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 E, JB275Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplB, TT_C1325
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Entity ID: 6
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50S ribosomal protein L3 F, KB206Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplC, TT_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 G, LB205Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplD, TT_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 H, MB182Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplE, TT_C1316
Find proteins for Q72I16 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 9
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50S ribosomal protein L6 I, NB180Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplF, TT_C1313
Find proteins for Q72I19 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 10
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50S ribosomal protein L9 J, OB148Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplI, TT_C1743
Find proteins for Q72GV5 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 11
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50S ribosomal protein L13 K, PB140Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplM, TT_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 L, QB122Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplN, TT_C1318
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Entity ID: 13
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50S ribosomal protein L15 M, RB150Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplO, TT_C1309
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Entity ID: 14
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50S ribosomal protein L16 N, SB141Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplP, TT_C1321
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Entity ID: 15
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50S ribosomal protein L17 O, TB118Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplQ, TT_C1299
Find proteins for Q72I33 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 16
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50S ribosomal protein L18 P, UB112Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplR, TT_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 Q, VB146Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplS, TT_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 R, WB118Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplT, TT_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 L21 S, XB101Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplU, TT_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 T, YB113Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplV, TT_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 U, ZB96Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplW, TT_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 L24 AC, V110Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplX, TT_C1317
Find proteins for Q72I15 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 23
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50S ribosomal protein L25 BC, W206Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplY, ctc, TT_C1225
Find proteins for Q72IA7 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 24
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50S ribosomal protein L27 CC, X85Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmA, TT_C1423
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Entity ID: 25
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50S ribosomal protein L28 DC, Y98Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmB, TT_C1964
Find proteins for Q72G84 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 26
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50S ribosomal protein L29 EC, Z72Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmC, TT_C1320
Find proteins for Q72I12 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 27
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50S ribosomal protein L30 AA, FC60Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmD, TT_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 BA, GC71Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmE, TT_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 CA, HC60Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmF, rpl32, TT_C0050
Find proteins for P62652 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 30
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50S ribosomal protein L33 DA, IC54Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmG, TT_C1735
Find proteins for Q72GW3 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 31
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50S ribosomal protein L34 EA, JC49Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 32
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50S ribosomal protein L35 FA, KC65Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmI, TT_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 GA, LC37Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmJ, TT_C1304
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide chain release factor 1 JA, KA, OC, PC365Escherichia coliMutation(s): 0 
Gene Names: prfA
Find proteins for B7MKB3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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Entity ID: 36
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30S ribosomal protein S2 LA, QC256Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsB, rps2, TT_C0509
Find proteins for P62662 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 37
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30S ribosomal protein S3 MA, RC239Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsC, rps3, TT_C1322
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Entity ID: 38
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50S ribosomal protein S4 NA, SC209Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsD, rps4, TT_C1301
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Entity ID: 39
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30S ribosomal protein S5 OA, TC162Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsE, rps5, TT_C1311
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Entity ID: 40
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30S ribosomal protein S6 PA, UC101Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsF, rps6, TT_C1740
Find proteins for P62666 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 41
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30S ribosomal protein S7 QA, VC156Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsG, rps7, TT_C1332
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Entity ID: 42
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30S ribosomal protein S8 RA, WC138Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsH, rps8, TT_C1314
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Entity ID: 43
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30S ribosomal protein S9 SA, XC128Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsI, rps9, TT_C1100
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Entity ID: 44
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30S ribosomal protein S10 TA, YC105Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsJ, rps10, TT_C1329
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Entity ID: 45
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30S ribosomal protein S11 UA, ZC129Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsK, rps11, TT_C1302
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Entity ID: 46
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30S ribosomal protein S12 AD, VA132Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsL, rps12, TT_C1333
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Entity ID: 47
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30S ribosomal protein S13 BD, WA126Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsM, rps13, TT_C1303
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Entity ID: 48
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30S ribosomal protein S14 type Z CD, XA61Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsZ, rps14, rpsN, TT_C1315
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Entity ID: 49
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30S ribosomal protein S15 DD, YA89Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsO, rps15, TT_C0773
Find proteins for P62657 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 50
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30S ribosomal protein S16 ED, ZA88Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsP, rps16, TT_C0673
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Entity ID: 51
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30S ribosomal protein S17 AB, FD105Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsQ, rps17, TT_C1319
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Entity ID: 52
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30S ribosomal protein S18 BB, GD88Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsR, rps18, TT_C1742
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Entity ID: 53
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30S ribosomal protein S19 CB, HD93Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsS, rps19, TT_C1324
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Entity ID: 54
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30S ribosomal protein S20 DB, ID106Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsT, rps20, TT_C1031
Find proteins for P62661 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 55
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30S ribosomal protein Thx EB, JD27Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsU, TT_C1030
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Entity ID: 1
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16S ribosomal RNAA, FB1507Thermus thermophilus HB27
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Entity ID: 2
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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
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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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