7QGR

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

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.70 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
50S ribosomal protein L2B [auth P]273Escherichia coliMutation(s): 0 
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50S ribosomal protein L3C [auth Q]209Escherichia coliMutation(s): 0 
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50S ribosomal protein L4D [auth R]201Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5E [auth S]179Escherichia coliMutation(s): 0 
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50S ribosomal protein L6F [auth T]177Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11G [auth V]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L13H [auth W]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14I [auth X]123Escherichia coliMutation(s): 0 
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50S ribosomal protein L15J [auth Y]144Escherichia coliMutation(s): 0 
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50S ribosomal protein L16K [auth Z]136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17L [auth a]127Escherichia coliMutation(s): 0 
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50S ribosomal protein L18M [auth b]117Escherichia coliMutation(s): 0 
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50S ribosomal protein L19N [auth c]115Escherichia coliMutation(s): 0 
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50S ribosomal protein L20O [auth d]118Escherichia coliMutation(s): 0 
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50S ribosomal protein L21P [auth e]103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22Q [auth f]110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23R [auth g]100Escherichia coliMutation(s): 0 
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50S ribosomal protein L24S [auth h]104Escherichia coliMutation(s): 0 
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50S ribosomal protein L25T [auth i]94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27U [auth j]85Escherichia coliMutation(s): 0 
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50S ribosomal protein L28V [auth k]78Escherichia coliMutation(s): 0 
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50S ribosomal protein L29W [auth l]63Escherichia coliMutation(s): 0 
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50S ribosomal protein L30X [auth m]59Escherichia coliMutation(s): 0 
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50S ribosomal protein L32Y [auth n]57Escherichia coliMutation(s): 0 
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50S ribosomal protein L33Z [auth o]55Escherichia coliMutation(s): 0 
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50S ribosomal protein L34AA [auth p]46Escherichia coliMutation(s): 0 
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50S ribosomal protein L35BA [auth q]65Escherichia coliMutation(s): 0 
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50S ribosomal protein L36CA [auth r]55Escherichia coliMutation(s): 0 
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50S ribosomal protein L31EA [auth L]70Escherichia coliMutation(s): 0 
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50S ribosomal protein L1FA [auth C]223Escherichia coliMutation(s): 0 
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50S ribosomal protein L9GA [auth U]149Escherichia coliMutation(s): 0 
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30S ribosomal protein S2KA [auth 1]239Escherichia coliMutation(s): 0 
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30S ribosomal protein S3LA [auth 2]218Escherichia coliMutation(s): 0 
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30S ribosomal protein S4MA [auth 3]206Escherichia coliMutation(s): 0 
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30S ribosomal protein S5NA [auth 4]162Escherichia coliMutation(s): 0 
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30S ribosomal protein S6, non-modified isoformOA [auth 5]131Escherichia coliMutation(s): 0 
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30S ribosomal protein S7PA [auth 6]152Escherichia coliMutation(s): 0 
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30S ribosomal protein S8QA [auth 7]130Escherichia coliMutation(s): 0 
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30S ribosomal protein S9RA [auth 8]130Escherichia coliMutation(s): 0 
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30S ribosomal protein S10SA [auth 9]103Escherichia coliMutation(s): 0 
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30S ribosomal protein S11TA [auth A]129Escherichia coliMutation(s): 0 
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30S ribosomal protein S12UA [auth B]124Escherichia coliMutation(s): 0 
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30S ribosomal protein S13VA [auth D]118Escherichia coliMutation(s): 0 
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30S ribosomal protein S14WA [auth E]101Escherichia coliMutation(s): 0 
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30S ribosomal protein S15XA [auth F]89Escherichia coliMutation(s): 0 
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30S ribosomal protein S16YA [auth G]82Escherichia coliMutation(s): 0 
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30S ribosomal protein S17ZA [auth H]84Escherichia coliMutation(s): 0 
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30S ribosomal protein S18AB [auth I]75Escherichia coliMutation(s): 0 
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30S ribosomal protein S19BB [auth J]92Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20CB [auth K]87Escherichia coliMutation(s): 0 
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Find proteins for P0A7U7 (Escherichia coli (strain K12))
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UniProt GroupP0A7U7
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21DB [auth s]71Escherichia coliMutation(s): 0 
UniProt
Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1EB [auth t]557Escherichia coliMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
UPF0115 protein YfcNGB [auth v]182Escherichia coliMutation(s): 0 
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

UniProt
Find proteins for Q6KCY1 (Escherichia coli)
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UniProt GroupQ6KCY1
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Entity ID: 1
MoleculeChains LengthOrganismImage
5S rRNAA [auth O]120Escherichia coli
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Entity ID: 30
MoleculeChains LengthOrganismImage
23S rRNADA [auth N]2,903Escherichia coli
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Entity ID: 34
MoleculeChains LengthOrganismImage
P-site tRNAHA [auth M]75Escherichia coli
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Entity ID: 35
MoleculeChains LengthOrganismImage
mRNAIA [auth x]692Vibrio alginolyticus
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Entity ID: 36
MoleculeChains LengthOrganismImage
16S rRNAJA [auth 0]1,539Escherichia coli
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Entity ID: 58
MoleculeChains LengthOrganismImage
A-site tRNAFB [auth u]73Escherichia coli
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.70 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: 2022-06-22
    Type: Initial release