4WT8

Crystal Structure of bactobolin A bound to 70S ribosome-tRNA complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

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This is version 1.4 of the entry. See complete history. 


Literature

Bactobolin A Binds to a Site on the 70S Ribosome Distinct from Previously Seen Antibiotics.

Amunts, A., Fiedorczuk, K., Truong, T.T., Chandler, J., Peter Greenberg, E., Ramakrishnan, V.

(2015) J Mol Biol 427: 753-755

  • DOI: https://doi.org/10.1016/j.jmb.2014.12.018
  • Primary Citation of Related Structures:  
    4WT8

  • PubMed Abstract: 

    The ribosome is the target of a large number of antibiotics. Here, we report a 3.4-Å-resolution crystal structure of bactobolin A bound to 70S ribosome-tRNA complex. The antibiotic binds at a previously unseen site in the 50S subunit and displaces tRNA bound at the P-site. It thus likely has a similar mechanism of action as blasticidin S despite binding to a different site. The structure also rationalizes previously identified resistance mutations.

    • Organizational Affiliation: 

    MRC Laboratory of Molecular Biology, Cambridge CB20QH, UK.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth AA],
Y [auth BA]		234Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth AC]238Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4AA [auth BD],
D [auth AD]		208Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5BA [auth BE],
E [auth AE]		150Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6CA [auth BF],
F [auth AF]		101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7DA [auth BG],
G [auth AG]		155Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8EA [auth BH],
H [auth AH]		138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9FA [auth BI],
I [auth AI]		127Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10GA [auth BJ],
J [auth AJ]		98Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11HA [auth BK],
K [auth AK]		119Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12IA [auth BL],
L [auth AL]		124Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13JA [auth BM],
M [auth AM]		124Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZKA [auth BN],
N [auth AN]		60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15LA [auth BO],
O [auth AO]		88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16MA [auth BP],
P [auth AP]		83Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17NA [auth BR],
Q [auth AR]		99Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18OA [auth BS],
R [auth AS]		70Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19PA [auth BT],
S [auth AT]		78Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20QA [auth BU],
T [auth AU]		99Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein ThxRA [auth BW],
U [auth AW]		24Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3Z [auth BC]206Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1VA [auth CA]206Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2GC [auth DB],
WA [auth CB]		271Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3HC [auth DC],
XA [auth CC]		204Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4IC [auth DD],
YA [auth CD]		207Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5JC [auth DE],
ZA [auth CE]		181Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6AB [auth CF],
KC [auth DF]		159Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9BB [auth CI],
LC [auth DI]		145Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal L10 proteinCB [auth CJ],
MC [auth DJ]		130Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13DB [auth CM],
NC [auth DM]		138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14EB [auth CN],
OC [auth DN]		122Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15FB [auth CO],
PC [auth DO]		146Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16GB [auth CP],
QC [auth DP]		141Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17HB [auth CQ],
RC [auth DQ]		117Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18IB [auth CR],
SC [auth DR]		98Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19JB [auth CS],
TC [auth DS]		137Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20KB [auth CT],
UC [auth DT]		117Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21LB [auth CU],
VC [auth DU]		101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22MB [auth CW]113Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23NB [auth CX],
XC [auth DX]		92Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24OB [auth CY],
YC [auth DY]		100Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25PB [auth CZ],
ZC [auth DZ]		176Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27AD [auth Da],
QB [auth Ca]		84Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28BD [auth DH],
RB [auth CH]		93Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29CD [auth DK],
SB [auth CK]		71Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30DD [auth DL],
TB [auth CL]		59Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31ED [auth D5],
UB [auth C5]		30Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32FD [auth D6],
VB [auth C6]		59Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33GD [auth D7],
WB [auth C7]		44Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34HD [auth D8],
XB [auth C8]		48Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35ID [auth D9],
YB [auth C9]		63Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36JD [auth D0],
ZB [auth C0]		36Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1FC [auth DA]206Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22WC [auth DW]113Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
mRNAA [auth A2]9Thermus thermophilus HB8
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Entity ID: 22
MoleculeChains LengthOrganismImage
RNA (1504-MER)V [auth Ab],
X [auth Bb]		1,504Thermus thermophilus HB8
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Entity ID: 23
MoleculeChains LengthOrganismImage
mRNAW [auth B2]10Thermus thermophilus HB8
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Entity ID: 25
MoleculeChains LengthOrganismImage
A site tNA, E site tNADC [auth D3],
SA [auth C2],
TA [auth C3]		76Thermus thermophilus HB8
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Entity ID: 26
MoleculeChains LengthOrganismImage
P site trNAUA [auth C4]77Thermus thermophilus HB8
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Entity ID: 58
MoleculeChains LengthOrganismImage
23S rRNA (2899-MER)AC [auth C1],
LD [auth D1]		2,899Thermus thermophilus HB8
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Entity ID: 59
MoleculeChains LengthOrganismImage
5S rRNA (119-MER)BC [auth Cs],
KD [auth Ds]		119Thermus thermophilus HB8
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Entity ID: 60
MoleculeChains LengthOrganismImage
tRNA (5'-D(*AP*UP*CP*CP*CP*CP*GP*UP*GP*UP*CP*CP*UP*UP*GP*GP*UP*UP*CP*G)-3')CC [auth D2]20Mitsuaria sp. 67
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Entity ID: 61
MoleculeChains LengthOrganismImage
tRNA (76-MER)EC [auth D4]76Mitsuaria sp. 67
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Entity ID: 64
MoleculeChains LengthOrganismImage
DNA (55-MER)MD [auth DV]55Mitsuaria sp. 67
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR
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ND [auth Ab],
OD [auth Bb]		PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
3V6
Query on 3V6
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PD [auth C1],
RD [auth D1]		Bactobolin A
C15 H22 Cl2 N2 O5
RREHSYIRMHYJHY-RQGKCFPDSA-N
MG
Query on MG
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QD [auth C1],
SD [auth D1]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 214.21α = 90
b = 457.45β = 90
c = 639.66γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-02-18
    Changes: Database references
  • Version 1.2: 2015-08-19
    Changes: Other
  • Version 1.3: 2018-07-18
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary