7ZRA

Crystal structure of E.coli LexA in complex with nanobody NbSOS1(Nb14497)

• PDB DOI: https://doi.org/10.2210/pdb7ZRA/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli, Lama glama
• Expression System: Escherichia coli BL21, Escherichia coli W
• Mutation(s): No 


• Deposited: 2022-05-04 Released: 2022-10-26 
• Deposition Author(s): Maso, L., Vascon, F., Chinellato, M., Pardon, E., Steyaert, J., Angelini, A., Tondi, D., Cendron, L.
• Funding Organization(s): Italian Ministry of Education

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.259 
• R-Value Work: 0.223 

Literature

Nanobodies targeting LexA autocleavage disclose a novel suppression strategy of SOS-response pathway.

Maso, L., Vascon, F., Chinellato, M., Goormaghtigh, F., Bellio, P., Campagnaro, E., Van Melderen, L., Ruzzene, M., Pardon, E., Angelini, A., Celenza, G., Steyaert, J., Tondi, D., Cendron, L.

(2022) Structure 30: 1479

• PubMed: 36240773 
• DOI: https://doi.org/10.1016/j.str.2022.09.004
• Primary Citation of Related Structures:  
  7B5G, 7OCJ, 7ZRA


• PubMed Abstract: 
  

  Antimicrobial resistance threatens the eradication of infectious diseases and impairs the efficacy of available therapeutics. The bacterial SOS pathway is a conserved response triggered by genotoxic stresses and represents one of the principal mechanisms that lead to resistance. The RecA recombinase acts as a DNA-damage sensor inducing the autoproteolysis of the transcriptional repressor LexA, thereby derepressing SOS genes that mediate DNA repair, survival to chemotherapy, and hypermutation. The inhibition of such pathway represents a promising strategy for delaying the evolution of antimicrobial resistance. We report the identification, via llama immunization and phage display, of nanobodies that bind LexA with sub-micromolar affinity and block autoproteolysis, repressing SOS response in Escherichia coli. Biophysical characterization of nanobody-LexA complexes revealed that they act by trapping LexA in an inactive conformation and interfering with RecA engagement. Our studies pave the way to the development of new-generation antibiotic adjuvants for the treatment of bacterial infections.

---

Organizational Affiliation: 

Dipartimento di Biologia, Università degli Studi di Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 148.13 kDa 
• Atom Count: 7,783 
• Modelled Residue Count: 1,001 
• Deposited Residue Count: 1,336 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LexA repressor	A, B [auth C], E [auth B], F [auth D]	202	Escherichia coli	Mutation(s): 0  Gene Names:  lexA_1, lexA, lexA_2, lexA_3, lexA_4, lexA_5, lexA_6, A6581_03840, A6592_09000, A6V01_14725, A8C65_05740, A9819_23115, A9P13_24790, A9R57_24265, A9X72_23540, AAW05_04940, AC067_05020, AC789_1c44530, ACN002_4144, ACN68_15885, ACN81_05765, ACU57_23725, ACU90_04800, AJ318_13980, AM270_18420, AM446_25905, AM464_13585, AM465_02855, AMK83_25365, AML07_00445, AML35_16500, APT94_01725, APU18_20100, APZ14_12275, ARC77_17360, AU473_00505, AUQ13_09675, AUS26_09870, AW059_18350, AW106_02825, AWB10_24615, AWE53_003010, AWF59_006810, AWG78_010890, AWG90_025185, AWP75_14755, AZZ83_003567, B6V57_23175, B7C53_16050, B9M99_07260, B9N33_14930, B9T59_11225, BANRA_02722, BANRA_02895, BANRA_05124, BB545_04745, BE963_11630, BEN53_25180, BER14_12995, BFD68_07790, BHF03_13425, BHF46_15090, BHJ80_01810, BHS81_24295, BHS87_22640, BIQ87_23185, BIU72_20655, BIZ41_02125, BJJ90_24770, BK248_24315, BK292_01025, BK296_23860, BK334_08815, BK373_03960, BK375_08450, BK383_21615, BMA87_07675, BMT49_20690, BMT91_12915, BN17_40181, BOH76_06090, BON63_06530, BON65_23060, BON66_03315, BON69_22095, BON71_16410, BON75_07080, BON76_04855, BON83_16235, BON86_25705, BON87_02545, BON91_12300, BON92_17725, BON94_08075, BON95_04860, BON96_03145, BON98_14025, BTQ04_27960, BTQ06_28255, BUE81_22465, BvCms12BK_04297, BvCms2454_00415, BvCms28BK_01342, BvCms35BK_01831, BvCmsC61A_01832, BvCmsHHP001_00842, BvCmsHHP019_03449, BvCmsHHP056_02653, BvCmsKKP036_01653, BvCmsKKP061_03212, BvCmsKSNP073_04428, BvCmsKSNP081_02209, BvCmsKSNP120_00016, BvCmsKSP011_01869, BvCmsKSP024_01390, BvCmsKSP026_03995, BvCmsKSP045_02606, BvCmsKSP058_01651, BvCmsKSP067_03973, BvCmsKSP076_00063, BvCmsNSNP036_01892, BvCmsNSP006_05193, BvCmsNSP007_02439, BvCmsNSP047_02150, BvCmsNSP072_02985, BvCmsOUP014_01488, BvCmsSINP011_01581, BvCmsSINP022_02516, BvCmsSIP019_02982, BvCmsSIP044_03653, BVL39_05000, BW690_17275, BWI89_17045, BWP17_09115, BXT93_20190, BZL31_27495, BZL69_04975, C2M16_18650, C2U48_12390, C4K41_22540, C4M78_06355, C5715_10070, C5F72_25480, C5F73_24600, C5N07_20195, C5P01_10950, C5P44_17630, C6669_07275, C6B13_20680, C7235_23375, C7B02_13860, C7B06_21440, C7B07_20950, C7B08_17115, C7B18_19350, C9098_11905, C9114_00185, C9141_04535, C9160_08095, C9162_23740, C9201_06385, C9306_11555, C9E25_05905, C9E67_28315, C9Z03_09215, C9Z23_10210, C9Z28_18985, C9Z29_15625, C9Z37_11110, C9Z39_12685, C9Z43_13055, C9Z68_12230, C9Z69_10275, C9Z70_15630, C9Z78_21525, C9Z89_05965, CA593_05680, CCZ14_07840, CDC27_21910, CDL37_20795, CF006_04145, CG692_11650, CI641_013760, CI693_02120, CI694_23155, CIG45_19390, CJU63_23870, CJU64_24205, CMR93_13445, CO706_19840, COD30_15395, COD46_18700, CQP61_25715, CR538_23835, CR539_02040, CRD98_27320, CRE06_21195, CRJUMX01_510039, CRM83_18295, CRT43_24270, CRX46_18555, CSB64_02010, CT146_24150, CUB99_11400, CV83915_01994, CVH05_06385, CWM24_08770, CWS33_15975, D0X26_12200, D1912_18705, D2184_21525, D2185_07080, D2188_17815, D3821_04640, D3822_08745, D3M98_15580, D3O91_19225, D3P01_12220, D3P02_10990, D4011_20000, D4023_17595, D4074_20080, D4628_12380, D4636_09720, D4638_24525, D4660_19160, D4718_13325, D4L91_18735, D4M06_19695, D4M76_10435, D4U49_11220, D4U85_19640, D4V08_08845, D5H35_01910, D5I97_18270, D6004_01850, D6C36_19740, D6D43_19725, D6T60_08900, D6T98_07050, D6W00_08775, D6X36_02250, D6X63_25780, D6X76_22790, D7K33_19360, D7K63_02835, D7K66_21305, D7W70_12300, D7Y10_01185, D7Z75_09495, D8Y65_18220, D9610_00735, D9C99_09310, D9D20_17210, D9D33_01860, D9D43_18385, D9D44_06445, D9D94_04730, D9E13_11180, D9E19_14095, D9E34_02075, D9E35_10415, D9E49_22250, D9E73_19440, D9F17_19275, D9F32_11525, D9F87_12490, D9G11_22460, D9G29_18660, D9G42_14820, D9G48_15290, D9G69_15475, D9G95_21630, D9H10_15220, D9H36_09830, D9H53_20975, D9H68_20260, D9H70_15350, D9H94_14230, D9I18_21060, D9I20_19240, D9I87_21035, D9I88_03895, D9I97_23010, D9J03_04410, D9J11_07590, D9J44_17675, D9J46_13285, D9J52_18345, D9J58_14965, D9J60_05135, D9J63_12310, D9J78_21390, D9K02_09285, D9K48_05710, D9K54_02940, D9L89_19960, D9L99_05045, D9S45_16730, D9X77_17715, D9X97_19985, D9Z28_19505, DAH18_17020, DAH26_23105, DAH30_16750, DAH32_05100, DAH34_09745, DAH37_23000, DAH43_08050, DB359_22770, DBQ99_24230, DD762_09570, DEN86_01240, DEN89_16940, DEN97_12815, DEO04_14355, DEO19_12485, DEO20_13045, DIV22_28315, DJ487_17695, DJ503_03205, DK132_10450, DL251_19160, DL257_06320, DL292_14670, DL326_18360, DL455_17780, DL479_04890, DL530_02190, DL545_23320, DL705_06290, DL800_28030, DL979_22465, DLT82_16100, DLU50_04305, DLU67_12520, DLU82_06835, DLW60_00780, DLW88_15040, DLX38_07225, DLX40_14200, DLY41_09575, DLY44_12300, DM102_07955, DM129_07275, DM155_00780, DM267_22275, DM272_08145, DM280_16450, DM296_05455, DM382_06365, DM820_11410, DM962_16745, DM973_17240, DMI04_18725, DMI53_18525, DMO02_19335, DMY83_08280, DMZ50_11405, DN627_13770, DN660_12190, DN700_09495, DN703_20325, DN808_20920, DNB37_17705, DNC98_13900, DND16_08380, DND79_11485, DNI21_02325, DNJ62_19610, DNK12_18155, DNQ45_03405, DNR35_06920, DNR41_16590, DNW42_02895, DNX19_05225, DOE35_19020, DOM23_10665, DOS18_18880, DOT81_19955, DOU81_18220, DOY22_18350, DOY56_18570, DOY61_11305, DOY67_06200, DP258_12750, DP265_01880, DP277_17730, DQE91_14650, DQF36_19215, DQF57_12540, DQF71_02370, DQF72_01950, DQG35_19915, DQO13_07445, DQP61_07285, DRP48_19990, DRW19_10040, DS143_02030, DS721_17960, DS732_01915, DS966_07340, DT034_16995, DTL43_19530, DTL90_18345, DTM10_17250, DTM45_22000, DTZ20_07940, DU309_08590, DU321_20700, DU333_20915, DVB38_00780, DW236_20350, DWB25_23105, DXT69_11240, DXT71_13455, DXT73_06680, DXX80_014420, E0I42_01715, E0K84_14705, E0L04_06555, E0L12_12475, E2112_13635, E2119_15925, E2127_04695, E2128_24955, E2129_11665, E2134_19225, E2135_15890, E2148_17730, E2855_05069, E2863_04868, E4A44_08405, E4K51_08400, E4K55_09280, E4K59_02705, E4K60_21225, E4K61_06350, E5P22_21020, E5P24_22750, E5P28_22440, E5P37_19690, E5S42_14590, E5S56_16625, E5S58_10005, E5S61_13810, E5S62_09140, EA159_09860, EA164_11895, EA167_12330, EA174_06160, EA184_14750, EA189_16420, EA191_11120, EA198_19920, EA200_15705, EA203_12170, EA213_12715, EA214_12670, EA218_06700, EA222_18665, EA223_05425, EA225_15150, EA231_21330, EA232_11815, EA233_13540, EA235_13150, EA239_14350, EA242_15215, EA245_21190, EA247_19925, EA250_22905, EA410_10735, EA429_14660, EA433_09295, EA434_07730, EA435_14070, EA834_14185, EAI42_11775, EAI46_13910, EAI52_14305, EAM59_19660, EAN70_04295, EAN77_18045, EAX79_14320, EB476_06510, EB509_23270, EB510_19485, EB515_21475, EB525_RS22295, EBA46_21785, EBA84_21540, EBJ06_20090, EBM08_00725, EC1094V2_4222, EC3234A_77c00360, EC3426_00367, EC382_06195, EC95NR1_03586, ECONIH1_23895, ECs5026, ECTO124_04687, ECTO6_04452, ED178_02160, ED225_20150, ED307_20800, ED600_11955, ED607_20180, ED611_21565, ED648_10135, ED903_21355, ED944_20920, EEA45_23665, EEP23_23665, EF082_14250, EF173_02775, EG075_18135, EG599_11110, EG796_08865, EG808_11410, EGC26_22390, EGT48_16960, EGU87_16570, EH186_18415, EH412_04435, EHD45_05640, EHD63_19000, EHD79_12175, EHH55_01035, EHJ36_05660, EHJ66_21070, EHV81_14020, EHV90_14340, EHW09_21540, EHX09_18295, EI021_16120, EI028_05870, EI032_15785, EI041_04290, EIA08_19795, EIA21_16610, EIZ93_23270, EJ366_21585, EJC75_19935, EKI52_13610, EL75_4145, EL79_4350, EL80_4257, ELT17_04335, ELT20_15125, ELT22_19765, ELT23_17595, ELT33_14365, ELT48_13885, ELT49_00210, ELT58_16885, ELU82_17295, ELU85_16290, ELU96_14010, ELV00_20075, ELV05_04290, ELV08_22365, ELV13_10080, ELV15_24385, ELV22_20245, ELV24_10490, ELV28_08325, ELX56_12745, ELX70_12445, ELX76_18040, ELX79_01350, ELX83_19330, ELY05_20415, ELY23_17950, ELY24_02305, ELY41_24075, ELY48_01785, ELY50_17875, EO241_22225, EPS91_05510, EPS94_15340, EPU41_22875, EQ820_09870, EQ823_07865, EQ825_11565, EQ830_09950, EQO00_24610, ERL57_14825, ERS085365_02976, ERS085366_03456, ERS085374_01624, ERS085379_03983, ERS085383_01448, ERS085386_02660, ERS085404_01243, ERS085406_04198, ERS085411_04446, ERS085416_00631, ERS139211_04672, ERS150873_01187, ERS150876_04135, EST51_23545, EVY14_11520, EWK56_09425, EXM29_06605, ExPECSC019_02605, ExPECSC038_04549, ExPECSC065_01920, EXX06_18435, EXX13_12090, EXX23_19315, EXX24_09955, EXX53_09260, EXX55_18970, EXX71_07865, EXX78_13230, EXX87_20000, EYD11_21280, EYX82_05305, EYX99_01640, EYY27_19365, EYY34_21065, EYY78_21440, F1E13_08855, F1E19_14155, F7F00_04830, F7F11_03715, F7F18_10310, F7F23_02515, F7F26_18655, F7F29_21255, F7F56_09730, F7G01_19665, F7G03_07710, F9040_10620, F9050_18985, F9225_08300, F9B07_06640, F9X20_06245, F9Z53_12245, F9Z74_02500, FAF34_027445, FE846_20710, FKO60_19090, FNJ67_24760, FNJ69_19430, FNJ83_25115, FORC82_4459, FPI65_24840, FQ021_13785, FQ022_13220, FQ915_20070, FQR64_21510, FQU83_25315, FQZ46_11420, FRV13_15940, FTV92_16270, FTV93_16625, FV293_00180, FV295_14155, FV438_02950, FVB16_13290, FY127_04780, FZ043_01435, FZC17_04895, FZN06_07660, FZN26_04905, FZN30_09565, G3565_23685, G3V64_10445, G5603_20840, G5608_21780, G5616_05135, G5632_08040, G5668_16270, G5670_04760, G5675_07615, G5680_02920, G5686_19405, G5688_11635, G5696_16625, G5697_10455, GFU40_20155, GFU45_18365, GFU47_11010, GHR40_03285, GII67_18535, GII91_01590, GIJ01_07080, GIY13_22705, GIY19_15100, GJ11_25525, GJ638_08800, GJD97_25670, GKE15_08795, GKE16_10270, GKE22_09815, GKE24_10940, GKE26_10295, GKE29_07830, GKE31_09080, GKE39_08675, GKE46_08475, GKE53_08285, GKE58_08305, GKE60_08375, GKE64_08350, GKE69_08185, GKE77_10555, GKE79_08190, GKE87_03580, GKE92_11980, GKE93_09555, GKE98_17470, GKF00_11225, GKF03_07640, GKF21_19525, GKF28_19545, GKF34_19920, GKF39_10130, GKF47_19635, GKF52_19185, GKF74_07005, GKF86_09530, GKF89_08240, GKG08_19925, GKG09_19795, GKG11_19965, GKG12_13240, GKG22_19630, GKG29_19840, GN312_11355, GNZ00_12570, GNZ02_08260, GNZ03_05545, GNZ05_23055, GP650_09375, GP654_14900, GP661_10840, GP662_05880, GP664_12905, GP666_14410, GP671_00680, GP678_14315, GP689_08955, GP698_02940, GP700_05045, GP711_15355, GP712_07365, GP720_18065, GP727_20045, GP892_04865, GP912_08340, GP935_16255, GP945_10980, GP946_12270, GP950_01700, GQA23_07565, GQA63_11350, GQA64_11565, GQE22_22480, GQE30_09515, GQE33_21095, GQE34_18985, GQE36_21390, GQE42_17480, GQE47_16615, GQE51_19030, GQE58_14030, GQE64_15035, GQE68_09185, GQE87_13955, GQE88_20795, GQE93_06065, GQF59_13075, GQL64_02840, GQM04_21825, GQM06_05485, GQM09_07375, GQM10_00185, GQM13_10075, GQM17_17755, GQM18_21055, GQM28_14230, GQN16_10665, GQN24_10350, GQN33_15605, GQS26_13850, GQY14_18825, GRW05_25935, GRW12_07495, GRW27_03680, GRW30_10035, GRW42_18565, GRW57_21705, GRW80_00680, GRW81_20425, GUB08_14505, GUB85_10045, GUB91_12015, GUB95_13125, GUC01_08305, GUC12_14155, GUC40_13020, GUI16_13780, GUI33_07450, GZS12_22285, HmCms169_03196, HmCms184_01443, HmCmsJML074_03763, HmCmsJML079_02438, HmCmsJML146_04299, HmCmsJML204_02607, HmCmsJML236_03697, HMPREF3040_01362, HW43_01890, MJ49_09110, MS6198_46970, MS8345_04507, NCTC10082_02015, NCTC10089_04675, NCTC10090_02705, NCTC10764_02888, NCTC10766_00857, NCTC10767_00646, NCTC10963_04726, NCTC10974_05266, NCTC11022_04367, NCTC11126_02097, NCTC11181_01887, NCTC11341_02866, NCTC12650_04928, NCTC12950_05138, NCTC13127_06081, NCTC13216_02170, NCTC13846_04407, NCTC7922_05075, NCTC7927_05177, NCTC7928_03743, NCTC8009_08326, NCTC8179_05022, NCTC8621_04799, NCTC8959_04132, NCTC8960_02264, NCTC8985_03936, NCTC9001_04561, NCTC9007_01043, NCTC9036_04577, NCTC9044_02378, NCTC9045_05471, NCTC9050_02746, NCTC9055_01590, NCTC9058_02211, NCTC9062_03515, NCTC9073_00755, NCTC9077_05829, NCTC9081_06397, NCTC9111_04889, NCTC9117_05822, NCTC9119_04984, NCTC9434_04602, NCTC9701_04926, NCTC9702_05565, NCTC9703_04146, NCTC9706_01937, NCTC9777_01051, NCTC9962_03719, NCTC9969_04855, PGD_03216, PU06_05790, RG28_25645, RK56_017085, RX35_03825, SAMEA3472043_01946, SAMEA3472044_04487, SAMEA3472047_04009, SAMEA3472055_01604, SAMEA3472056_04390, SAMEA3472070_04043, SAMEA3472080_00231, SAMEA3472090_02852, SAMEA3472108_01696, SAMEA3472110_00875, SAMEA3472112_01208, SAMEA3472114_02039, SAMEA3472147_04803, SAMEA3484427_03830, SAMEA3484429_02475, SAMEA3484434_03756, SAMEA3485101_02956, SAMEA3752372_01305, SAMEA3752553_02498, SAMEA3752557_02189, SAMEA3752559_00285, SAMEA3752620_03709, SAMEA3753064_01449, SAMEA3753097_04412, SAMEA3753164_04167, SAMEA3753290_01938, SAMEA3753300_00786, SK85_04379, SY51_23235, U12A_04345, U14A_04341, UC41_10590, UN86_02805, UN91_08555, WQ89_14700, WR15_07670, YDC107_2768 EC: 3.4.21.88
UniProt
Find proteins for C3SHL2 (Escherichia coli) Explore C3SHL2  Go to UniProtKB:  C3SHL2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody NbSOS1 (Nb14497)	C [auth E], D [auth G], G [auth F], H	132	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	I [auth A], J [auth C], K [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.259 
• R-Value Work: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.918	α = 90
b = 110.75	β = 90
c = 231.796	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-10-26 
Deposition Author(s): Maso, L., Vascon, F., Chinellato, M., Pardon, E., Steyaert, J., Angelini, A., Tondi, D., Cendron, L.

---

Funding Organization	Location	Grant Number
Italian Ministry of Education	Italy	--

Revision History  

• Version 1.0: 2022-10-26
  Type: Initial release
  
• Version 1.1: 2022-11-16
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description