2025-09-10 REL RCSB INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_PubMed _citation.title _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update RCSB RCSB 2025-06-06 2025-08-13 2025-08-13 2025-09-10 Cancer Prevention and Research Institute of Texas (CPRIT) RP220582 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01AI167967 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01AI150776 United States Welch Foundation I-1948-20240404 United States Howard Hughes Medical Institute (HHMI) United States Cryo-EM structure of S. Mansoni p97 bound to compound 739 Stephens DR Han Y Chen Z Liang J Ready J Collins JJ Fung HYJ AAA-ATPase, Endoplasmic Reticulum, Hexamer, Inhibitor, CHAPERONE Stephens DR Fung HYJ Han Y Liang J Chen Z Ready J Collins 3rd JJ A genome-scale drug discovery pipeline uncovers therapeutic targets and a unique p97 allosteric binding site in Schistosoma mansoni. Proc.Natl.Acad.Sci.USA US 122 e2505710122 e2505710122 2025 40880532 doi:10.1073/pnas.2505710122 1091-6490 0040 PNASA6 9p02 FULLOVERLAP PDB 9OX9 unspecified
In the same study
 EMDB EMD-71064 associated EM volume
Cryo-EM structure of S. Mansoni p97 bound to compound 739
 Hexamer of p97 conjugated to inhibitor 739 Hexamer of p97 conjugated to inhibitor 739 0 1 Schistosoma mansoni vesicle-fusing ATPase Schistosoma mansoni 0.092755594
First 37 residues are expression tags.
6 Escherichia coli BL21(DE3) LEVO MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSEFMCALNANPSNDPSSGEKVKFHRLIVDEPVKDDNSVVYLSQAKMD SMNLFRGDTVLVKGKKRKETVCVAIVDESCPDDKIRLNRCIRSNLRVKPGDIISIKSLPDILYGKRIHVLPIDDTIVGLT GNLYEAFLKPYFLAAYRPVHKGDIFIVRGGMRAVEFKVIETDPSPYCIVSPDTTIHTEGDPVKREDEEEKLNEIGYDDIG GCRKQLAQIKEMVELPLRHPQLFKAIGVKPPRGILLYGPPGTGKTLVARAVANESGSFFFLINGPEIMSKLAGESESNLR KAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRSHVIVMAATNRPNSVDPALRRFGRFDREI EIGIPDSIGRLEILRIHTRNIRLAEDVELEKIANEAHGHVGADLASLCSEAALQQIRNKMNLIDLEDDTIDAEVLNSLAV TMDDFRWALGKSNPSALRETTVEVPNVTWDDIGGLENVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLL AKAIANECQANFISIKGPELLTMWFGESEANVRDIFDKARQAAPCVLFFDELDSIAKARGGSVGDAGGAADRVINQLLTE MDGMSAKKNVFIIGATNRPDIIDGAILRPGRLDQLIYIPLPDEASRVNILKANLRKSPIARDVDINFLAKATQGFSGADL TEICQRACKQAIRESIEAEIRAESEKKNKPNAMEDDFDPVPEITRRHFEEAMRFARRSVTENDVRKYEMFAQTLQQSRGI GNNFRFPGSDGSGIPTSTGGQGGGGSVYGSQNDAEDLYN G4M0P7 3.6.4.6 (2E)-3-(pyridin-4-yl)-N-[2-(pyridin-2-yl)-1,3-benzoxazol-5-yl]prop-2-enamide 0.00034235099999999996 6 A1CGC singleParticle particle 1 7.4
20mM Tris (pH 7.4), 180mM NaCl, 5mM MgCl2, and 1mM tris(2-carboxyethyl)phosphine (TCEP)
 Quantifoil R1.2/1.3 COPPER 300 GLOW DISCHARGE ETHANE FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.9 2.2 TFS Selectris 10 TFS FALCON 4i (4k x 4k) 60.0 1 2812039
Template pick with templates generated used the CB-5083-bound map
 cryoSPARC PHASE FLIPPING AND AMPLITUDE CORRECTION EMD-70961
CB-5083-bound map
 C6 3.06 FSC 0.143 CUT-OFF cryoSPARC
Non-uniform refinement with C6 symmetry applied, with global and CTF refinements. Unsharpened map was used for modeling
101602 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC 3 cryoSPARC
With C6 symmetry
 emd_71064.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 448 448 448 0 0 0 448 448 448 330.624 330.624 330.624 90.0 90.0 90.0 X Y Z -0.16404785 0.34170598 0.00020318084 0.008700134 0.738 0.738 0.738 0.06 AUTHOR structure of S. Mansoni p97 bound to compound 739 9P00 PDB experimental model
Apo structure was docked as initial model, then went through multiple rounds of manual fitting in coot and refinement in Phenix.
 emd_71064_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 448 448 448 0 0 0 448 448 448 330.624 330.624 330.624 90.0 90.0 90.0 X Y Z -0.31541887 0.4871697 0.00039267348 0.03122303 0.738 0.738 0.738 AUTHOR Half Map A emd_71064_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 448 448 448 0 0 0 448 448 448 330.624 330.624 330.624 90.0 90.0 90.0 X Y Z -0.37326464 0.4380406 0.00039711499 0.031199282 0.738 0.738 0.738 AUTHOR Half Map B