2024-11-06 REL PDBe PDBe PDBe 2018-06-28 2018-08-22 2018-10-24 2024-11-06 Wellcome Trust 098302 United Kingdom Sao Paulo Research Foundation 2011/07777-5 Brazil Sao Paulo Research Foundation 2017/17303-7 Brazil Costa TRD Sgro GG Farah CS Waksman G core complex, bacterial killing, protein transport, bacterial Type IV Secretion System, MEMBRANE PROTEIN Sgro GG Costa TRD Cenens W Souza DP Cassago A Coutinho de Oliveira L Salinas RK Portugal RV Farah CS Waksman G Nat Microbiol UK 3 1429 1440 2018 30349081 doi:10.1038/s41564-018-0262-z 2058-5276 6gyb FULLOVERLAP Core complex of a bacterial killing type IV secretion system from Xanthomonas Core complex of a bacterial killing type IV secretion system from Xanthomonas 0 1 2 3

Fourteen copies of each of the following three subunits: VirB7, VirB9 and VirB10

Xanthomonas axonopodis pv. citri str. 306 VirB7 Xanthomonas axonopodis pv. citri (strain 306) 0.014762794999999999 14 Escherichia coli BL21(DE3) LEVO MNPMYVSKLSLVLVAAALVGACATKPAPDFGGRWKHVNHFDEAPTEIPLYTSYTYQATPMDGTLKTMLERWAADSNMQLS YNLPSDYTLIGPVSAISTTSVQQAATELSAVYAAQGVSVSVSANKLLVQPVPVSSGAKL Q8PJB3 VirB9 protein Xanthomonas axonopodis pv. citri (strain 306) 306 0.029359384999999998 14 Escherichia coli BL21(DE3) LEVO MKLFNRYRVALLSALPLALCALSAAAQVVQEYEYAPDRIYQVRTGLGITTQVELSPNEKILDYSTGFTGGWELTRRENVF YLKPKNVDVDTNMMIRTATHSYILELKVVATDWQRLEQAKQAGVQYKVVFTYPKDTSFNNVADADTSKNGPLLNAKILKD RRYYYDYDYATRTKKSWLIPSRVYDDGKFTYINMDLTRFPTGNFPAVFAREKEHAEDFLVNTTVEGNTLIVHGTYPFLVV RHGDNVVGLRRNKQK Q8PJB5 VirB10 protein Xanthomonas axonopodis pv. citri (strain 306) 306 0.043392468999999996 14 Escherichia coli BL21(DE3) LEVO MNSNIPNSPDERIQNHGGDEQHNGDHNERNNPYFARQQASAEPDLDANEPILRSSDIKRLNRKALVFLAAIAALLILAIF WLATQSGEDSAPPKPRTETVVAPALPQSMTAPVEEAPVPLAQQPSLPPLPPMPTDNSEEVSSAPERQRGPTLLERRILAE SAANGGGVPGQLGAQPAPTQEDGPVTLAKPISNPDGLLVRGTYIRCILETRIISDFGGYTSCIVTEPVYSINGHNLLLPK GSKMLGQYSAGEPTSHRLQVVWDRVTTPTGLDVTLMGPGIDTLGSSGHPGNYNAHWGNKIASALFISLLSDAFKYAAAEY GPETTTIGVGSGIVTQQPFESNTARSMQQLAEQAVEKSGRRPATLTINQGTVLNVYVAKDVDFSAVLPKAAALEGLSAWS HPQFEK Q8PJB6 singleParticle particle 0.3 8.0 20.0 NH2C(CH2OH)3HCl Tris-HCl 200.0 NaCl Sodium Chloride 10.0 CH3(CH2)11N(O)(CH3)2 LDAO ETHANE 100 295.2 FEI VITROBOT MARK IV

Blot for 4.5 seconds after 30 seconds of incubation..

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 QUANTUM (4k x 4k) SUPER-RESOLUTION 1 1469 12.0 60.0 1 185079 1 C14 BACK PROJECTION 3.28 FSC 0.143 CUT-OFF RELION 2.0 142306 MAXIMUM LIKELIHOOD cryoSPARC 1.0 MAXIMUM LIKELIHOOD RELION 2.0 1 142306.0 RELION 2.0

The electron density was clearly interpretable, which allowed us to build a de novo structural model. This process began by fitting the crystallographic model of the X. citri VirB7 C-terminal N0 domain (PDB:3OV5) and the NMR model of the X. citri VirB9CTD-VirB7NTD complex (PDB:2N01) in order to identify the map with the correct handedness. Models were positioned using Fit in map tool in Chimera, and saved relative to the map. Using these as starting points, we were able to manually build the rest of the model for VirB7 and VirB9CTD, and the de novo models for VirB10CTD, VirB10NTD_150-161 and VirB9NTD using Coot. In this manner, we obtained a combined model for a single VirB7-VirB9-VirB10 heterotrimer unit, which was submitted to iterative rounds of real space refinement and building using PHENIX and Coot software, respectively. Thirteen more copies of the refined heterotrimer were then fit into the density map using Chimera and new rounds of real space refinement (now using NCS for the 42 chains contained in the structure) and building using PHENIX and Coot, respectively, were executed until we obtained good parameters for Ramachandran plot and MolProbity. Chimera and PyMol were used for map and model visualization and figure production.

Cross-correlation coefficient REAL 138.0