7QGN

Structure of the SmrB-bound E. coli disome - stalled 70S ribosome

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Ribosome collisions induce mRNA cleavage and ribosome rescue in bacteria.

Saito, K., Kratzat, H., Campbell, A., Buschauer, R., Burroughs, A.M., Berninghausen, O., Aravind, L., Green, R., Beckmann, R., Buskirk, A.R.

(2022) Nature 603: 503-508

  • DOI: https://doi.org/10.1038/s41586-022-04416-7
  • Primary Citation of Related Structures:  
    7QG8, 7QGH, 7QGN, 7QGR, 7QGU, 7QH4

  • PubMed Abstract: 

    Ribosome rescue pathways recycle stalled ribosomes and target problematic mRNAs and aborted proteins for degradation 1,2 . In bacteria, it remains unclear how rescue pathways distinguish ribosomes stalled in the middle of a transcript from actively translating ribosomes 3-6 . Here, using a genetic screen in Escherichia coli, we discovered a new rescue factor that has endonuclease activity. SmrB cleaves mRNAs upstream of stalled ribosomes, allowing the ribosome rescue factor tmRNA (which acts on truncated mRNAs 3 ) to rescue upstream ribosomes. SmrB is recruited to ribosomes and is activated by collisions. Cryo-electron microscopy structures of collided disomes from E. coli and Bacillus subtilis show distinct and conserved arrangements of individual ribosomes and the composite SmrB-binding site. These findings reveal the underlying mechanisms by which ribosome collisions trigger ribosome rescue in bacteria.

    • Organizational Affiliation: 

    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
UPF0115 protein YfcN183Escherichia coliMutation(s): 2 
Gene Names: 
yfcN, mutS2, smrB, smrB_1, smrB_2, A5U30_004390, A8499_001840, A9819_13690, A9X72_07680, ABE90_016875, ACN68_23030, ACN81_17810, ACU57_26745, AT845_000599, AWP93_07555, BANRA_00899, BANRA_03120, BANRA_03372, BF481_001004, BG944_000572, BGZ_01188, BGZ_03662, BHS81_14420, BIZ41_10480, BJI68_12470, BK292_05530, BMT49_14945, BN17_16361, BO068_000573, BOB65_001429, BOH76_07895, BON63_04725, BON64_17650, BON65_13895, BON66_23670, BON67_14425, BON68_20955, BON70_19955, BON72_07945, BON73_17545, BON74_06335, BON75_03320, BON76_16635, BON77_02335, BON78_04290, BON79_05115, BON80_19510, BON84_07205, BON88_15485, BON89_17570, BON90_11325, BON93_24455, BON94_16970, BON95_09375, BON97_08585, BON98_08660, BR158_002903, BSR05_08700, BTQ06_04170, BvCmsF30A_00313, BvCmsHHP019_01505, BvCmsHHP019_04741, BvCmsHHP056_04467, BvCmsKKP061_01272, BvCmsKSNP073_04721, BvCmsNSP072_04545, BVL39_15455, C2121_000219, C2U48_22750, C5N07_03940, C5Y87_03970, C9114_16420, C9160_05935, CCS08_07685, CCV12_002627, CDC27_12170, CG692_16040, CG831_000106, CIG67_19185, CQB02_04630, CR538_08010, CT143_04915, CV83915_03834, CWS33_01470, D3G36_02825, D9D77_18555, D9H94_01080, D9J61_20205, DAH18_01290, DAH19_01275, DAH20_01625, DAH22_02175, DAH27_09560, DAH28_11500, DAH29_05910, DAH30_16955, DAH31_06915, DAH32_12865, DAH34_11100, DAH35_01300, DAH36_15590, DAH37_19730, DAH41_07365, DAH50_05250, DEN88_00035, DEN89_08320, DEN90_05265, DEN91_02555, DEN92_02065, DEN93_02685, DEN94_01290, DEN95_01315, DEN96_01750, DEN97_01415, DEN98_01420, DEN99_05995, DEO00_00270, DEO01_17030, DEO02_01830, DEO03_03920, DEO04_00005, DEO05_00005, DEO06_08185, DEO07_00005, DEO08_00005, DEO09_00005, DEO10_00005, DEO11_00005, DEO12_00005, DEO13_01820, DEO14_01755, DEO15_01085, DEO17_01750, DEO18_04800, DEO19_01300, DEO20_01795, DIV22_21330, DN627_21615, DNQ45_19055, DRW19_09740, DS732_17835, DTL90_12855, DTM16_09590, DXT69_04490, DXT70_01870, DXT71_03185, E2112_03655, E2113_09810, E2117_01065, E2119_16395, E2121_01160, E2134_04330, E3N34_02270, E5P23_02715, E5P24_14725, E5P25_01670, E5P30_14800, E5P31_09445, E5P32_05070, E5P33_05410, E5P35_06605, E5P36_01995, E5P37_00385, E5P39_08050, E5P40_09805, E5P41_10890, E5P42_00250, E5P43_12380, E5P44_13535, E5P45_12690, E5P46_02815, E5P47_11675, E5P48_09480, E5P49_00460, E5P50_14395, E5P51_21390, E5S35_19735, E5S36_02955, E5S38_02620, E5S39_01460, E5S42_01695, E5S43_19350, E5S44_00375, E5S45_16565, E5S47_01205, E5S48_14270, E5S51_02300, E5S52_02190, E5S53_18875, E5S55_19065, E5S56_02640, E5S57_06985, EA239_07420, EA435_01595, EAN77_01305, EAX79_20205, EC1094V2_1345, EC3234A_175c01110, EC95NR1_01492, ED648_12345, EHD79_00295, EHH55_04655, EI021_18035, EIZ93_06290, EKI52_23470, ELT16_18350, ELT20_15195, ELT24_01425, ELT26_03990, ELT30_01440, ELT32_01920, ELT34_02590, ELT35_07845, ELT36_06875, ELT39_20410, ELT40_03580, ELT44_07815, ELT45_01435, ELT46_01450, ELT48_05880, ELT54_16840, ELT55_13610, ELT59_03260, ELT60_09215, ELT61_19220, ELT63_16105, ELT72_01435, ELU07_15110, ELU82_03765, ELU88_16655, ELU89_04385, ELU91_15800, ELU94_18550, ELU96_02215, ELU97_18185, ELU98_09905, ELV00_03615, ELV01_12085, ELV03_05730, ELV04_06410, ELV05_03280, ELV07_11430, ELV11_03535, ELV12_11720, ELV13_16905, ELV22_00040, ELV23_22840, ELV24_07090, ELV29_06140, ELX56_00135, ELX68_00090, ELX70_01865, ELX79_14975, ELX83_13520, ELX85_05845, ELY02_00645, ELY05_05535, ELY23_09510, ELY24_08500, ELY31_00705, ELY50_09115, ERS085406_02073, ERS139208_00454, EYV17_01290, EYV18_11375, F0L67_02300, F2N31_09430, F7F11_19875, F9V24_13620, F9X20_21990, FDM60_03010, FE587_23440, FEJ01_05060, FEL34_15690, FOI11_001300, FOI11_18750, FQ007_23030, FQF29_20000, FTV90_21245, FV293_07005, G3565_01615, G9448_22280, GF699_03390, GFY34_16620, GIB53_14855, GKF86_02695, GKF89_15515, GKG12_06190, GNZ05_23665, GP650_07760, GP662_01570, GP711_04770, GP946_05950, GQA06_05730, GQE64_02945, GQM09_01760, GQM13_01410, GQW07_19785, GRC73_01145, GRO95_21555, GRW57_06930, GRW81_01820, GUB92_01975, GUI33_05790, H0O53_19725, H0O72_00040, H6Y26_004289, HI055_002425, HIE29_002473, HIN64_001808, HKA49_003965, HLZ50_13880, HmCms169_00759, HMU06_04960, HMV41_01130, HV109_07165, HV146_16035, HV209_11120, HVV39_03830, HVX32_14355, HVY77_08085, HVZ29_14235, HX136_07310, I6H02_06990, IAI11_22020, IFB95_000286, IH772_06500, J0541_000123, J5U05_001006, JE86ST02C_27550, JE86ST05C_28400, JFD_00470, JNP96_19200, NCTC10089_01526, NCTC10767_02776, NCTC10865_01974, NCTC11181_03768, NCTC13148_02067, NCTC13216_05049, NCTC7928_01110, NCTC8008_00929, NCTC8009_02822, NCTC8179_04654, NCTC8333_01761, NCTC8450_03992, NCTC8621_01639, NCTC8622_03767, NCTC8960_04324, NCTC9001_01891, NCTC9036_01593, NCTC9045_01822, NCTC9073_04248, NCTC9111_01754, NCTC9775_05405, ND22_002524, PGD_00891, RG28_10175, SAMEA3472044_01606, SAMEA3472056_00624, SAMEA3472067_00013, SAMEA3472080_03598, SAMEA3751407_01308, SAMEA3752557_00674, WR15_08435

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VemP nascent chainC [auth s]179Vibrio alginolyticusMutation(s): 0 
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50S ribosomal protein L2F [auth P]273Escherichia coliMutation(s): 0 
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50S ribosomal protein L3G [auth Q]209Escherichia coliMutation(s): 0 
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50S ribosomal protein L4H [auth R]201Escherichia coliMutation(s): 0 
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50S ribosomal protein L5I [auth S]179Escherichia coliMutation(s): 0 
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50S ribosomal protein L6J [auth T]177Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9K [auth U]149Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11L [auth V]142Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13M [auth W]142Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14N [auth X]123Escherichia coliMutation(s): 0 
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50S ribosomal protein L15O [auth Y]144Escherichia coliMutation(s): 0 
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50S ribosomal protein L16P [auth Z]136Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L17Q [auth a]127Escherichia coliMutation(s): 1 
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Entity ID: 18
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50S ribosomal protein L18R [auth b]117Escherichia coliMutation(s): 0 
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50S ribosomal protein L19S [auth c]115Escherichia coliMutation(s): 0 
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50S ribosomal protein L20T [auth d]118Escherichia coliMutation(s): 0 
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50S ribosomal protein L21U [auth e]103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22V [auth f]110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23W [auth g]100Escherichia coliMutation(s): 1 
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50S ribosomal protein L24X [auth h]104Escherichia coliMutation(s): 0 
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50S ribosomal protein L25Y [auth i]94Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27Z [auth j]85Escherichia coliMutation(s): 0 
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50S ribosomal protein L28AA [auth k]78Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29BA [auth l]63Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30CA [auth m]59Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32DA [auth n]57Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33EA [auth o]55Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34FA [auth p]46Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35GA [auth q]65Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36HA [auth r]55Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31JA [auth L]70Escherichia coliMutation(s): 1 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1KA [auth C]223Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2MA [auth 1]239Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3NA [auth 2]218Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4OA [auth 3]206Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5PA [auth 4]162Escherichia coliMutation(s): 1 
UniProt
Find proteins for A0A377C6M5 (Escherichia coli)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6QA [auth 5]131Escherichia coli K-12Mutation(s): 1 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S7RA [auth 6]156Escherichia coliMutation(s): 1 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8SA [auth 7]130Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9TA [auth 8]130Escherichia coliMutation(s): 1 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10UA [auth 9]103Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11VA [auth D]129Escherichia coliMutation(s): 1 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12WA [auth E]124Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13XA [auth F]118Escherichia coliMutation(s): 1 
UniProt
Find proteins for A0A7U9IV78 (Escherichia coli HVH 36)
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14YA [auth G]101Escherichia coliMutation(s): 1 
UniProt
Find proteins for A0A090BZT4 (Escherichia coli)
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15ZA [auth H]89Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16AB [auth I]82Escherichia coli UMEA 3162-1Mutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17BB [auth J]84Escherichia coliMutation(s): 1 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18CB [auth K]75Escherichia coliMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19DB [auth t]92Escherichia coliMutation(s): 2 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20EB [auth u]87Escherichia coliMutation(s): 1 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21FB [auth v]88Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
A-site tRNA73Escherichia coli
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Entity ID: 4
MoleculeChains LengthOrganismImage
P-site tRNAD [auth M]75Escherichia coli
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Entity ID: 5
MoleculeChains LengthOrganismImage
5S rRNAE [auth O]120Escherichia coli
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Entity ID: 35
MoleculeChains LengthOrganismImage
23S rRNAIA [auth N]2,903Escherichia coli
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Entity ID: 38
MoleculeChains LengthOrganismImage
16S rRNALA [auth 0]1,539Escherichia coli
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-27
    Type: Initial release