6BOH

Antibiotic blasticidin S and E. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosome

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 
    0.281 (DCC) 
  • R-Value Work: 
    0.243 (DCC) 

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Ligand Structure Quality Assessment 

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Literature

Conformational Control of Translation Termination on the 70S Ribosome.

Svidritskiy, E., Korostelev, A.A.

(2018) Structure 26: 821

  • DOI: https://doi.org/10.1016/j.str.2018.04.001
  • Primary Citation of Related Structures:  
    6BOH, 6BOK

  • PubMed Abstract: 

    Translation termination ensures proper lengths of cellular proteins. During termination, release factor (RF) recognizes a stop codon and catalyzes peptide release. Conformational changes in RF are thought to underlie accurate translation termination. However, structural studies of ribosome termination complexes have only captured RFs in a conformation that is consistent with the catalytically active state. Here, we employ a hyper-accurate RF1 variant to obtain crystal structures of 70S termination complexes that suggest a structural pathway for RF1 activation. We trapped RF1 conformations with the catalytic domain outside of the peptidyl-transferase center, while the codon-recognition domain binds the stop codon. Stop-codon recognition induces 30S decoding-center rearrangements that precede accommodation of the catalytic domain. The separation of codon recognition from the opening of the catalytic domain suggests how rearrangements in RF1 and in the ribosomal decoding center coordinate stop-codon recognition with peptide release, ensuring accurate translation termination.

    • 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, JB
275Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3
F, KB
206Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4
G, LB
205Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5
H, MB
182Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6
I, NB
180Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9
J, OB
148Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13
K, PB
140Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14
L, QB
122Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15
M, RB
150Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16
N, SB
141Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17
O, TB
118Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18
P, UB
112Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19
Q, VB
146Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20
R, WB
118Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21
S, XB
101Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22
T, YB
113Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23
U, ZB
96Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24
AC, V
110Thermus thermophilus HB27Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25
BC, W
206Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27
CC, X
85Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28
DC, Y
98Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29
EC, 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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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3565Thermus thermophilus HB27Mutation(s): 0 
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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 1
JA, KA, OC, PC
365Escherichia coliMutation(s): 0 
Gene Names: prfA
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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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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein S4209Thermus thermophilus HB27Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5162Thermus thermophilus HB27Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6101Thermus thermophilus HB27Mutation(s): 0 
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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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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 
UniProt
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UniProt GroupP62657
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1688Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17105Thermus thermophilus HB27Mutation(s): 0 
UniProt
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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
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BLS
Query on BLS
Download Ideal Coordinates CCD File 
BNA [auth GB],
LK [auth B]		BLASTICIDIN S
C17 H26 N8 O5
CXNPLSGKWMLZPZ-ZNIXKSQXSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
AFB [auth IC]
EFB [auth LC]
LDA [auth V]
SEB [auth AC]
TDA [auth BA]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AAA [auth B]
AAB [auth GB]
ABA [auth B]
ABB [auth GB]
ACA [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
0TD
Query on 0TD
AD, VA
L-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free:  0.281 (DCC) 
  • R-Value Work:  0.243 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.86α = 90
b = 450.69β = 90
c = 615.88γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BLSClick on this verticalbar to view details

View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM107465
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK047757

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.4: 2025-02-19
    Changes: Data collection, Database references, Derived calculations, Structure summary