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 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 De novo calcium channel heptamer, CalC6_3 with DHR extensions. Off target multimerization state Weidle C Liu Y Borst AJ Calcium Channel, CalC6_3, De novo, Membrane protein, CalC6_3 with DHR extensions, heptamer, 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 EMD-47340 other EM volume
hexamer map
 9e0h FULLOVERLAP EMDB EMD-47340 other EM volume
hexamer map
 EMDB EMD-47356 associated EM volume
De novo calcium channel heptamer, CalC6_3 with DHR extensions. Off target multimerization state
 PDB 9DZW unspecified
hexamer strucutre
 CalC6_3 with DHR extensions, hepatmer CalC6_3 with DHR extensions, hepatmer 0 1 synthetic construct 0.25276902 CalC6_3 with DHR extension synthetic construct 0.036163828 7 Escherichia coli BL21(DE3) LEVO MAELRERLLRAARWILLLGLLVLVGFVVLAYLERSPLIRAFVLSAGVVLVALFAAALAWLYLAAALLGRSPLLALVALAL GLITLAAASAAMAATFAHLLLEAPPEYREAMLYVFGIAVLIVGLLLLGLVWLLEEALEALLEEEKRREEEEKRRELVKRA EEALQKAQEAEKQGDVEKAVKAAQEAVRAAKESGDNDVLRRVAEQALQIAKEAEKQGNVEVAVKAARVAVEAAKQAGDND VLRKVAEQALRIAKEAEKQGNVEVAVKAARVAVEAAKQAGDQDVLRKVSEQAERISKEAKKQGNSEVSEEARKVADEAKK QTGGSGGSHHHHHH singleParticle particle 1 8.0 20.0 Tris/HCl tris(hydroxymethyl)aminomethane / Hydrogen Chloride 150.0 NaCl Sodium Chloride 0.006 GDN Glyco-Diosgenin
20 mM Tris/HCl pH 8.0, 150 mM NaCl, 0.006% GDN
 Quantifoil R2/2 COPPER 300 GRAPHENE CONTINUOUS 2.0 CARBON HOLEY 40.0 GLOW DISCHARGE AIR 39.0
5 mA current
 ETHANE 100 295.15 FEI VITROBOT MARK IV
membrane protein in purified detergent micelle
 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 cryoSPARC PHASE FLIPPING AND AMPLITUDE CORRECTION
Ab Initio
 C7 FOURIER SPACE 4.62 FSC 0.143 CUT-OFF cryoSPARC 45077 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC 3 10470.0 cryoSPARC
Ab Initio, C7
 emd_47356.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 -0.0018723768 2.0103915 -0.00074011995 0.027550498 0.84000003 0.84000003 0.84000003 0.15 AUTHOR Non uniform refinement in C7, sharpened with DeepEMhancer, Main map for structure building. 4.62 Angstrom Other in silico model
Design protein, see paper
 FLEXIBLE FIT
For the heptamer, CalC6_3 with DHR extension hexamer design model was used as a starting model. A single chain for the heptamer was isolated in PyMOL, and 7 copies of this chain were fitted to the map in UCSF Chimera to reform the channel. The heptamer 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_47356_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 -0.17882445 0.33313614 -0.0002342131 0.010400457 0.84000003 0.84000003 0.84000003 AUTHOR Non uniform refinement in C1, un-sharpened. 5.13 Angstrom emd_47356_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 -0.7290098 1.0156877 -0.00024804974 0.021695195 0.84000003 0.84000003 0.84000003 AUTHOR Non uniform refinement in C7, auto sharpened. 4.62 Angstrom emd_47356_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 -0.11451797 0.31075832 -0.0002480497 0.009964271 0.84000003 0.84000003 0.84000003 AUTHOR Non uniform refinement in C7, un-sharpened. 4.62 Angstrom emd_47356_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 -0.5312766 0.9384719 -0.00023421309 0.020090539 0.84000003 0.84000003 0.84000003 AUTHOR Non uniform refinement in C1, sharpened. 5.13 Angstrom emd_47356_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 -0.36785462 0.63006705 0.00044592298 0.038468212 0.84000003 0.84000003 0.84000003 AUTHOR Non uniform refinement in C1, half map A. emd_47356_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 -0.3556388 0.54991835 0.00045119636 0.038041648 0.84000003 0.84000003 0.84000003 AUTHOR Non uniform refinement in C1, half map B emd_47356_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 -0.18489811 0.38485128 0.00043773119 0.016586777 0.84000003 0.84000003 0.84000003 AUTHOR Non uniform refinement in C7, half map B. emd_47356_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 -0.17814729 0.38027275 0.0004398647 0.016593324 0.84000003 0.84000003 0.84000003 AUTHOR Non uniform refinement in C7, half map A.