2026-08-12 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update DATABASE_REFERENCES citation _citation.journal_volume _citation.page_first _citation.page_last _citation.year DATA_COLLECTION chem_comp_atom chem_comp_bond pdbx_validate_chiral REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY em_admin pdbx_entry_details pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order _em_admin.last_update _pdbx_entry_details.has_protein_modification RCSB RCSB 2021-09-21 2021-12-22 2021-12-22 2026-08-12 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM47909 Childrens Discovery Institute of Washington University and St. Louis Childrens Hospital 2015-505 Childrens Discovery Institute of Washington University and St. Louis Childrens Hospital 2019-813 Foundation for Barnes-Jewish Hospital 3770 Chan Zuckerberg Initiative 2020-225726 Helicobacter Hepaticus CcsBA Open Conformation Mendez DL Lowder EP Cytochrome c biogenesis, Heme transporter, Heme lyase, MEMBRANE PROTEIN Mendez DL Lowder EP Tillman DE Sutherland MC Collier AL Rau MJ Fitzpatrick JAJ Kranz RG Cryo-EM of CcsBA reveals the basis for cytochrome c biogenesis and heme transport. Nat.Chem.Biol. US 18 101 108 2022 34931065 doi:10.1038/s41589-021-00935-y 1552-4469 7s9y FULLOVERLAP EMDB EMD-24941 associated EM volume
Helicobacter Hepaticus CcsBA Open Conformation
 Complex of CcsBA with two hemes present Complex of CcsBA with two hemes present 0 1
Purified from E. coli in DDM
Helicobacter hepaticus Cytochrome c biogenesis protein Helicobacter hepaticus 0.10729146899999999 1 Escherichia coli BL21(DE3) LEVO MMNIIKTLFCSMKMVLLLIGIYATACGIATFIEKYEGTLAARLWVYDAFWFEILHIWLVACLIGCFITSKAWQRKKYASL LLHASFIVIIIGAGITRYYGFEGLMNLREGQSVNFISTNTHYIFIQIKNPQGDVESVRIPTYIDEKVNHKINQHLTFFGK PLTLHTEEFTAKQVNMSELFILNASIDFLGKNEKTLIMRDGNNAPTKENITMLEIEGYKIFLAWGIDNIALPFSIKLKKF ELERYPGSNSPASYTSEVEVLDGQNPPLPFRIFMNNVLDYGGYRFFQSSYHPDEKGSILSVNNDPGKTPTYIGYAMLILG VIWLLFDKNGRFATLGRFLKTQKFFSLMLCSALCYALSSPQIAYASTQSQTDFQPLSENEIPPLQDIPSMIKALADTSSL TNDFDRILVQDFGGRIKPMHTLANEYIHKLTQQRTFKGLNPSQVFLGMLFYPQEWQSIQMIATKSPKLRQILGLDENQKH IAYIDVFTPQGQYILQNYVEAANLKSPSLRDTFEKDVISVDERINYAFLIYTGQVLRIFPDNKSPNNQWLYPLQAISSAV AQDDTKKAKELMQIYKKFAQGMQQGINTHNWQEAAQATRDIRTFQQNNGGSLLISPAKVDSEIWLNLYNPFYQLTYPYIF ISIVLFIIVLVGILKNTPTRPLIHKVFYILLFALFILHTCGLGLRWYVSEHAPWSNAYESMLYIAWAAILSGVVFFRRSN LALCASSFLAGMTLFVANLGDMDPQIGNLMPVLKSYWLNIHVSVITASYGFLGLCFMLGLITLIMFLLRNEKRSQVDCSI LSLSALNEMSMILGLFLLSVGNFLGGIWANESWGRYWGWDSKETWALISIGVYAIILHLRFVVPKNFPFIFASASVIGFF SVLMTYFGVNYYLTGMHSYAAGEAEPVPLWVELMVAGIILLIIIASRKRVLDMPHLHHHHHH Q7VHG9 HEME B/C 0.0006185030000000001 2 HEB PHOSPHATIDYLETHANOLAMINE 0.0007340389999999999 1 PTY singleParticle particle 2.8 8.0 20.0 C4H11NO3 Tris 100.0 NaCL Sodium chloride 0.03 C24H46O11 DDM Quantifoil R2/2 COPPER 300 PLASMA CLEANING OTHER 0.009300000000000001 ETHANE 100 277.15 FEI VITROBOT MARK IV
Blot for 2 seconds at a blot force of -1 and plunge frozen.
TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 150.0 0.01 1.0 1.0 2.5 2.5 105000.0 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 82.0 84.0 Microscope is outfitted with a Cs image corrector with two hexapole elements. GIF Bioquantum 20
Specific energy filter was a Gatan BioQuantum 968.
Preliminary grid screening was performed manually.
GATAN K2 QUANTUM (4k x 4k) COUNTING 3832 3704 1 8676 8.0 66.0 1 1778157
Initial particle picking was accomplished using blob picker in cryoSPARC. Picked particles were then subjected to 2D classification. Once converged, a sub-set of 2D classes were manually picked and reclassified using a smaller number of classes.
 cryoSPARC 3.2 PHASE FLIPPING AND AMPLITUDE CORRECTION Initial model was created using the ab initio approach in Cryosparc v3.2 1 C1 FOURIER SPACE 3.56 FSC 0.143 CUT-OFF cryoSPARC 3.2 140727 MAXIMUM LIKELIHOOD cryoSPARC 3.2 MAXIMUM LIKELIHOOD cryoSPARC 3.2 4 72000.0 cryoSPARC 3.2 emd_24941.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 281.6 281.6 281.6 90.0 90.0 90.0 X Y Z -1.0209982 1.5434968 0.00088474626 0.029381098 1.1 1.1 1.1 0.199 AUTHOR FLEXIBLE FIT
De novo modelling was undertaken using COOT. Both Phenix and ISOLDE were used for refinement
REAL