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MolNFT v2 · #169878 · protein + RNA

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

6WD3: “Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure II-B1)”. Electron microscopy at 3.6, 3 ligands (FME, PHE, GDP). MolNFT v2 #169878 on GenesisL1: 3D structure, binding sites and pockets in…

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
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

Structure

electron microscopy · resolution 3.6 · 58 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
b—protein271—P60422
c—protein209—P60438
d—protein201—D7Z9F6
e—protein177—S1EUW9
f—protein176—A0A5B7PA13
g—protein149—D7ZI15
h—protein131—A0A073FNB4
i—protein141—S1ERR4
j—protein142—D7ZET0
k—protein122—U9YFU2
l—protein143—A0A037Y8L6
m—protein136—P0ADY7
n—protein120—A0A1X3LC97
o—protein116—F4TL27
p—protein114—A0A4P8C2I6
q—protein117—L3CCT0
r—protein103—D7ZEN7
s—protein110—D7Z9G0
t—protein93—D6I208
u—protein102—D7XKZ6
v—protein94—D7XH79
w—protein75—A0A069XRX8
x—protein77—J7RMJ2
y—protein63—D7Z9G3
z—protein58—I2X1N4
B—protein56—E3PJQ3
C—protein50—L3NSS9
D—protein46—B7MGC4
E—protein64—G0F552
F—protein38—A0A0E2L017
G—protein225—C3TPN2
H—protein206—A0A376HTV6
I—protein205—L3PZ69
J—protein157—F4TL26
K—protein100—S1CG62
L—protein151—S1D5F0
M—protein129—D8A1L7
N—protein127—T9TH92
O—protein98—D7X302
P—protein116—I2UH22
Q—protein123—V6FZ95
R—protein114—A0A1X3KX08
S—protein100—I2X0X3
T—protein88—D7XN21
U—protein82—B7MIU7
V—protein80—A0A080IK26
W—protein65—A0A222QU44
X—protein79—F4SQ43
Y—protein85—T6N332
Z—protein65—E9TH65
a—protein134—A0A4Y8DMK0
3—rna1539——
1—rna2903——
2—rna120——
5, 6—rna77——
4—rna18——
7—rna76——
8—protein383—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.

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