2025-12-24 REL RCSB 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 INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID _em_admin.last_update RCSB RCSB 2024-10-17 2025-10-01 2025-10-01 2025-12-24 Howard Hughes Medical Institute (HHMI) United States National Science Foundation (NSF, China) DGE-2140004 China Human Frontier Science Program (HFSP) LT000880/2019 France Defense Advanced Research Projects Agency (DARPA) HR001120S0052 United States De novo calcium channel hexamer, CalC6_3 with DHR extensions Weidle C Liu Y Borst AJ Calcium Channel, CalC6_3, De novo, Membrane protein, CalC6_3 with DHR extensions, hexamer, pore, De novo protein, Ca Liu Y Weidle C Mihaljevic L Watson JL Li Z Yu LT Majumder S Borst AJ Carr KD Kibler RD Gamal El-Din TM Catterall WA Baker D Bottom-up design of Ca 2+ channels from defined selectivity filter geometry. Nature UK 648 468 476 2025 41125887 doi:10.1038/s41586-025-09646-z 1476-4687 0006 NATUAS 9dzw FULLOVERLAP EMDB EMD-47340 associated EM volume
De novo calcium channel hexamer, CalC6_3 with DHR extensions
 CalC6_3 with DHR extension CalC6_3 with DHR extension 0 1
6 monomers assemble to form a calcium channel
synthetic construct 0.21665916 CalC6_3 with DHR extension synthetic construct 0.036163828 6 Escherichia coli BL21(DE3) LEVO MAELRERLLRAARWILLLGLLVLVGFVVLAYLERSPLIRAFVLSAGVVLVALFAAALAWLYLAAALLGRSPLLALVALAL GLITLAAASAAMAATFAHLLLEAPPEYREAMLYVFGIAVLIVGLLLLGLVWLLEEALEALLEEEKRREEEEKRRELVKRA EEALQKAQEAEKQGDVEKAVKAAQEAVRAAKESGDNDVLRRVAEQALQIAKEAEKQGNVEVAVKAARVAVEAAKQAGDND VLRKVAEQALRIAKEAEKQGNVEVAVKAARVAVEAAKQAGDQDVLRKVSEQAERISKEAKKQGNSEVSEEARKVADEAKK QTGGSGGSHHHHHH singleParticle particle 1 8.0 20.0 TRIS tris(hydroxymethyl)aminomethane 150.0 NaCl sodium chloride 0.006 GDN glyco-diosgenin Quantifoil R2/2 COPPER 300 GRAPHENE CONTINUOUS 2.0 CARBON HOLEY 40.0 GLOW DISCHARGE 39.0 ETHANE 100 295.15 FEI VITROBOT MARK IV
20 mM Tris/HCl pH 8, 150 mM NaCl, 0.006% GDN
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.8 1.8 NITROGEN GIF Bioquantum GATAN K3 (6k x 4k) 1 6893 4.0 47.32 1 886110 PHASE FLIPPING AND AMPLITUDE CORRECTION
Ab Initio
 1 C6 FOURIER SPACE 3.75 FSC 0.143 CUT-OFF
Non Uniform Refinement
67181 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD 8 10470.0
Heterogeneous Refinement
 emd_47340.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 285.6 285.6 285.6 90.0 90.0 90.0 X Y Z -0.0018169921 1.8135867 0.0007987067 0.020220935 0.84000003 0.84000003 0.84000003 0.0463 AUTHOR Non Uniform Refinement, DeepEMhancer sharpened map. C6 symmetry. Main map used for structure refinement. 3.75 Angstrom Other in silico model
Design protein, see methods
 AB INITIO MODEL
The design model was used as an initial reference for building the final cryo-EM structure. For the hexamer the design model of the CalC6_3 was used as an initial reference model fit with UCSF Chimera. Hexamer was refined using several rounds of relaxation and minimization, performed on the complete structures, which were manually inspected for errors each time using ISOLDE in UCSF ChimeraX, Coot, and PHENIX real-space refinement. The final model quality was analyzed using MolProbity.
REAL emd_47340_additional_7.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 285.6 285.6 285.6 90.0 90.0 90.0 X Y Z -0.050989702 0.10426826 -0.00030143122 0.003210551 0.84000003 0.84000003 0.84000003 AUTHOR Non Uniform Refinement, un-sharpened map. C1 symmetry. 3.98 Angstrom emd_47340_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 285.6 285.6 285.6 90.0 90.0 90.0 X Y Z -0.10095559 0.15065788 0.0000839002 0.009720378 0.84000003 0.84000003 0.84000003 AUTHOR Non Uniform Refinement, half map B. C1 symmetry. 3.98 Angstrom emd_47340_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 285.6 285.6 285.6 90.0 90.0 90.0 X Y Z -0.09730352 0.14059153 0.00008255444 0.009694537 0.84000003 0.84000003 0.84000003 AUTHOR Non Uniform Refinement, half map B. C1 symmetry. 3.98 Angstrom emd_47340_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 285.6 285.6 285.6 90.0 90.0 90.0 X Y Z -0.16078018 0.19411016 -0.00030143122 0.005013243 0.84000003 0.84000003 0.84000003 AUTHOR Non Uniform Refinement, auto sharpened map. C1 symmetry. 3.98 Angstrom emd_47340_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 285.6 285.6 285.6 90.0 90.0 90.0 X Y Z -0.0017131126 1.8515943 0.0008272064 0.021481277 0.84000003 0.84000003 0.84000003 AUTHOR Non Uniform Refinement, DeepEMhancer sharpened map. C1 symmetry. 3.98 Angstrom emd_47340_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 285.6 285.6 285.6 90.0 90.0 90.0 X Y Z -0.3009382 0.41418245 -0.00029980444 0.007130694 0.84000003 0.84000003 0.84000003 AUTHOR Non Uniform Refinement, auto sharpened map. C6 symmetry. 3.75 Angstrom emd_47340_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 285.6 285.6 285.6 90.0 90.0 90.0 X Y Z -0.06466642 0.11250176 -0.0002998044 0.003378711 0.84000003 0.84000003 0.84000003 AUTHOR Non Uniform Refinement, un-sharpened map. C6 symmetry. 3.75 Angstrom emd_47340_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 285.6 285.6 285.6 90.0 90.0 90.0 X Y Z -0.08940141 0.123170406 0.00008363234 0.0057673813 0.84000003 0.84000003 0.84000003 AUTHOR Non Uniform Refinement, half map B. C6 symmetry. 3.75 Angstrom emd_47340_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 285.6 285.6 285.6 90.0 90.0 90.0 X Y Z -0.08071625 0.14327542 0.00008154084 0.0058053355 0.84000003 0.84000003 0.84000003 AUTHOR Non Uniform Refinement, half map A. C6 symmetry. 3.75 Angstrom