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Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure IV-A)

Analyse Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WDB
Type: protein + RNA
Length: 10,830 residues
Chains: 58
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 4.0
Source: Escherichia coli; SYNTHETIC CONSTRUCT
Molecule: 50S ribosomal protein L2; 50S ribosomal protein L3; 50S ribosomal protein L4; 50S…
UniProt: P60422, P60438, P60723, P62399, P0AG55, P0A7R1, P0A7J3, P0A7J7, P0AA10, P0ADY3, P02413, P0ADY7, P0AG44, P0C018, P0A7K6, P0A7L3, P0AG48, P61175, P0ADZ0, P60624, P68919, P0A7L8, P0A7M2, P0A7M6, P0AG51, P0A7N4, P0A7N9, P0A7P5, P0A7Q1, P0A7Q6, P0A7V0, P0A7V3, P0A7V8, P0A7W1, P02358, P02359, P0A7W7, P0A7X3, P0A7R5, P0A7R9, P0A7S3, P0A7S9, P0AG59, P0ADZ4, P0A7T3, P0AG63, P0A7T7, P0A7U3, P0A7U7, P68679, P0A7L0
Ligands: FME
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · resolution 4.0 · 57 distinct chains · 29% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
b	50S ribosomal protein L2	protein	271	5% helix, 29% strand	P60422
c	50S ribosomal protein L3	protein	209	8% helix, 35% strand	P60438
d	50S ribosomal protein L4	protein	201	32% helix, 7% strand	P60723
e	50S ribosomal protein L5	protein	177	31% helix, 17% strand	P62399
f	50S ribosomal protein L6	protein	176	17% helix, 32% strand	P0AG55
g	50S ribosomal protein L9	protein	149	33% helix, 18% strand	P0A7R1
h	50S ribosomal protein L10	protein	131	34% helix, 2% strand	P0A7J3
i	50S ribosomal protein L11	protein	141	36% helix, 12% strand	P0A7J7
j	50S ribosomal protein L13	protein	142	26% helix, 15% strand	P0AA10
k	50S ribosomal protein L14	protein	122	7% helix, 34% strand	P0ADY3
l	50S ribosomal protein L15	protein	143	15% helix, 11% strand	P02413
m	50S ribosomal protein L16	protein	136	19% helix, 25% strand	P0ADY7
n	50S ribosomal protein L17	protein	120	43% helix, 18% strand	P0AG44
o	50S ribosomal protein L18	protein	116	41% helix, 16% strand	P0C018
p	50S ribosomal protein L19	protein	114	15% helix, 39% strand	P0A7K6
q	50S ribosomal protein L20	protein	117	74% helix, 0% strand	P0A7L3
r	50S ribosomal protein L21	protein	103	0% helix, 45% strand	P0AG48
s	50S ribosomal protein L22	protein	110	35% helix, 38% strand	P61175
t	50S ribosomal protein L23	protein	93	28% helix, 34% strand	P0ADZ0
u	50S ribosomal protein L24	protein	102	0% helix, 39% strand	P60624
v	50S ribosomal protein L25	protein	94	20% helix, 41% strand	P68919
w	50S ribosomal protein L27	protein	75	0% helix, 37% strand	P0A7L8
x	50S ribosomal protein L28	protein	77	26% helix, 31% strand	P0A7M2
y	50S ribosomal protein L29	protein	63	70% helix, 0% strand	P0A7M6
z	50S ribosomal protein L30	protein	58	29% helix, 26% strand	P0AG51
B	50S ribosomal protein L32	protein	56	13% helix, 11% strand	P0A7N4
C	50S ribosomal protein L33	protein	50	0% helix, 32% strand	P0A7N9
D	50S ribosomal protein L34	protein	46	50% helix, 0% strand	P0A7P5
E	50S ribosomal protein L35	protein	64	27% helix, 13% strand	P0A7Q1
F	50S ribosomal protein L36	protein	38	16% helix, 8% strand	P0A7Q6
G	30S ribosomal protein S2	protein	225	49% helix, 14% strand	P0A7V0
H	30S ribosomal protein S3	protein	206	37% helix, 30% strand	P0A7V3
I	30S ribosomal protein S4	protein	205	39% helix, 6% strand	P0A7V8
J	30S ribosomal protein S5	protein	157	25% helix, 25% strand	P0A7W1
K	30S ribosomal protein S6	protein	100	31% helix, 23% strand	P02358
L	30S ribosomal protein S7	protein	151	54% helix, 5% strand	P02359
M	30S ribosomal protein S8	protein	129	28% helix, 29% strand	P0A7W7
N	30S ribosomal protein S9	protein	127	25% helix, 17% strand	P0A7X3
O	30S ribosomal protein S10	protein	98	23% helix, 36% strand	P0A7R5
P	30S ribosomal protein S11	protein	116	18% helix, 26% strand	P0A7R9
Q	30S ribosomal protein S12	protein	123	5% helix, 21% strand	P0A7S3
R	30S ribosomal protein S13	protein	114	48% helix, 2% strand	P0A7S9
S	30S ribosomal protein S14	protein	100	40% helix, 7% strand	P0AG59
T	30S ribosomal protein S15	protein	88	72% helix, 0% strand	P0ADZ4
U	30S ribosomal protein S16	protein	82	21% helix, 23% strand	P0A7T3
V	30S ribosomal protein S17	protein	80	0% helix, 39% strand	P0AG63
W	30S ribosomal protein S18	protein	65	42% helix, 3% strand	P0A7T7
X	30S ribosomal protein S19	protein	79	23% helix, 13% strand	P0A7U3
Y	30S ribosomal protein S20	protein	85	86% helix, 0% strand	P0A7U7
Z	30S ribosomal protein S21	protein	65	40% helix, 3% strand	P68679
a	50S ribosomal protein L1	protein	134	28% helix, 28% strand	P0A7L0
3	16S ribosomal RNA	rna	1539	—	—
1	23S ribosomal RNA	rna	2903	—	—
2	5S ribosomal RNA	rna	120	—	—
5, 6	tRNAfMet	rna	77	—	—
4	mRNA	rna	18	—	—
7	tRNAPhe	rna	73	—	—

Ligands and binding sites

FME · N-formylmethionine · ligand · chains 1, 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	1013	0.89	0.91	117	empty
2	1157	0.88	0.91	143	empty
3	1022	0.88	0.90	88	FME
4	1107	0.88	0.90	108	empty
5	1073	0.87	0.89	88	empty

Interfaces

142 interfaces between chains.

b–1 · 7473 Å² buried · 172 hydrogen bonds · protein-nucleic
c–1 · 5248 Å² buried · 126 hydrogen bonds · protein-nucleic
l–1 · 4605 Å² buried · 107 hydrogen bonds · protein-nucleic
d–1 · 4369 Å² buried · 85 hydrogen bonds · protein-nucleic
q–1 · 4226 Å² buried · 95 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

P0A7L0 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L1 (P0A7L0) · a predicted model of the same protein · chain a against A, TM-score 0.95
P0A7J3 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L10 (P0A7J3) · a predicted model of the same protein · chain h against A, TM-score 0.81

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