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

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Conformational Control of Translation Termination on the 70S Ribosome.

Svidritskiy, E.Korostelev, A.A.

(2018) Structure 26: 821

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

  • 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. How ...

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



Macromolecules

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2 EJB275Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplBTT_C1325
Find proteins for Q72I07 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 6
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50S ribosomal protein L3 FKB206Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplCTT_C1328
Find proteins for Q72I04 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4 GLB205Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplDTT_C1327
Find proteins for Q72I05 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5 HMB182Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplETT_C1316
Find proteins for Q72I16 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6 INB180Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplFTT_C1313
Find proteins for Q72I19 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9 JOB148Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplITT_C1743
Find proteins for Q72GV5 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13 KPB140Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplMTT_C1101
Find proteins for Q72IN1 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 12
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50S ribosomal protein L14 LQB122Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplNTT_C1318
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Entity ID: 13
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50S ribosomal protein L15 MRB150Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplOTT_C1309
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16 NSB141Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplPTT_C1321
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Entity ID: 15
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50S ribosomal protein L17 OTB118Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplQTT_C1299
Find proteins for Q72I33 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18 PUB112Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplRTT_C1312
Find proteins for Q72I20 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19 QVB146Thermus 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 L20 RWB118Thermus 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
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21 SXB101Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplUTT_C1424
Find proteins for Q72HR2 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 20
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50S ribosomal protein L22 TYB113Thermus 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 L23 UZB96Thermus 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
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24 ACV110Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplXTT_C1317
Find proteins for Q72I15 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25 BCW206Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplYctcTT_C1225
Find proteins for Q72IA7 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27 CCX85Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmATT_C1423
Find proteins for Q72HR3 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28 DCY98Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmBTT_C1964
Find proteins for Q72G84 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29 ECZ72Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmCTT_C1320
Find proteins for Q72I12 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30 AAFC60Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmDTT_C1310
Find proteins for Q72I22 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 28
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50S ribosomal protein L31 BAGC71Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmETT_C0708
Find proteins for Q72JR0 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 29
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50S ribosomal protein L32 CAHC60Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmFrpl32TT_C0050
Find proteins for P62652 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33 DAIC54Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmGTT_C1735
Find proteins for Q72GW3 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34 EAJC49Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35 FAKC65Thermus 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 L36 GALC37Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmJTT_C1304
Find proteins for Q72I28 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide chain release factor 1 JAKAOCPC365Escherichia coliMutation(s): 0 
Gene Names: prfA
Find proteins for B7MKB3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2 LAQC256Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsBrps2TT_C0509
Find proteins for P62662 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3 MARC239Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsCrps3TT_C1322
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein S4 NASC209Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsDrps4TT_C1301
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5 OATC162Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsErps5TT_C1311
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6 PAUC101Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsFrps6TT_C1740
Find proteins for P62666 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7 QAVC156Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsGrps7TT_C1332
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8 RAWC138Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsHrps8TT_C1314
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9 SAXC128Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsIrps9TT_C1100
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10 TAYC105Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsJrps10TT_C1329
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Entity ID: 45
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30S ribosomal protein S11 UAZC129Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsKrps11TT_C1302
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12 ADVA132Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsLrps12TT_C1333
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Entity ID: 47
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30S ribosomal protein S13 BDWA126Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsMrps13TT_C1303
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Entity ID: 48
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30S ribosomal protein S14 type Z CDXA61Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsZrps14rpsNTT_C1315
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15 DDYA89Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsOrps15TT_C0773
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16 EDZA88Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsPrps16TT_C0673
Find proteins for P62238 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17 ABFD105Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsQrps17TT_C1319
Find proteins for P62658 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18 BBGD88Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsRrps18TT_C1742
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19 CBHD93Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsSrps19TT_C1324
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20 DBID106Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsTrps20TT_C1031
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein Thx EBJD27Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsUTT_C1030
Find proteins for P62613 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAA, FB1507Thermus thermophilus HB27
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Entity ID: 2
MoleculeChainsLengthOrganismImage
23S ribosomal RNAB, GB2880Thermus thermophilus HB27
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Entity ID: 3
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5S ribosomal RNAC, HB120Thermus thermophilus HB27
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Entity ID: 4
MoleculeChainsLengthOrganismImage
tRNAD, IA, IB, NC77Escherichia coli K-12
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Entity ID: 34
MoleculeChainsLengthOrganismImage
mRNAHA, MC27synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BLS
Query on BLS

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

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AC, BA, CA, DA, GA, GC, HC, IC, LC, V
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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