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MolNFT v2 · #151961 · protein + RNA

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

6HA8: “Cryo-EM structure of the ABCF protein VmlR bound to the Bacillus subtilis ribosome”. Electron microscopy at 3.5, 2 ligands (ATP, TEL). MolNFT v2 #151961 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

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
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

Structure

electron microscopy · resolution 3.5 · 53 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
A—rna2887——
B—rna112——
C—protein272—P42919
D—protein206—P42920
E—protein205—P42921
F—protein176—P12877
G—protein175—P46898
J—protein142—P70974
K—protein122—P12875
L—protein146—P19946
M—protein135—P14577
N—protein119—P20277
O—protein120—P46899
P—protein115—O31742
Q—protein117—P55873
R—protein101—P26908
S—protein109—P42060
T—protein90—P42924
U—protein101—P0CI78
V—protein541—P39115
W—protein82—P05657
X—protein58—P37807
Y—protein65—P12873
Z—protein58—P19947
0—protein54—O34687
1—protein48—P56849
2—protein44—P05647
3—protein64—P55874
4—protein37—P20278
6—protein63—Q03223
7—rna3——
8—protein212—Q06797
a—rna1533——
b—protein218—P21464
c—protein206—P21465
d—protein195—P21466
e—protein164—P21467
f—protein92—P21468
g—protein149—P21469
h—protein131—P12879
i—protein125—P21470
j—protein95—P21471
k—protein114—P04969
l—protein136—P21472
m—protein108—P20282
n—protein60—P12878
o—protein85—P21473
p—protein88—P21474
q—protein84—P12874
r—protein64—P21475
s—protein78—P21476
t—protein83—P21477
x—rna75——

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.

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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