2025-07-09 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name PDBe PDBe 2024-04-17 2025-06-04 2025-06-04 2025-07-09 Wellcome Trust United Kingdom CryoEM map of the F plasmid relaxosome in its pre-initiation state. ds-27_+143-R Locally-refined Map 3.76 A Williams SM Waksman G Relaxosome, Bacterial Conjugation, DNA processing, Relaxase, DNA binding proteins, DNA BINDING PROTEIN Williams SM Raffl S Kienesberger S Ilangovan A Zechner EL Waksman G Cryo-EM Structure of the relaxosome, a complex essential for bacterial mating and the spread of antibiotic resistance genes. Nat Commun UK 16 4906 4906 2025 40425557 doi:10.1038/s41467-025-60116-6 2041-1723 EMD-50098 other EM volume
Initial 3D Map of relaxosome complex with oriT DNA ds-27_+143
 9f0x FULLOVERLAP Complex of the relaxosome containing oriT DNA, accessory proteins TraY and TraM, host protein IHF and relaxase TraI in its pre-initiation state Complex of the relaxosome containing oriT DNA, accessory proteins TraY and TraM, host protein IHF and relaxase TraI in its pre-initiation state 0 1 2 3 4 5 6 dsOriT DNA, nic site not present in the interpretable DNA density 1 1 2
Prepared by restriction digestion of oriT fragment cloned in pUC57-Mini vector
Escherichia coli K-12 IHF heterodimer 1 3 4 Escherichia coli K-12 Train of three TraY proteins 1 5 Escherichia coli K-12 Relaxase/helicase protein TraI 1 6 Escherichia coli K-12 TraM tetramer 1
Used for complex formation, but density was excluded from the local refinement. TraM is therefore not present in the model.
Escherichia coli K-12 T-strand DNA (83-MER) Escherichia coli K-12 0.052621707 1 (DC)(DC)(DT)(DA)(DC)(DA)(DA)(DA)(DA)(DC)(DG)(DG)(DT)(DG)(DT)(DC)(DG)(DG)(DC)(DG) (DC)(DG)(DT)(DT)(DG)(DT)(DT)(DG)(DT)(DA)(DG)(DC)(DC)(DG)(DC)(DG)(DC)(DC)(DG)(DA) (DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DT)(DT)(DT)(DT)(DA)(DA)(DA)(DT)(DA)(DT)(DC)(DA) (DT)(DA)(DA)(DA)(DG)(DA)(DG)(DA)(DG)(DT)(DA)(DA)(DG)(DA)(DG)(DA)(DA)(DA)(DC)(DT) (DA)(DA)(DT)(DT)(DT)(DT)(DT)(DC)(DA)(DT)(DA)(DA)(DC)(DA)(DC)(DT)(DC)(DT)(DA)(DT) (DT)(DT)(DA)(DT)(DA)(DA)(DA)(DG)(DA)(DA)(DA)(DA)(DA)(DT)(DC)(DA)(DG)(DC)(DA)(DA) (DA)(DA)(DA)(DC)(DT)(DT)(DG)(DT)(DT)(DT)(DT)(DT)(DG)(DC)(DG)(DT)(DG)(DG)(DG)(DG) (DT)(DG)(DT)(DG)(DG)(DT)(DG)(DC)(DT)(DT)(DT)(DT)(DG)(DG)(DT)(DG)(DG)(DT)(DG)(DA) (DG)(DA)(DA)(DC)(DC)(DA)(DC)(DC)(DA)(DA) DNA R-strand DNA (83-MER) Escherichia coli K-12 0.052314465 1 (DT)(DT)(DG)(DG)(DT)(DG)(DG)(DT)(DT)(DC)(DT)(DC)(DA)(DC)(DC)(DA)(DC)(DC)(DA)(DA) (DA)(DA)(DG)(DC)(DA)(DC)(DC)(DA)(DC)(DA)(DC)(DC)(DC)(DC)(DA)(DC)(DG)(DC)(DA)(DA) (DA)(DA)(DA)(DC)(DA)(DA)(DG)(DT)(DT)(DT)(DT)(DT)(DG)(DC)(DT)(DG)(DA)(DT)(DT)(DT) (DT)(DT)(DC)(DT)(DT)(DT)(DA)(DT)(DA)(DA)(DA)(DT)(DA)(DG)(DA)(DG)(DT)(DG)(DT)(DT) (DA)(DT)(DG)(DA)(DA)(DA)(DA)(DA)(DT)(DT)(DA)(DG)(DT)(DT)(DT)(DC)(DT)(DC)(DT)(DT) (DA)(DC)(DT)(DC)(DT)(DC)(DT)(DT)(DT)(DA)(DT)(DG)(DA)(DT)(DA)(DT)(DT)(DT)(DA)(DA) (DA)(DA)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG)(DT)(DC)(DG)(DG)(DC)(DG)(DC)(DG)(DG)(DC) (DT)(DA)(DC)(DA)(DA)(DC)(DA)(DA)(DC)(DG)(DC)(DG)(DC)(DC)(DG)(DA)(DC)(DA)(DC)(DC) (DG)(DT)(DT)(DT)(DT)(DG)(DT)(DA)(DG)(DG) DNA Integration host factor subunit alpha Escherichia coli K-12 0.011373951999999998 1 Escherichia coli BL21(DE3) LEVO MALTKAEMSEYLFDKLGLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVT FRPGQKLKSRVENASPKDE P0A6X7 Integration host factor subunit beta Escherichia coli K-12 0.010671178 1 Escherichia coli BL21(DE3) LEVO MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIEIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHF KPGKELRDRANIYG P0A6Y1 Relaxosome protein TraY Escherichia coli K-12 0.015210423 3 Escherichia coli BL21(DE3) LEVO MKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVKYLTMRLDDETNQ LLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL P06627 Multifunctional conjugation protein TraI Escherichia coli K-12 0.193050859
TraI in its trans-esterase or relaxase conformation
1 Escherichia coli BL21(DE3) LEVO MEFELGTMMSIAQVRSAGSAGNFYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQDGS NRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLVMALFNHDTSRDQE PQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEALGYETEVVGKHGMWEMPGVPVEA FSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMAEWMQTLKETGFDIRAYRDAADQRADLRTLTPGPASQDG PDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPENGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVR ALSRDIMKQNRVTVHPEKSVPRTAGYSDAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQ MNMKQDERLSGELITGRRQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDA GVNTYRWQGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGLPEVTMTA LSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDSSWSLFRPEKMPVA DGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVSDSPFTALKLENGWVETPGHSVSDSATVFASVT QMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQIKTRAGETSLETAISHQKSALHTPAQQAIHLALP VVESKKLAFSMVDLLTEAKSFAAEGTGFTELGGEINAQIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEA VMPLMERVPGELMEKLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEM RSAGVDAQTLASFLHDTQLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFR LQQTRSAADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEAQQK AMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDVREKAGELGKEQVMVPVLNTANIRDGE LRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVTLYTPDTIRVGTGDRMRFTKSDRE RGYVANSVWTVTAVSGDSVTLSDGQQTREIRPGQEQAEQHIDLAYAITAHGAQGASETFAIALEGTEGNRKLMAGFESAY VALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVFEPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPA RFIAPGRKYPQPYVALPAFDRNGKSAGIWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVR IARDNPDSGVVVRIAGEGRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMA ENKPDLPDGKTEQAVREIAGQERDRAAITEREAALPEGVLREPQRVREAVREIARENLLQERLQQMERDMVRDLQKEKTL GGD P14565 5.6.2.1 singleParticle particle 7.5
20 mM Hepes pH 7.5, 100 mM NaCl
 Quantifoil R2/2 GOLD 200 GLOW DISCHARGE ETHANE 95 277 FEI VITROBOT MARK IV
The complex after assembly and gel filtration was subjected to glutaraldehyde cross-linking
 FEI TITAN KRIOS OTHER OTHER FIELD EMISSION GUN 300 1.5 3.3000000000000003 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 (6k x 4k) 50.0
Movies were collected in counting mode fractionated over 50 frames
 1 20752847 PHASE FLIPPING AND AMPLITUDE CORRECTION
CryoSPARC ab-initio
 3.78 FSC 0.143 CUT-OFF 337238 MAXIMUM LIKELIHOOD
CryoSPARC ab-initio
 MAXIMUM LIKELIHOOD
Local refinement
 emd_50117.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 560 560 560 0 0 0 560 560 560 462.0 462.0 462.0 90.0 90.0 90.0 X Y Z -1.277998 2.063611 0.001291354 0.030630102 0.825 0.825 0.825 0.4 AUTHOR F plasmid relaxosome pre-initiation state: Local refinement map AB INITIO MODEL emd_50117_msk_1.map emd_50117_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 560 560 560 0 0 0 560 560 560 462.0 462.0 462.0 90.0 90.0 90.0 X Y Z -0.0017467048 2.4612737 0.00029698422 0.010933819 0.825 0.825 0.825 AUTHOR DeepEMhancer Post-processed Map emd_50117_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 560 560 560 0 0 0 560 560 560 462.0 462.0 462.0 90.0 90.0 90.0 X Y Z -0.6759484 1.3168831 0.0012913593 0.024889672 0.825 0.825 0.825 AUTHOR F plasmid relaxosome pre-initiation state: Local refinement map Unsharpened emd_50117_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 560 560 560 0 0 0 560 560 560 462.0 462.0 462.0 90.0 90.0 90.0 X Y Z -0.8595272 1.4854255 0.0012917541 0.03183758 0.825 0.825 0.825 AUTHOR Local refinement map - Half-B emd_50117_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 560 560 560 0 0 0 560 560 560 462.0 462.0 462.0 90.0 90.0 90.0 X Y Z -0.7453236 1.4652362 0.001287039 0.03174424 0.825 0.825 0.825 AUTHOR Local refinement map - Half-A