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MolNFT v2 · #151525 · protein + RNA

Cryo-EM structure of a rotated E. coli 70S ribosome in complex with RF3-GDPCP, RF1(GAQ) and P/E-tRNA (State IV)

6GXO: “Cryo-EM structure of a rotated E. coli 70S ribosome in complex with RF3-GDPCP, RF1(GAQ) and P/E-tRNA (State…”. Electron microscopy at 3.9, 1 ligand (GCP). MolNFT v2 #151525 on GenesisL1: 3D structure, binding sites and pockets in…

PDB
6GXO
Type
protein + RNA
Length
11,286 residues
Chains
58
Method
electron microscopy
Collection
MolNFT v2 / PDB Bank
Contract
0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner
0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution
3.9
Source
Escherichia coli; SYNTHETIC CONSTRUCT
UniProt
P60422, P60438, P60723, P62399, P0AG55, P0A7R1, P0A7J7, P0AA10, P0ADY3, P02413, P0ADY7, P0AG44, P0C018, P0A7K6, P0A7L3, P0AG48, P61175, P0ADZ0, P60624, P68919, P0A7L8, P0A7M2, P0A7M6, P0AG51, P0A7N4, P0A7N9, P0A7P5, P0A7Q1, P0A7Q6, P0A7J3, P0A7V0, P0A7V3, P0A7V8, P0A7W1, P02358, P02359, P0A7W7, P0A7X3, P0A7R5, P0A7R9, P0A7S3, P0A7S9, P0AG59, P0ADZ4, P0A7T3, P0AG63, P0A7T7, P0A7U3, P0A7U7, P68679, P0A7I0, P0A7I4, Q8WSY8
Ligands
GCP

Structure

electron microscopy · resolution 3.9 · 58 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
A—rna2900——
B—rna120——
C—protein271—P60422
D—protein209—P60438
E—protein201—P60723
F—protein177—P62399
G—protein176—P0AG55
H—protein149—P0A7R1
I—protein141—P0A7J7
J—protein142—P0AA10
K—protein122—P0ADY3
L—protein143—P02413
M—protein136—P0ADY7
N—protein120—P0AG44
O—protein116—P0C018
P—protein114—P0A7K6
Q—protein117—P0A7L3
R—protein103—P0AG48
S—protein110—P61175
T—protein93—P0ADZ0
U—protein102—P60624
V—protein94—P68919
W—protein75—P0A7L8
X—protein77—P0A7M2
Y—protein63—P0A7M6
Z—protein58—P0AG51
0—protein56—P0A7N4
1—protein50—P0A7N9
2—protein46—P0A7P5
3—protein64—P0A7Q1
4—protein38—P0A7Q6
5—protein131—P0A7J3
7—rna7——
a—rna1539——
b—protein218—P0A7V0
c—protein206—P0A7V3
d—protein205—P0A7V8
e—protein157—P0A7W1
f—protein100—P02358
g—protein151—P02359
h—protein129—P0A7W7
i—protein127—P0A7X3
j—protein98—P0A7R5
k—protein116—P0A7R9
l—protein123—P0A7S3
m—protein114—P0A7S9
n—protein101—P0AG59
o—protein88—P0ADZ4
p—protein82—P0A7T3
q—protein80—P0AG63
r—protein65—P0A7T7
s—protein79—P0A7U3
t—protein85—P0A7U7
u—protein65—P68679
v—protein248—P0A7I0
w—protein498—P0A7I4
x—rna77——
z—protein14—Q8WSY8

Ligands and binding sites

  • GCP · Phosphomethylphosphonic acid guanylate ester · ligand · chains w

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Compared structures

  • P60422 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L2 (P60422) · a predicted model of the same protein · chain C against A, TM-score 0.99
  • P0AA10 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L13 (P0AA10) · a predicted model of the same protein · chain J against A, TM-score 0.98
  • P0ADY7 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L16 (P0ADY7) · a predicted model of the same protein · chain M against A, TM-score 0.98
  • P0A7I0 · AlphaFold monomer V2.0 prediction for peptide chain release factor RF1 (P0A7I0) · a predicted model of the same protein · chain v against A, TM-score 0.96
  • P60723 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L4 (P60723) · a predicted model of the same protein · chain E against A, TM-score 0.96
  • P0AG51 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L30 (P0AG51) · a predicted model of the same protein · chain Z against A, TM-score 0.96
  • P0ADZ0 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L23 (P0ADZ0) · a predicted model of the same protein · chain T against A, TM-score 0.94
  • P61175 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L22 (P61175) · a predicted model of the same protein · chain S against A, TM-score 0.94
  • P0A7X3 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S9 (P0A7X3) · a predicted model of the same protein · chain i against A, TM-score 0.93
  • P0AG48 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L21 (P0AG48) · a predicted model of the same protein · chain R against A, TM-score 0.93
  • P0A7I4 · AlphaFold monomer V2.0 prediction for peptide chain release factor RF3 (P0A7I4) · a predicted model of the same protein · chain w against A, TM-score 0.92
  • P0A7P5 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L34 (P0A7P5) · a predicted model of the same protein · chain 2 against A, TM-score 0.90

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