6B4V

Antibiotic blasticidin S and E. coli release factor 1 bound to the 70S ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanism of Inhibition of Translation Termination by Blasticidin S.

Svidritskiy, E.Korostelev, A.A.

(2018) J Mol Biol 430: 591-593

  • DOI: https://doi.org/10.1016/j.jmb.2018.01.007
  • Primary Citation of Related Structures:  
    6B4V

  • PubMed Abstract: 

    Understanding the mechanisms of inhibitors of translation termination may inform development of new antibacterials and therapeutics for premature termination diseases. We report the crystal structure of the potent termination inhibitor blasticidin S bound to the ribosomal 70S•release factor 1 (RF1) termination complex. Blasticidin S shifts the catalytic domain 3 of RF1 and restructures the peptidyl transferase center. Universally conserved uridine 2585 in the peptidyl transferase center occludes the catalytic backbone of the GGQ motif of RF1, explaining the structural mechanism of inhibition. Rearrangement of domain 3 relative to the codon-recognition domain 2 provides insight into the dynamics of RF1 implicated in termination accuracy.


  • Organizational Affiliation

    RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation St., Worcester, MA 01605, USA.


Macromolecules

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2
E, IB
275Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3
F, JB
206Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4
G, KB
205Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5
H, LB
182Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6
I, MB
180Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9
J, NB
148Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13
K, OB
140Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14
L, PB
122Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15
M, QB
150Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16
N, RB
141Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17
O, SB
118Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18
P, TB
112Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19
Q, UB
146Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20
R, VB
118Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21
S, WB
101Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22
T, XB
113Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23
U, YB
96Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24
V, ZB
110Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25
AC, W
206Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27
BC, X
85Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28
CC, Y
98Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29
DC, Z
72Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3060Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3171Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3260Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3354Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3449Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3565Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3637Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide chain release factor 1368Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2256Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3239Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4209Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5162Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6101Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7156Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8138Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9128Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10105Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11129Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12132Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13126Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type Z61Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1589Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1688Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for P62238 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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UniProt GroupP62238
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17105Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for P62658 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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UniProt GroupP62658
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1888Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1993Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20106Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein Thx27Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for P62613 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNA
A, EB
1,507Thermus thermophilus HB27
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Entity ID: 2
MoleculeChains LengthOrganismImage
23S ribosomal RNA
B, FB
2,880Thermus thermophilus HB27
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S ribosomal RNA
C, GB
120Thermus thermophilus HB27
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Entity ID: 4
MoleculeChains LengthOrganismImage
tRNA
D, HB, IA, MC
77Escherichia coli K-12
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Entity ID: 34
MoleculeChains LengthOrganismImage
mRNA23synthetic construct
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BLS
Query on BLS

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OL [auth B],
YTA [auth FB]
BLASTICIDIN S
C17 H26 N8 O5
CXNPLSGKWMLZPZ-ZNIXKSQXSA-N
ZN
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BKA [auth CA]
DKA [auth DA]
GOB [auth ZB]
HKA [auth GA]
MJA [auth V]
BKA [auth CA],
DKA [auth DA],
GOB [auth ZB],
HKA [auth GA],
MJA [auth V],
TOB [auth FC],
VOB [auth GC],
WOB [auth HC],
YOB [auth KC],
ZJA [auth BA]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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