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: 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 ...

    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. Electronic address: andrei.korostelev@umassmed.edu.



Macromolecules

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2EIB275Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplBTT_C1325
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Entity ID: 6
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50S ribosomal protein L3FJB206Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplCTT_C1328
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Entity ID: 7
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50S ribosomal protein L4GKB205Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplDTT_C1327
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5HLB182Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplETT_C1316
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6IMB180Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplFTT_C1313
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Entity ID: 10
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50S ribosomal protein L9JNB148Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplITT_C1743
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Entity ID: 11
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50S ribosomal protein L13KOB140Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplMTT_C1101
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Entity ID: 12
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50S ribosomal protein L14LPB122Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplNTT_C1318
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Entity ID: 13
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50S ribosomal protein L15MQB150Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplOTT_C1309
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Entity ID: 14
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50S ribosomal protein L16NRB141Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplPTT_C1321
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Entity ID: 15
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50S ribosomal protein L17OSB118Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplQTT_C1299
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Entity ID: 16
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50S ribosomal protein L18PTB112Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplRTT_C1312
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19QUB146Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplSTT_C0669
Find proteins for Q72JU9 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20RVB118Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplTTT_C0185
Find proteins for Q72L76 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 19
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50S ribosomal protein L21SWB101Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplUTT_C1424
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Entity ID: 20
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50S ribosomal protein L22TXB113Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplVTT_C1323
Find proteins for Q72I09 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 21
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50S ribosomal protein L23UYB96Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplWTT_C1326
Find proteins for Q72I06 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 22
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50S ribosomal protein L24VZB110Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplXTT_C1317
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25ACW206Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplYctcTT_C1225
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27BCX85Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmATT_C1423
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Entity ID: 25
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50S ribosomal protein L28CCY98Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmBTT_C1964
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Entity ID: 26
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50S ribosomal protein L29DCZ72Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmCTT_C1320
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Entity ID: 27
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50S ribosomal protein L30AAEC60Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmDTT_C1310
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31BAFC71Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmETT_C0708
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32CAGC60Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmFrpl32TT_C0050
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33DAHC54Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmGTT_C1735
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34EAIC49Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35FAJC65Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmITT_C0184
Find proteins for Q72L77 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36GAKC37Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmJTT_C1304
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide chain release factor 1JANC368Escherichia coliMutation(s): 0 
Find proteins for A7ZKY5 (Escherichia coli O139:H28 (strain E24377A / ETEC))
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Entity ID: 36
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30S ribosomal protein S2KAOC256Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsBrps2TT_C0509
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Entity ID: 37
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30S ribosomal protein S3LAPC239Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsCrps3TT_C1322
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Entity ID: 38
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30S ribosomal protein S4MAQC209Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsDrps4TT_C1301
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5NARC162Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsErps5TT_C1311
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Entity ID: 40
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30S ribosomal protein S6OASC101Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsFrps6TT_C1740
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Entity ID: 41
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30S ribosomal protein S7PATC156Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsGrps7TT_C1332
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Entity ID: 42
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30S ribosomal protein S8QAUC138Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsHrps8TT_C1314
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9RAVC128Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsIrps9TT_C1100
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Entity ID: 44
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30S ribosomal protein S10SAWC105Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsJrps10TT_C1329
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Entity ID: 45
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30S ribosomal protein S11TAXC129Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsKrps11TT_C1302
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Entity ID: 46
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30S ribosomal protein S12UAYC132Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsLrps12TT_C1333
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Entity ID: 47
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30S ribosomal protein S13VAZC126Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsMrps13TT_C1303
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Entity ID: 48
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30S ribosomal protein S14 type ZADWA61Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsZrps14rpsNTT_C1315
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Entity ID: 49
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30S ribosomal protein S15BDXA89Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsOrps15TT_C0773
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Entity ID: 50
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30S ribosomal protein S16CDYA88Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsPrps16TT_C0673
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Entity ID: 51
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30S ribosomal protein S17DDZA105Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsQrps17TT_C1319
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Entity ID: 52
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30S ribosomal protein S18ABED88Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsRrps18TT_C1742
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Entity ID: 53
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30S ribosomal protein S19BBFD93Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsSrps19TT_C1324
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Entity ID: 54
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30S ribosomal protein S20CBGD106Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsTrps20TT_C1031
Find proteins for P62661 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein ThxDBHD27Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsUTT_C1030
Find proteins for P62613 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Explore P62613 
Go to UniProtKB:  P62613
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAA, EB1507Thermus thermophilus HB27
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Entity ID: 2
MoleculeChainsLengthOrganismImage
23S ribosomal RNAB, FB2880Thermus thermophilus HB27
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Entity ID: 3
MoleculeChainsLengthOrganismImage
5S ribosomal RNAC, GB120Thermus thermophilus HB27
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Entity ID: 4
MoleculeChainsLengthOrganismImage
tRNAD, HB, IA, MC77Escherichia coli K-12
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Entity ID: 34
MoleculeChainsLengthOrganismImage
mRNAHA, LC23synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BLS
Query on BLS

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B, FB
BLASTICIDIN S
C17 H26 N8 O5
CXNPLSGKWMLZPZ-ZNIXKSQXSA-N
 Ligand Interaction
ZN
Query on ZN

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BA, CA, DA, FC, GA, GC, HC, KC, V, ZB
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, AA, AB, AD, B, BA, BC, BD, C, CA, CB, CC, CD, D, DA, DC, E, EA, EB, EC, F, FB, FC, G, GB, H, HA, HB, I, IA, IB, J, JA, JB, JC, K, KA, KB, L, LA, LC, M, MA, MB, MC, NA, NB, NC, O, OB, OC, PB, PC, Q, QA, QC, RB, RC, S, SA, SB, SC, T, TA, TB, TC, U, UA, UB, UC, V, VB, VC, W, WB, WC, X, XA, XC, Y, YC, Z, ZA, ZB
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
0TD
Query on 0TD
UA,YCL-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.849α = 90
b = 452.539β = 90
c = 624.45γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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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 

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Author supporting evidence
  • Version 1.2: 2018-03-14
    Changes: Database references
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence