7AK9

Structure of Salmonella TacT3 toxin bound to TacA3 antitoxin C-terminal peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Auxiliary interfaces support the evolution of specific toxin-antitoxin pairing.

Grabe, G.J., Giorgio, R.T., Hall, A.M.J., Morgan, R.M.L., Dubois, L., Sisley, T.A., Rycroft, J.A., Hare, S.A., Helaine, S.

(2021) Nat Chem Biol 17: 1296-1304

  • DOI: https://doi.org/10.1038/s41589-021-00862-y
  • Primary Citation of Related Structures:  
    7AK7, 7AK8, 7AK9

  • PubMed Abstract: 

    Toxin-antitoxin (TA) systems are a large family of genes implicated in the regulation of bacterial growth and its arrest in response to attacks. These systems encode nonsecreted toxins and antitoxins that specifically pair, even when present in several paralogous copies per genome. Salmonella enterica serovar Typhimurium contains three paralogous TacAT systems that block bacterial translation. We determined the crystal structures of the three TacAT complexes to understand the structural basis of specific TA neutralization and the evolution of such specific pairing. In the present study, we show that alteration of a discrete structural add-on element on the toxin drives specific recognition by their cognate antitoxin underpinning insulation of the three pairs. Similar to other TA families, the region supporting TA-specific pairing is key to neutralization. Our work reveals that additional TA interfaces beside the main neutralization interface increase the safe space for evolution of pairing specificity.

    • Organizational Affiliation: 

    Department of Microbiology, Harvard Medical School, Boston, MA, USA.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acetyltransferase
A, B
176Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 1 
Gene Names: 
A2O69_14710, A3104_08525, A3111_02365, A3122_05715, A3146_07085, A3S30_20570, A3T81_15835, A3U32_19315, A3V03_13160, A3V89_13630, A3W57_15915, A3W75_13520, A3W86_09800, A3X15_14395, A3X55_09260, A3Y76_11330, A3Z96_17730, A4J27_06855, A4N07_06735, A4O05_06540, A4R48_05595, A6D61_06495, A9C21_11525, A9T39_06955, A9U46_17515, A9U64_03850, AAA76_13150, AAB27_19890, AAB39_07250, AAB79_09875, AAC08_00420, AAC35_15875, AAC42_08845, AAC44_05970, AAC95_11790, AAC98_08180, AAK29_13035, AAP89_06290, AAQ24_13230, AB424_06630, ABO94_10350, ABP87_20380, ADQ28_09230, ADQ45_03525, AE787_08375, AF480_02650, AF488_02445, AF489_05145, AF497_15340, AGC55_04185, AGM99_07505, AGQ32_07045, AH984_01035, AHN93_09010, AIC76_09285, AKH62_10520, AKH68_10580, AKI16_02015, AL144_10105, AL151_10950, AL166_11665, AL168_09635, AL170_09510, AL174_03655, AL184_10950, APY91_06225, AQ530_13930, AS118_08370, AT354_02285, AU613_08485, AU805_10975, AU830_04485, AU839_11895, AU951_07445, AU965_16560, AVA38_07605, AVB77_13980, AVB94_15035, AVC05_01920, AVC09_03465, AVD08_11675, AVD75_12175, AVD94_11625, AVL02_10280, AVL16_05965, AVM19_04730, AWT30_06955, AXM10_11690, AXM23_13930, AXR84_07880, AXU58_02150, AXX99_11930, B1265_07265, B1398_23385, B1642_13580, B1B86_06045, B1B89_02010, B1I91_06440, B1P38_03325, B1Q82_05910, B2E31_15360, B4V59_13460, B4W90_04250, B5A40_05340, B6362_07445, B6G98_04770, B6M25_12980, B6M43_01870, B7071_02280, B7890_10645, B7J30_02750, B7Q27_07260, B8Y16_10555, B8Y36_04530, B8Z46_07685, B9653_20405, B9C61_09950, B9C71_14620, B9C90_09640, B9C91_13400, B9C96_07470, B9M14_11835, B9O84_04625, B9U29_15940, BBQ66_03420, BEL47_20970, BGP52_08870, BIC00_01965, BIC01_05330, BIC03_09930, BIC13_10285, BK110_07455, BKM50_12355, BLB03_01740, BMS46_04300, BMU56_05250, BSC80_02300, BSD55_06335, BZ203_09215, BZ210_07060, BZG47_06310, BZN20_02445, BZZ88_18440, C4E88_02445, C5U54_02150, C5W43_12245, CA117_08410, CB102_08185, CB161_12015, CB198_02180, CB380_14500, CB383_01935, CB416_07355, CB530_05450, CB535_13640, CB570_08575, CB646_10705, CB657_09085, CBH20_06435, CBM40_20070, CBM67_16515, CBM76_14910, CBN77_16785, CBO42_11245, CBR08_04950, CBU32_07665, CBZ90_11485, CC403_06280, CC453_06265, CC594_15440, CC652_14675, CC725_04865, CC886_14180, CC918_07945, CC944_02215, CC971_01735, CCF93_10575, CCP17_12420, CCW27_01035, CD48_09215, CD977_05545, CDJ75_04635, CDT37_10325, CDZ72_03910, CE355_06180, CE615_05710, CE70_11930, CE806_07385, CE87_05355, CE896_10245, CEC46_10535, CEC56_05725, CED07_07405, CEQ70_02125, CER78_09050, CET98_05350, CEY64_12815, CFB16_10680, CFB28_09520, CFE76_07290, CFE79_02120, CFF58_10820, CFF59_05970, CFJ48_10970, CGG73_06885, CHN22_06165, CI444_05360, CIX60_02145, CJC42_03195, CPR79_16280, CPS79_11185, CPX68_05100, CQE35_07680, CQO33_16090, CR370_08455, CRB02_05340, CSG22_12020, CTJ81_12735, CVR97_12650, D3147_08940, D3174_07820, D3F31_20020, D3T68_17985, D3Y48_07440, D4361_09990, D4369_10995, D4380_01880, D4387_15140, D4422_12965, D4E62_16105, D4E68_14820, D4E74_13085, D4X64_15240, D4Y62_17435, D5823_15645, D5949_23340, D5B48_13110, D5C67_12005, D5C71_16355, D5N86_08970, D5N95_10230, D5O82_16440, D5P17_16530, D5X47_15185, D5Y28_18520, D6360_15430, D6367_13695, D6371_04230, D6373_15865, D6395_13525, D6421_15010, D6422_15625, D6J79_16905, D6K10_25570, D6P67_17865, D6Q64_15695, D6S43_13590, D6T00_01880, D6T40_09010, D7F20_20100, D7H43_13140, D7O44_15935, D8Q90_16805, D8S24_11150, D9O84_11660, DD95_05355, DJ388_12295, DJ702_05335, DK061_11060, DK631_03160, DK641_12245, DK642_13480, DK689_12875, DK696_12630, DK698_11875, DKJ10_12870, DKR95_21490, DKS55_05145, DKU45_05690, DKU57_07335, DKU80_06725, DLB14_13735, DLB57_11890, DLB93_11425, DLR28_16975, DM322_06960, DMI89_25655, DMO92_02670, DMV40_12195, DMZ93_26675, DN165_11055, DN204_16500, DN359_23735, DNB97_00775, DNL62_15760, DNM27_05590, DNU59_05715, DNV08_01875, DNV12_09940, DNV30_14235, DNY92_13980, DNZ37_15375, DO350_06855, DO533_06050, DO585_16180, DO640_14410, DO698_08950, DO766_06390, DO828_16965, DO960_09160, DOC60_02105, DOH72_07130, DOI32_13580, DOI92_13210, DOJ39_17520, DOJ91_12145, DOQ54_06625, DOQ88_13030, DOR12_06235, DOV43_10320, DOW25_12865, DP680_15120, DPB42_03780, DPB45_13780, DPB48_08570, DPB57_07290, DPD91_09220, DPD95_09935, DPD99_23550, DPF41_13030, DPF68_13810, DPJ93_05515, DPK32_07545, DPK79_14260, DPL02_04340, DPP94_15975, DPP97_15415, DPS76_00440, DPT18_14130, DPU20_13855, DPY58_11745, DQ848_11335, DQ947_01880, DQ951_13955, DQC39_17415, DQC52_23390, DQD03_08180, DQD22_04750, DQE65_01875, DQK42_05460, DQQ98_08490, DQR10_25350, DQR61_13365, DQS14_11730, DQY10_10410, DQZ46_12325, DQZ56_08295, DR982_12275, DRL45_08460, DRM14_13595, DRM16_12360, DRR75_02370, DRT38_02095, DRT61_15355, DRT65_10140, DRV05_05570, DRW84_08295, DRX66_12300, DS270_13440, DS296_06505, DS451_14735, DS453_11540, DS521_04860, DS619_14375, DSF69_15770, DSF94_01875, DSG41_06680, DSM38_13920, DSN15_14610, DSR36_07530, DTE73_08970, DTF68_01875, DTG22_06850, DTG27_07270, DTW13_15655, DTW14_17675, DTW26_10525, DU071_02620, DU223_03775, DU657_08025, DU821_15060, DU879_12775, DU924_00430, DUQ28_15105, DUQ56_12120, DUQ92_16070, DUR36_05660, DUW10_17140, DUW48_07425, DVF14_10520, DVF88_05805, DVG01_14880, DVZ53_02690, DWU22_21650, DY580_03860, DYM27_25875, DYS82_16110, DZG11_12860, E0584_17725, E0595_12520, E0935_16805, E0989_11820, E0M34_00770, E0U75_12350, E0V94_13550, E1A11_13990, E1A20_08715, E5196_10530, E6W45_11290, EBB93_08225, EBC01_14215, EBD14_10775, EBD99_16245, EBK21_12495, EBL31_10765, EBO41_07985, EBP31_13400, EC404_10185, EC52_10650, ECA50_06355, ECC89_10360, ED424_12910, ED467_14455, EDL18_12335, EEK73_07615, EEQ30_03190, EER35_13455, EGL32_13215, EGN81_14320, EGU67_16280, EGU98_01815, EHB09_17685, EHB24_06860, EHB55_04625, EHC98_13055, EIE48_07335, EIW53_10865, EJI18_11855, EJO08_15295, EJO98_03745, EKA25_05275, EL822_10545, ELO47_06300, ELR28_12910, ELS01_13730, EM832_14630, EM840_15510, EMN66_11055, EMY79_07110, EO190_01820, EP115_08910, EP446_17725, EPB30_04875, EPH81_13125, EQG93_17545, EQG94_14990, ERM04_12360, EU349_14435, EU873_14810, EUB95_06180, EUQ56_12620, EUQ65_14085, EUQ74_12140, EUS13_11340, EVY71_02270, EW905_11445, EWB18_13125, EWE52_09515, EWJ47_12360, EWZ09_10265, EXA47_14060, EXB31_10305, EXB41_12245, EYA29_09815, EYJ91_01000, F0D96_04670, F2O93_06050, F2P00_05765, F3Q46_12455, F3Q59_03865, F3Q88_17410, F3Q97_01745, F3R12_04520, F3R61_14650, F3R63_08825, F9G02_11745, F9O44_07395, FE758_05780, FEM52_10645, FGZ46_12865, FJM64_15875, FL833_14220, FQC24_10790, FQD13_05150, GCH31_04025, GCQ81_09835, GCZ80_06975, GEZ01_15490, GW08_02135, JO10_05360, KP44_07640, LZ63_05160, NG02_08975, NG06_24275, NG18_05800, NU83_05230, QA89_10955, QB40_04985, R035_04270, RJ78_02450, SAMEA4398682_01021, SE14_03092, Y934_04800, YG50_06085, YT65_12255, Z700_09660, ZT09_11460, ZT28_14425, ZT74_12940, ZT89_06430, ZU86_13060, ZU92_03155, ZV33_12500, ZV34_13970, ZV38_09350, ZV58_11905, ZV70_14285, ZV78_10390, ZW74_09615, ZX03_03830, ZY23_09620, ZY27_14455, ZY40_09835, ZY51_10295, ZZ18_13325, ZZ43_10110, ZZ77_05435, ZZ79_07510

UniProt
Find proteins for Q7CPW9 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q7CPW9 
Go to UniProtKB:  Q7CPW9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7CPW9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ABC transporter
C, D
36Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: DD95_05360, SE14_03091, STMLT2P22_CBEKMEGD_03680
UniProt
Find proteins for Q8ZMH5 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q8ZMH5 
Go to UniProtKB:  Q8ZMH5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZMH5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.671α = 90
b = 76.633β = 90
c = 119.655γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data scaling
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/M009629/1
European Research Council (ERC)United Kingdom757369
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/D524840/1
Wellcome TrustUnited Kingdom202926/Z/16/Z

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-18
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2021-12-01
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description