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Cryo-EM structure of the ABCF protein VmlR bound to the Bacillus subtilis ribosome

Analyse Cryo-EM structure of the ABCF protein VmlR bound to the Bacillus subtilis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6HA8
Type: protein + RNA
Length: 10,662 residues
Chains: 53
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.5
Source: Bacillus subtilis (strain 168); Escherichia coli; SYNTHETIC CONSTRUCT
Molecule: 23S rRNA; 5S rRNA; 50S ribosomal protein L2; 50S ribosomal protein L3; 50S ribosomal…
UniProt: P42919, P42920, P42921, P12877, P46898, P70974, P12875, P19946, P14577, P20277, P46899, O31742, P55873, P26908, P42060, P42924, P0CI78, P39115, P05657, P37807, P12873, P19947, O34687, P56849, P05647, P55874, P20278, Q03223, Q06797, P21464, P21465, P21466, P21467, P21468, P21469, P12879, P21470, P21471, P04969, P21472, P20282, P12878, P21473, P21474, P12874, P21475, P21476, P21477
Ligands: ATP, TEL
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · resolution 3.5 · 53 distinct chains · 29% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	23S rRNA	rna	2887	—	—
B	5S rRNA	rna	112	—	—
C	50S ribosomal protein L2	protein	272	2% helix, 24% strand	P42919
D	50S ribosomal protein L3	protein	206	10% helix, 36% strand	P42920
E	50S ribosomal protein L4	protein	205	34% helix, 8% strand	P42921
F	50S ribosomal protein L5	protein	176	31% helix, 16% strand	P12877
G	50S ribosomal protein L6	protein	175	19% helix, 34% strand	P46898
J	50S ribosomal protein L13	protein	142	31% helix, 20% strand	P70974
K	50S ribosomal protein L14	protein	122	7% helix, 39% strand	P12875
L	50S ribosomal protein L15	protein	146	16% helix, 13% strand	P19946
M	50S ribosomal protein L16	protein	135	20% helix, 24% strand	P14577
N	50S ribosomal protein L17	protein	119	49% helix, 17% strand	P20277
O	50S ribosomal protein L18	protein	120	34% helix, 19% strand	P46899
P	50S ribosomal protein L19	protein	115	13% helix, 39% strand	O31742
Q	50S ribosomal protein L20	protein	117	75% helix, 0% strand	P55873
R	50S ribosomal protein L21	protein	101	0% helix, 37% strand	P26908
S	50S ribosomal protein L22	protein	109	37% helix, 32% strand	P42060
T	50S ribosomal protein L23	protein	90	23% helix, 34% strand	P42924
U	50S ribosomal protein L24	protein	101	3% helix, 39% strand	P0CI78
V	Nucleotide-binding protein ExpZ	protein	541	36% helix, 18% strand	P39115
W	50S ribosomal protein L27	protein	82	0% helix, 34% strand	P05657
X	50S ribosomal protein L28	protein	58	5% helix, 21% strand	P37807
Y	50S ribosomal protein L29	protein	65	77% helix, 0% strand	P12873
Z	50S ribosomal protein L30	protein	58	31% helix, 26% strand	P19947
0	50S ribosomal protein L32	protein	54	20% helix, 19% strand	O34687
1	50S ribosomal protein L33 1	protein	48	0% helix, 50% strand	P56849
2	50S ribosomal protein L34	protein	44	55% helix, 0% strand	P05647
3	50S ribosomal protein L35	protein	64	41% helix, 13% strand	P55874
4	50S ribosomal protein L36	protein	37	8% helix, 35% strand	P20278
6	50S ribosomal protein L31	protein	63	8% helix, 19% strand	Q03223
7	mRNA	rna	3	—	—
8	50S ribosomal protein L1	protein	212	20% helix, 16% strand	Q06797
a	16S rRNA	rna	1533	—	—
b	30S ribosomal protein S2	protein	218	43% helix, 11% strand	P21464
c	30S ribosomal protein S3	protein	206	31% helix, 28% strand	P21465
d	30S ribosomal protein S4	protein	195	38% helix, 6% strand	P21466
e	30S ribosomal protein S5	protein	164	29% helix, 30% strand	P21467
f	30S ribosomal protein S6	protein	92	26% helix, 38% strand	P21468
g	30S ribosomal protein S7	protein	149	57% helix, 8% strand	P21469
h	30S ribosomal protein S8	protein	131	31% helix, 28% strand	P12879
i	30S ribosomal protein S9	protein	125	31% helix, 21% strand	P21470
j	30S ribosomal protein S10	protein	95	25% helix, 38% strand	P21471
k	30S ribosomal protein S11	protein	114	25% helix, 30% strand	P04969
l	30S ribosomal protein S12	protein	136	7% helix, 19% strand	P21472
m	30S ribosomal protein S13	protein	108	50% helix, 2% strand	P20282
n	30S ribosomal protein S14	protein	60	33% helix, 12% strand	P12878
o	30S ribosomal protein S15	protein	85	74% helix, 0% strand	P21473
p	30S ribosomal protein S16	protein	88	32% helix, 27% strand	P21474
q	30S ribosomal protein S17	protein	84	0% helix, 45% strand	P12874
r	30S ribosomal protein S18	protein	64	48% helix, 3% strand	P21475
s	30S ribosomal protein S19	protein	78	24% helix, 17% strand	P21476
t	30S ribosomal protein S20	protein	83	83% helix, 0% strand	P21477
x	P-tRNA(Leu)	rna	75	—	—

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains V
TEL · Telithromycin · ligand · 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	1073	0.86	0.88	96	empty
2	1010	0.86	0.88	81	empty
3	918	0.86	0.88	99	empty
4	1189	0.85	0.87	105	empty
5	1137	0.85	0.87	107	empty

Interfaces

120 interfaces between chains.

A–C · 7594 Å² buried · 180 hydrogen bonds · protein-nucleic
A–D · 5126 Å² buried · 113 hydrogen bonds · protein-nucleic
A–E · 4534 Å² buried · 97 hydrogen bonds · protein-nucleic
A–L · 4526 Å² buried · 115 hydrogen bonds · protein-nucleic
A–Q · 4136 Å² buried · 92 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 3 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

P42919 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L2 (P42919) · a predicted model of the same protein · chain C against A, TM-score 0.99
P20277 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L17 (P20277) · a predicted model of the same protein · chain N against A, TM-score 0.99
P42920 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L3 (P42920) · a predicted model of the same protein · chain D against A, TM-score 0.99
P70974 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L13 (P70974) · a predicted model of the same protein · chain J against A, TM-score 0.98
P42060 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L22 (P42060) · a predicted model of the same protein · chain S against A, TM-score 0.98
P14577 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L16 (P14577) · a predicted model of the same protein · chain M against A, TM-score 0.98
P21467 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S5 (P21467) · a predicted model of the same protein · chain e against A, TM-score 0.98
P42921 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L4 (P42921) · a predicted model of the same protein · chain E against A, TM-score 0.98
P21470 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S9 (P21470) · a predicted model of the same protein · chain i against A, TM-score 0.98
P12879 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S8 (P12879) · a predicted model of the same protein · chain h against A, TM-score 0.98
P12875 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L14 (P12875) · a predicted model of the same protein · chain K against A, TM-score 0.97
P46898 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L6 (P46898) · a predicted model of the same protein · chain G against A, TM-score 0.97

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