, A0A8E0IYC4, S1EW51, C3SQZ2, A0A037Y8L6, P0ADY7, A0A2T1LEK9, A0A1X3KXD9, S1PSA3, L4J8J1, C3SSG2, P61175, S1EUY1, S1E9P3, D7XH79, C3SSG7, A0A0E2KZD0, D6IEL0, P0AG51, U9ZNW8, V0Y888, C3SR62, F4TL26, P02358, P02359, A0A828U358, V0A2W7, A0A0H3EQD3, P0A7R9, I2UHF1, S1P5F8, A0A090BZT4, D7XN21, C3SYP2, A0A080IK26, W1EY92, A0A7U9LGZ0, C3TRH7, A0A5C9AJ78, A0A2X1MT45, C3SG37
Ligands: GTP
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · resolution 3.2 · 52 distinct chains · 30% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	50S ribosomal protein L32	protein	56	13% helix, 11% strand	A0A828UBL8
1	50S ribosomal protein L33	protein	50	0% helix, 52% strand	A0A891SPC3
2	50S ribosomal protein L34	protein	46	59% helix, 0% strand	B7MGC4
3	50S ribosomal protein L35	protein	64	31% helix, 13% strand	E9XJC8
4	50S ribosomal protein L36	protein	38	0% helix, 37% strand	A0A0E2L017
A	5S	rna	117	—	—
B	23S	rna	2903	—	—
C	50S ribosomal protein L2	protein	271	4% helix, 27% strand	A0A1X3JB59
D	50S ribosomal protein L3	protein	209	6% helix, 34% strand	P60438
E	50S ribosomal protein L4	protein	201	36% helix, 13% strand	A1AGK6
F	50S ribosomal protein L5	protein	178	25% helix, 12% strand	D6IEK6
G	50S ribosomal protein L6	protein	176	22% helix, 29% strand	A0A8E0IYC4
J	50S ribosomal protein L13	protein	142	32% helix, 18% strand	S1EW51
K	50S ribosomal protein L14	protein	121	6% helix, 31% strand	C3SQZ2
L	50S ribosomal protein L15	protein	143	19% helix, 13% strand	A0A037Y8L6
M	50S ribosomal protein L16	protein	136	21% helix, 29% strand	P0ADY7
N	50S ribosomal protein L17	protein	120	46% helix, 17% strand	A0A2T1LEK9
O	50S ribosomal protein L18	protein	116	46% helix, 18% strand	A0A1X3KXD9
P	50S ribosomal protein L19	protein	114	10% helix, 39% strand	S1PSA3
Q	50S ribosomal protein L20	protein	117	77% helix, 0% strand	L4J8J1
R	Ribosomal protein L21	protein	103	0% helix, 52% strand	C3SSG2
S	50S ribosomal protein L22	protein	110	41% helix, 38% strand	P61175
T	50S ribosomal protein L23	protein	93	28% helix, 25% strand	S1EUY1
U	50S ribosomal protein L24	protein	102	0% helix, 40% strand	S1E9P3
V	50S ribosomal protein L25	protein	94	23% helix, 46% strand	D7XH79
W	50S ribosomal protein L27	protein	79	0% helix, 33% strand	C3SSG7
X	50S ribosomal protein L28	protein	77	27% helix, 34% strand	A0A0E2KZD0
Y	50S ribosomal protein L29	protein	63	68% helix, 0% strand	D6IEL0
Z	50S ribosomal protein L30	protein	58	38% helix, 22% strand	P0AG51
w	30S ribosomal protein S2	protein	218	40% helix, 6% strand	U9ZNW8
x	30S ribosomal protein S3	protein	206	35% helix, 29% strand	V0Y888
c	30S ribosomal protein S4	protein	205	43% helix, 9% strand	C3SR62
d	30S ribosomal protein S5	protein	150	27% helix, 35% strand	F4TL26
e	30S ribosomal protein S6, non-modified isoform	protein	100	30% helix, 37% strand	P02358
f	30S ribosomal protein S7	protein	151	58% helix, 7% strand	P02359
g	30S ribosomal protein S8	protein	129	30% helix, 30% strand	A0A828U358
h	30S ribosomal protein S9	protein	127	31% helix, 13% strand	V0A2W7
i	30S ribosomal protein S10	protein	98	23% helix, 41% strand	A0A0H3EQD3
j	30S ribosomal protein S11	protein	117	29% helix, 30% strand	P0A7R9
k	30S ribosomal protein S12	protein	123	5% helix, 24% strand	I2UHF1
l	30S ribosomal protein S13	protein	114	51% helix, 0% strand	S1P5F8
m	30S ribosomal protein S14	protein	96	52% helix, 4% strand	A0A090BZT4
n	30S ribosomal protein S15	protein	88	75% helix, 0% strand	D7XN21
o	30S ribosomal protein S16	protein	82	23% helix, 33% strand	C3SYP2
p	30S ribosomal protein S17	protein	80	0% helix, 54% strand	A0A080IK26
q	30S ribosomal protein S18	protein	55	51% helix, 4% strand	W1EY92
r	30S ribosomal protein S19	protein	79	24% helix, 18% strand	A0A7U9LGZ0
s	30S ribosomal protein S20	protein	85	87% helix, 0% strand	C3TRH7
t	30S ribosomal protein S21 (Fragment)	protein	51	43% helix, 0% strand	A0A5C9AJ78
u	Transcription termination/antitermination protein NusG	protein	59	0% helix, 24% strand	A0A2X1MT45
v	16S	rna	1539	—	—
6	GTPase HflX	protein	426	41% helix, 15% strand	C3SG37

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · chains 6

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	1158	0.88	0.90	113	empty
2	968	0.87	0.90	79	empty
3	779	0.87	0.91	80	empty
4	1004	0.87	0.89	82	empty
5	903	0.87	0.90	82	empty

Interfaces

109 interfaces between chains.

B–C · 7197 Å² buried · 170 hydrogen bonds · protein-nucleic
B–D · 5137 Å² buried · 124 hydrogen bonds · protein-nucleic
B–L · 4631 Å² buried · 114 hydrogen bonds · protein-nucleic
B–E · 4251 Å² buried · 110 hydrogen bonds · protein-nucleic
B–Q · 4219 Å² buried · 104 hydrogen bonds · protein-nucleic

Compared structures

A1AGK6 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L4 (A1AGK6) · a predicted model of the same protein · chain E against A, TM-score 0.96
B7MGC4 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L34 (B7MGC4) · a predicted model of the same protein · chain 2 against A, TM-score 0.91

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