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Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure II-B1)

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: 6WD3
Type: protein + RNA
Length: 11,216 residues
Chains: 59
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.6
Source: Escherichia coli; SYNTHETIC CONSTRUCT
Molecule: 50S ribosomal protein L2; 50S ribosomal protein L3; 50S ribosomal protein L4; 50S…
UniProt: P60422, P60438, D7Z9F6, S1EUW9, A0A5B7PA13, D7ZI15, A0A073FNB4, S1ERR4, D7ZET0, U9YFU2, A0A037Y8L6, P0ADY7, A0A1X3LC97, F4TL27, A0A4P8C2I6, L3CCT0, D7ZEN7, D7Z9G0, D6I208, D7XKZ6, D7XH79, A0A069XRX8, J7RMJ2, D7Z9G3, I2X1N4, E3PJQ3, L3NSS9, B7MGC4, G0F552, A0A0E2L017, C3TPN2, A0A376HTV6, L3PZ69, F4TL26, S1CG62, S1D5F0, D8A1L7, T9TH92, D7X302, I2UH22, V6FZ95, A0A1X3KX08, I2X0X3, D7XN21, B7MIU7, A0A080IK26, A0A222QU44, F4SQ43, T6N332, E9TH65, A0A4Y8DMK0, E2QFJ4
Ligands: FME, PHE, GDP
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · resolution 3.6 · 58 distinct chains · 28% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
b	50S ribosomal protein L2	protein	271	5% helix, 26% strand	P60422
c	50S ribosomal protein L3	protein	209	9% helix, 34% strand	P60438
d	50S ribosomal protein L4	protein	201	34% helix, 9% strand	D7Z9F6
e	50S ribosomal protein L5	protein	177	30% helix, 16% strand	S1EUW9
f	50S ribosomal protein L6	protein	176	18% helix, 32% strand	A0A5B7PA13
g	50S ribosomal protein L9	protein	149	34% helix, 17% strand	D7ZI15
h	50S ribosomal protein L10	protein	131	36% helix, 6% strand	A0A073FNB4
i	50S ribosomal protein L11	protein	141	38% helix, 14% strand	S1ERR4
j	50S ribosomal protein L13	protein	142	30% helix, 10% strand	D7ZET0
k	50S ribosomal protein L14	protein	122	7% helix, 34% strand	U9YFU2
l	50S ribosomal protein L15	protein	143	18% helix, 13% strand	A0A037Y8L6
m	50S ribosomal protein L16	protein	136	18% helix, 26% strand	P0ADY7
n	50S ribosomal protein L17	protein	120	40% helix, 11% strand	A0A1X3LC97
o	50S ribosomal protein L18	protein	116	44% helix, 16% strand	F4TL27
p	50S ribosomal protein L19	protein	114	17% helix, 37% strand	A0A4P8C2I6
q	50S ribosomal protein L20	protein	117	68% helix, 0% strand	L3CCT0
r	50S ribosomal protein L21	protein	103	0% helix, 51% strand	D7ZEN7
s	50S ribosomal protein L22	protein	110	35% helix, 34% strand	D7Z9G0
t	50S ribosomal protein L23	protein	93	26% helix, 38% strand	D6I208
u	50S ribosomal protein L24	protein	102	0% helix, 40% strand	D7XKZ6
v	50S ribosomal protein L25	protein	94	20% helix, 41% strand	D7XH79
w	50S ribosomal protein L27	protein	75	0% helix, 35% strand	A0A069XRX8
x	50S ribosomal protein L28	protein	77	22% helix, 34% strand	J7RMJ2
y	50S ribosomal protein L29	protein	63	71% helix, 0% strand	D7Z9G3
z	50S ribosomal protein L30	protein	58	33% helix, 26% strand	I2X1N4
B	50S ribosomal protein L32	protein	56	13% helix, 13% strand	E3PJQ3
C	50S ribosomal protein L33	protein	50	0% helix, 36% strand	L3NSS9
D	50S ribosomal protein L34	protein	46	54% helix, 0% strand	B7MGC4
E	50S ribosomal protein L35	protein	64	25% helix, 11% strand	G0F552
F	50S ribosomal protein L36	protein	38	8% helix, 26% strand	A0A0E2L017
G	30S ribosomal protein S2	protein	225	45% helix, 15% strand	C3TPN2
H	30S ribosomal protein S3	protein	206	34% helix, 29% strand	A0A376HTV6
I	30S ribosomal protein S4	protein	205	38% helix, 8% strand	L3PZ69
J	30S ribosomal protein S5	protein	157	23% helix, 21% strand	F4TL26
K	30S ribosomal protein S6	protein	100	30% helix, 24% strand	S1CG62
L	30S ribosomal protein S7	protein	151	54% helix, 4% strand	S1D5F0
M	30S ribosomal protein S8	protein	129	29% helix, 28% strand	D8A1L7
N	30S ribosomal protein S9	protein	127	25% helix, 19% strand	T9TH92
O	30S ribosomal protein S10	protein	98	16% helix, 28% strand	D7X302
P	30S ribosomal protein S11	protein	116	18% helix, 26% strand	I2UH22
Q	30S ribosomal protein S12	protein	123	7% helix, 24% strand	V6FZ95
R	30S ribosomal protein S13	protein	114	48% helix, 2% strand	A0A1X3KX08
S	30S ribosomal protein S14	protein	100	32% helix, 3% strand	I2X0X3
T	30S ribosomal protein S15	protein	88	70% helix, 0% strand	D7XN21
U	30S ribosomal protein S16	protein	82	23% helix, 34% strand	B7MIU7
V	30S ribosomal protein S17	protein	80	0% helix, 48% strand	A0A080IK26
W	30S ribosomal protein S18	protein	65	42% helix, 3% strand	A0A222QU44
X	30S ribosomal protein S19	protein	79	23% helix, 11% strand	F4SQ43
Y	30S ribosomal protein S20	protein	85	85% helix, 0% strand	T6N332
Z	30S ribosomal protein S21	protein	65	37% helix, 3% strand	E9TH65
a	50S ribosomal protein L1	protein	134	28% helix, 28% strand	A0A4Y8DMK0
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	76	—	—
8	Elongation factor Tu	protein	383	23% helix, 32% strand	E2QFJ4

Ligands and binding sites

FME · N-formylmethionine · ligand · chains 1, 5
PHE · Phenylalanine · ligand · chains 7, 8
GDP · Guanosine-5'-diphosphate · ligand · chains 8

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	633	0.87	0.94	78	empty
2	1018	0.87	0.89	97	empty
3	881	0.87	0.90	76	empty
4	584	0.86	0.92	69	empty
5	983	0.86	0.88	91	empty

Interfaces

143 interfaces between chains.

b–1 · 7371 Å² buried · 169 hydrogen bonds · protein-nucleic
c–1 · 5227 Å² buried · 125 hydrogen bonds · protein-nucleic
l–1 · 4610 Å² buried · 87 hydrogen bonds · protein-nucleic
d–1 · 4266 Å² buried · 86 hydrogen bonds · protein-nucleic
q–1 · 4262 Å² buried · 94 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

B7MGC4 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L34 (B7MGC4) · a predicted model of the same protein · chain D against A, TM-score 0.92
B7MIU7 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S16 (B7MIU7) · a predicted model of the same protein · chain U against A, TM-score 0.92

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