6LKQ

The Structural Basis for Inhibition of Ribosomal Translocation by Viomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The structural basis for inhibition of ribosomal translocation by viomycin.

Zhang, L.Wang, Y.H.Zhang, X.Lancaster, L.Zhou, J.Noller, H.F.

(2020) Proc Natl Acad Sci U S A 117: 10271-10277

  • DOI: 10.1073/pnas.2002888117
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Viomycin, an antibiotic that has been used to fight tuberculosis infections, is believed to block the translocation step of protein synthesis by inhibiting ribosomal subunit dissociation and trapping the ribosome in an intermediate state of intersubu ...

    Viomycin, an antibiotic that has been used to fight tuberculosis infections, is believed to block the translocation step of protein synthesis by inhibiting ribosomal subunit dissociation and trapping the ribosome in an intermediate state of intersubunit rotation. The mechanism by which viomycin stabilizes this state remains unexplained. To address this, we have determined cryo-EM and X-ray crystal structures of Escherichia coli 70S ribosome complexes trapped in a rotated state by viomycin. The 3.8-Å resolution cryo-EM structure reveals a ribosome trapped in the hybrid state with 8.6° intersubunit rotation and 5.3° rotation of the 30S subunit head domain, bearing a single P/E state transfer RNA (tRNA). We identify five different binding sites for viomycin, four of which have not been previously described. To resolve the details of their binding interactions, we solved the 3.1-Å crystal structure of a viomycin-bound ribosome complex, revealing that all five viomycins bind to ribosomal RNA. One of these (Vio1) corresponds to the single viomycin that was previously identified in a complex with a nonrotated classical-state ribosome. Three of the newly observed binding sites (Vio3, Vio4, and Vio5) are clustered at intersubunit bridges, consistent with the ability of viomycin to inhibit subunit dissociation. We propose that one or more of these same three viomycins induce intersubunit rotation by selectively binding the rotated state of the ribosome at dynamic elements of 16S and 23S rRNA, thus, blocking conformational changes associated with molecular movements that are required for translocation.


    Organizational Affiliation

    Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064 jiezh@zju.edu.cn harry@nuvolari.ucsc.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
A
218Escherichia coliMutation(s): 0 
Gene Names: 
rpsBA6581_19565A6592_02990A8C65_17850A9819_00790A9P13_21180A9R57_04400AC067_04635AJ318_03080AM446_22760AM464_17645AM465_25885AML35_22875APT94_19995APU18_02555ARC77_20180AU473_25970AUQ13_07500AW059_09840AWE53_010740AWF59_003780AWG78_007095AWG90_002345AWP75_13480AZZ83_003980B6V57_00930B7C53_01360B9M99_16250B9N33_22515B9T59_07520BANRA_00547BANRA_02273BANRA_03339BE963_14830BEN53_03085BER14_07785BFD68_21815BHF03_16550BHF46_07885BHS87_00800BIQ87_00790BIU72_13410BIZ41_19080BJJ90_21360BK248_07255BK334_15020BK373_09595BK375_04645BK383_20240BMT49_02175BMT91_01365BON65_09430BON66_02955BON75_17145BON83_24855BON86_04410BON87_26695BON91_06960BON92_02750BON96_17215BTQ04_14405BUE81_01710BvCms12BK_00034BvCms2454_04107BvCms35BK_02145BvCmsC61A_04364BvCmsHHP001_04838BvCmsHHP019_00044BvCmsHHP056_04094BvCmsKKP036_03788BvCmsKSNP120_00104BvCmsKSP026_04711BvCmsKSP058_03767BvCmsKSP076_03014BvCmsNSP007_03764BvCmsSINP022_00326BW690_02470BWI89_14055BWP17_11915BXT93_00705BZL31_14940BZL69_20205C2M16_10795C2U48_09610C4K41_20910C4M78_19960C5715_17350C5N07_08575C5P44_18010C6669_04250C6B13_04325C7B06_05860C7B07_04280C7B08_09695C7B18_05305C9E25_15390C9E67_25210C9Z23_08405C9Z29_10375C9Z39_04990C9Z43_09525C9Z68_04785C9Z70_08115C9Z78_00165C9Z78_02775CA593_02870CCZ14_20505CCZ17_20470CDC27_24690CDL37_07245CG692_09500CI693_15090CI694_28160CIG45_06990CQP61_22090CR539_04935CRE06_00170CRT43_00990CRX46_05020CSB64_09595CT146_12115CUB99_08015CVH05_24475CWM24_05035D0X26_09420D1912_13690D2185_20130D2188_12785D3821_06210D3822_17335D3O91_03185D3P01_06970D3Y67_16405D4M06_01450D4V08_16070D6T60_04050D6X76_09800D7K63_00165D7K66_11610D7Y10_00165D9D20_18630D9D31_08885D9D33_03385D9D43_02305D9E34_01105D9E35_14530D9E49_02145D9F17_00165D9G11_19100D9G42_07585D9G48_08785D9H36_21790D9H53_14245D9H68_13775D9H70_04355D9I20_08115D9I37_13510D9I87_01640D9I88_06435D9I97_03805D9J03_00165D9J11_16825D9J60_02075D9J78_12380D9K54_16750D9L89_00165D9L99_05940D9X97_00165DAH26_11215DAH34_04190DAH37_16335DAH43_04025DBQ99_21360DD762_01090DEN86_04070DJ487_06020DJ492_12760DJ503_00895DL455_01615DLW88_03755DM102_18365DM129_14540DMI04_00170DMZ50_04115DN627_10245DNB37_01435DND16_04815DNR41_13200DNX30_02270DOY56_00170DP258_09355DQE83_10255DS966_12905DTL43_05925DTL90_09735DTM10_02780DTM45_12630DU309_06140DU321_03650DU333_05950DW236_10615DWB25_20305DXT73_18920DXX80_017135E0L04_16465E0L12_05055E2112_01240E2115_17375E2116_17400E2119_15580E2127_15010E2128_01350E2129_02860E2134_11975E2135_11635E2148_14070E4K55_06965E5P22_04090E5P28_13975E5P37_21190E5S46_19535E5S58_05605E5S61_20145EA250_20395EA410_04885EA834_19145EAI42_08300EAI52_11005EB509_04560EB510_04565EB515_00165EC3234A_2c01500EC3426_00920EC382_02955ECONIH1_00890ECs0171ECTO124_04042ECTO6_03894ED225_10455ED607_02625ED611_09635ED648_00165ED903_08485ED944_00165EEA45_04510EEP23_00165EF173_00165EGT48_20250EI021_19845EI028_17525EI032_14690EIA08_06325EIA21_00165EIZ93_07925EL75_3596EL79_3705EL80_3652ELT20_04470ELT23_12175ELT33_15870ELT34_19890ELT48_12180ELT49_18475ELT58_11815ELU82_16775ELU85_21270ELU96_20275ELV05_06475ELV13_13145ELV15_10275ELV24_19200ELV28_04185ELX79_12490ELX83_20605ELY23_06765ELY24_11290ELY50_16140EO241_11800EPS76_09885EPS91_15145EPS94_12740EPT01_02595EPU41_00950EQ820_08895EQ823_16635EQ825_22910EQ830_01905ERL57_05895ERS085365_03087ERS085366_02719ERS085383_01177ERS085386_01543ERS085404_00708ERS085406_00569ERS085411_00031ERS085416_03650ERS139211_02987ERS150873_01111EST51_20100EVY14_15615EWK56_14885EXM29_15760ExPECSC019_03545ExPECSC038_03990ExPECSC065_04179EXX06_08815EXX13_05315EXX23_14665EXX53_06965EXX55_08280EXX71_19560EXX87_03335EYD11_18540EYX82_24365EYX99_20960EYY27_25445EYY34_22885F7F11_02075F7G01_02645F7G03_01455FAF34_018075FKO60_12340FNJ67_21465FNJ69_22375FNJ83_02345FORC82_3871FQU83_21885FRV13_02390FV293_02895FV295_13970FV438_03735FY127_02945GJ11_00885HmCms184_03911HmCmsJML074_03001HmCmsJML146_01754HmCmsJML204_00825HMPREF3040_02610MJ49_06195MS6198_01840MS8345_00167NCTC10082_01383NCTC10089_04076NCTC10090_02160NCTC10767_03962NCTC10974_04616NCTC11126_03634NCTC12950_04424NCTC13127_05455NCTC13148_05196NCTC13846_03878NCTC7922_05813NCTC7927_04507NCTC7928_04613NCTC8450_01117NCTC8500_04546NCTC8621_04202NCTC8959_04843NCTC9007_00459NCTC9044_03184NCTC9045_04711NCTC9050_02026NCTC9058_02797NCTC9062_04214NCTC9117_05053NCTC9119_04267NCTC9434_02610NCTC9701_04378NCTC9702_04760NCTC9706_01337NCTC9777_00472NCTC9969_04265PGD_03810RK56_028000SAMEA3472044_04157SAMEA3472047_02498SAMEA3472056_00973SAMEA3472080_03752SAMEA3472090_04487SAMEA3472108_03201SAMEA3472110_04513SAMEA3472112_04653SAMEA3472147_00380SAMEA3484427_01375SAMEA3484429_01106SAMEA3484434_01147SAMEA3485113_00840SAMEA3752372_04458SAMEA3752557_00874SAMEA3752559_03712SAMEA3752620_02090SAMEA3753097_03905SAMEA3753164_02433SAMEA3753300_01863SK85_00168SY51_00965U12A_00178U14A_00177UC41_07420UN91_10580WQ89_09555YDC107_3394

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
B
206Escherichia coliMutation(s): 0 
Gene Names: rpsCNCTC9094_00425
Find proteins for A0A376HTV6 (Escherichia coli)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
C
205Escherichia coliMutation(s): 0 
Find proteins for A0A4P8BV83 (Escherichia coli O145:NM)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
D
150Escherichia coliMutation(s): 0 
Find proteins for F4SQ30 (Escherichia coli H736)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
E
100Escherichia coliMutation(s): 0 
Gene Names: rpsFD9J60_11985
Find proteins for A0A3L2GT12 (Escherichia coli)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
F
151Escherichia coliMutation(s): 0 
Find proteins for D6I218 (Escherichia coli B088)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
G
129Escherichia coliMutation(s): 0 
Find proteins for U9ZUM7 (Escherichia coli 907713)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
H
127Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
I
98Escherichia coliMutation(s): 0 
Gene Names: rpsJFTV90_00850
Find proteins for A0A5B9AU26 (Escherichia coli)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
J
117Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
K
123Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
L
114Escherichia coliMutation(s): 0 
Find proteins for A0A069XLE9 (Escherichia coli 3-373-03_S4_C2)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
M
100Escherichia coliMutation(s): 0 
Gene Names: rpsNBvCmsNSP072_04005D9J44_12955ERS085374_04715SAMEA3485113_04711
Find proteins for A0A090BZT4 (Escherichia coli)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
N
88Escherichia coliMutation(s): 0 
Find proteins for A0A029IK47 (Escherichia coli 2-005-03_S4_C2)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
O
82Escherichia coliMutation(s): 0 
Find proteins for A0A029IMB2 (Escherichia coli 2-005-03_S4_C2)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
P
80Escherichia coliMutation(s): 0 
Find proteins for T6LV72 (Escherichia coli HVH 87)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
Q
55Escherichia coliMutation(s): 0 
Find proteins for E9TDX6 (Escherichia coli MS 117-3)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
R
79Escherichia coliMutation(s): 0 
Find proteins for S1EA57 (Escherichia coli KTE73)
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
S
85Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
T
51Escherichia coliMutation(s): 0 
Gene Names: rpsUFWK02_18995
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
U
271Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
V
209Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
W
201Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
X
177Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
Y
176Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
Z
141Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
0
142Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
1
122Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
2
143Escherichia coliMutation(s): 0 
Gene Names: 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
3
136Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
4
120Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
5
116Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
6
114Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
8
117Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
9
103Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
a
110Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
b
93Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
c
102Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
d
94Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
e
79Escherichia coliMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
f
77Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
g
63Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
h
58Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
i
56Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
j
50Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
k
46Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
l
64Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
m
38Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
n
163Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7/L12
o, p, q, r
30Escherichia coliMutation(s): 0 
Gene Names: rplLBvCmsKKP036_03582CQB02_21450
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor 3
v
525Escherichia coliMutation(s): 0 
Gene Names: 
prfCA6592_04090A9819_24895A9P13_22280AM446_23880APT94_26745APU18_05660ARC77_19140AU473_27010AW059_08770AWE53_009720AWF59_004815AWG78_008420AWG90_001320B6V57_25825B7C53_16745B9M99_13090B9T59_08605BE963_13730BEN53_02000BIQ87_25000BK292_12635BK296_03565BK334_23560BK375_05695BK383_08010BON66_13380BON69_06980BON83_25940BON86_14100BON87_19305BON91_08050BTQ04_23865BvCms35BK_02339BvCmsC61A_04169BvCmsKSP076_01357BvCmsSINP022_00133BWP17_03290BZL69_04535C4M78_04330C6B13_05410C7B06_04825C7B07_05320C7B08_12205C9E25_18240C9Z29_11365C9Z70_09130C9Z78_01140C9Z78_01800CDC27_23620CO706_22040CQP61_23130CRE06_01225CRM83_16110CRX46_08470CSB64_20240CVH05_08650D3P01_08040D4M06_02510D4V08_15195D6X76_13610D7K63_01185D7K66_00530D9D31_02535D9D33_04435D9E34_05080D9E49_03180D9F17_01140D9G11_20135D9G42_08575D9H36_11075D9I20_09105D9J03_08845D9J46_24105D9J78_18550D9K54_15750D9L89_01175D9X97_01175DAH43_02965DJ487_07090DJ492_15720DM102_03510DM129_14235DMI04_01235DN627_19210DNB37_02495DND16_26005DNX30_03355DOY56_01235DP258_19205DS966_19590DTL90_19440DTM10_01760DU321_02625DW236_09545DWB25_21390DXX80_016145E0L12_12060E2115_07710E2116_05915E5S46_05040E5S58_22630E5S61_04945EA250_12685EA410_05935EAI52_14785EB509_11720EB510_06525EB515_01160ECs5333ED225_13205ED607_14660ED611_13460ED903_11920ED944_01160EEA45_16055EF173_01160ELT33_16890ELT58_08165ELU85_12220ELV05_08500ELV15_04515ELV28_15045EPU41_24455EQ820_17955EQ823_02985EQ830_02930EXM29_16750ExPECSC019_03346ExPECSC038_04189EXX13_04315EXX23_13025EXX53_09860EYX82_09370EYY27_03920F7F11_03075F7G01_01655F7G03_00465FKO60_13500FNJ69_21335FNJ83_01320FV295_13040HmCmsJML074_02111HmCmsJML146_04652HmCmsJML204_00635MJ49_07195MS6198_51560NCTC9058_02594NCTC9434_02405NCTC9701_04578PGD_03617SAMEA3472090_00813SAMEA3484434_03165SAMEA3485101_00902SAMEA3752620_01894SAMEA3753164_02629UC41_15680UN86_17350

Find proteins for C3SE77 (Escherichia coli)
Go to UniProtKB:  C3SE77
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
Viomycin
7, AA, BA, y, z
6synthetic constructMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 51
MoleculeChainsLengthOrganism
16S ribosomal RNAs1532Escherichia coli

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Entity ID: 52
MoleculeChainsLengthOrganism
23S ribosomal RNAt2903Escherichia coli

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Entity ID: 53
MoleculeChainsLengthOrganism
5S ribosomal RNAu118Escherichia coli
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 55
MoleculeChainsLengthOrganism
messenger RNAw6Escherichia coli
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000226
Query on PRD_000226
7, AA, BA, y, zViomycinOligopeptide /  Antibiotic

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Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
5OH
Query on 5OH
7,AA,BA,y,z
L-PEPTIDE LINKINGC6 H12 N4 O3ALA
DPP
Query on DPP
7,AA,BA,y,z
L-PEPTIDE LINKINGC3 H8 N2 O2ALA
KBE
Query on KBE
7,AA,BA,y,z
L-PEPTIDE LINKINGC6 H14 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 257.6α = 90
b = 312.9β = 90
c = 328.6γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31971226

Revision History 

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2020-05-13
    Changes: Source and taxonomy, Structure summary
  • Version 1.2: 2020-05-27
    Changes: Database references