2025-05-28 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 EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name REMEDIATION REPOSITORY Carbohydrate remediation STRUCTURE_SUMMARY atom_site chem_comp entity pdbx_branch_scheme pdbx_chem_comp_identifier pdbx_entity_branch pdbx_entity_branch_descriptor pdbx_entity_branch_link pdbx_entity_branch_list pdbx_entity_nonpoly pdbx_nonpoly_scheme pdbx_struct_assembly_gen pdbx_unobs_or_zero_occ_atoms struct_asym struct_conn struct_site struct_site_gen _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.label_asym_id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_entity_id _atom_site.type_symbol _chem_comp.name _chem_comp.type _pdbx_struct_assembly_gen.asym_id_list _pdbx_unobs_or_zero_occ_atoms.label_asym_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_role _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id STRUCTURE_SUMMARY atom_site chem_comp database_2 entity pdbx_entity_nonpoly pdbx_nonpoly_scheme pdbx_unobs_or_zero_occ_atoms struct_conn _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.pdbx_formal_charge _atom_site.type_symbol _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.type _database_2.pdbx_DOI _database_2.pdbx_database_accession _entity.formula_weight _entity.pdbx_description _pdbx_entity_nonpoly.comp_id _pdbx_entity_nonpoly.name _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _struct_conn.pdbx_leaving_atom_flag STRUCTURE_SUMMARY atom_site chem_comp database_PDB_caveat pdbx_entity_nonpoly pdbx_nonpoly_scheme pdbx_validate_chiral _atom_site.auth_comp_id _atom_site.label_comp_id _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.type _pdbx_entity_nonpoly.comp_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_mon_id STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond em_admin pdbx_entry_details pdbx_modification_feature _em_admin.last_update DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name RCSB RCSB 2019-01-28 2019-02-06 2019-02-20 2025-05-28 Cryo-EM structure of a human-cockroach hybrid Nav channel. Clairfeuille T Rohou A Sodium channel, scorpion toxin, electrical signaling, fast inactivation, MEMBRANE PROTEIN Clairfeuille T Rohou A Payandeh J Cryo-EM structures of a human-cockroach hybrid Nav channel in the presence and absence of the alpha-scorpion toxin AaH2. Science US 2019 1095-9203 0038 SCIEAS 6nt3 FULLOVERLAP NavPas-VSD4 NavPas-VSD4 0 1 Periplaneta americana 0.155 Sodium channel protein type 9 subunit alpha, Sodium channel protein PaFPC1, chimeric construct Periplaneta americana 0.178763656 1 Homo sapiens LEVO WSHPQFEKGGGSGGGSGGSAWSHPQFEKGGSGGDYKDDDDKGGSGGDYKDDDDKMADNSPLIREERQRLFRPYTRAMLTA PSAQPAKENGKTEENKDNSRDKGRGANKDRDGSAHPDQALEQGSRLPARMRNIFPAELASTPLEDFDPFYKNKKTFVVVT KAGDIFRFSGEKSLWMLDPFTPIRRVAISTMVQPIFSYFIMITILIHCIFMIMPATQTTYILELVFLSIYTIEVVVKVLA RGFILHPFAYLRDPWNWLDFLVTLIGYITLVVDLGHLYALRAFRVLRSWRTVTIVPGWRTIVDALSLSITSLKDLVLLLL FSLSVFALIGLQLFMGNLKHKCVKHFPADGSWGNFTDERWFNYTSNSSHWYIPDDWIEYPLCGNSSGAGMCPPGYTCLQG YGGNPNYGYTSFDTFGWAFLSVFRLVTLDYWEDLYQLALRSAGPWHILFFIIVVFYGTFCFLNFILAVVVMSYTHMVKRA DEEKAAERELKKEKKAASVANNTANGQEQTTIEMNGDEAVVIDNNDQAARQQSDPETPAPSVTQRLTDFLCVWDCCVPWQ KLQGAIGAVVLSPFFELFIAVIIVLNITFMALDHHDMNIEFERILRTGNYIFTSIYIVEAVLKIIALSPKFYFKDSWNVF DFIIVVFAILELGLEGVQGLSVFRSFRLLRVFRLAKFWPTLNNFMSVMTKSYGAFVNVMYVMFLLLFIFAIIGMQLFGMN YIDNMERFPDGDLPRWNFTDFLHSFMIVFRALCGEWIESMWDCMLVGDWSCIPFFVAVFFVGNLVILNLLIALLLNNYGS FCTSPTSDEEDSKDEDALAQIVRIFKRFKPNLNAVKLSPMKPDSEDIVESQEIQGNNIADAEDVLAGEFPPDCCCNAFYK CFPSRPARDSSVQRMWSNIRRVCFLLAKNKYFQKFVTAVLVITSVLLALEDIYLPQRPVLVNITLYVDYVLTAFFVIEMI IMLFAVGFKKYFTSKWYWLDFIVVVAYLLNFVLMCAGIEALQTLRLLRVFRLFRPLSKVNGMQVVTSTLVEAVPHIFNVI LVGIFFWLVFAIMGVQLFAGKFYKCVDENSTVLSHEITMDRNDCLHENYTWENSPMNFDHVGNAYLSLLQVATFKGWLQI MNDAIDSREVHKQPIRETNIYMYLYFIFFIVFGSFFILKLFVCILIDIFRQQRRKAEGLSATDSRTQLIYRRAVMRTMSA KPVKRIPKPGNKIQGCIFDLVTNQAFDISIMVLICLNMVTMMVEKEGQSQHMTEVLYWINVVFIILFTGECVLKLISLRH YYFTVGWNIFDFVVVIISIVGMFLADLIETYFVSPTLFRVIRLARIGRILRLVKGAKGIRLLLLALRKALRTLFNVSFLL FVIMFVYAVFGMEFFMHIRDAGAIDDVYNFKTFGQSIILLFQLATSAGWDGVYFAIANEEDCRAPDHELGYPGNCGSRAL GIAYLVSYLIITCLVVINMYAAVILDYVLEVYEDSKEGLTDDDYDMFFEVWQQFDPEATQYIRYDQLSELLEALQPPLQV QKPNKYKILSMNIPICKDDHIFYKDVLEALVKDVFSRRG D0E0C2 Q15858 D0E0C2 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 4 NAG CHOLESTEROL HEMISUCCINATE 0.000486726 1 Y01 (7E,21R,24S)-27-amino-24-hydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaheptacos-7-en-21-yl (9Z,12E)-octadeca-9,12-dienoate 0.000742018 4 76F 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 1 LHG Digitonin 0.0012293119999999998 1 AJP singleParticle particle 1.5 7.5 C-flat-2/1 COPPER 200 CARBON HOLEY ARRAY PLASMA CLEANING
Grids were plasma etched using the Solarus plasma cleaner (Gatan) in the hydrogen-oxygen setting. Grids were etched for 4 minutes on each side to remove burrs from hole edges. The grids were then coated on both sides with 5nm of Au/Pd which was plasma deposited using the Leica ACE600 (Leica).
 ETHANE 100 277 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 1 10421 10.0 40.0 1
Automated picking using a soft-edged disc as a template yielded 591739 candidate coordinates. 2D classification led to the selection of 334055 particles for further analysis.
 cisTEM PHASE FLIPPING AND AMPLITUDE CORRECTION EMD-6698
The startup map was low-pass filtered to 40A and resolution-limited automatic refinement in cisTEM was used (beginning at 20A)
 1 C1 FOURIER SPACE 3.4 FSC 0.143 CUT-OFF cisTEM
No information from spatial frequencies higher than 1/5A were ever used during refinement.
150583 OTHER cisTEM OTHER cisTEM cisTEM emd_0500.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 250 250 250 0 0 0 250 250 250 250.0 250.0 250.0 90.0 90.0 90.0 X Y Z -15.94242 23.608826000000001 0.048209425 1.1041741 1.0 1.0 1.0 3.8 AUTHOR Sharpened and masked map used for model building. emd_0500_msk_1.map emd_0500_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 250 250 250 0 0 0 250 250 250 250.0 250.0 250.0 90.0 90.0 90.0 X Y Z -3.4230137 7.180583 0.040679917 0.32210472 1.0 1.0 1.0 AUTHOR emd_0500_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 250 250 250 0 0 0 250 250 250 250.0 250.0 250.0 90.0 90.0 90.0 X Y Z -5.432905 8.643335 -0.0032683648 0.46295217 1.0 1.0 1.0 AUTHOR em-half-volume_P2 emd_0500_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 250 250 250 0 0 0 250 250 250 250.0 250.0 250.0 90.0 90.0 90.0 X Y Z -5.667403 8.672696999999999 -0.004107717 0.46362567 1.0 1.0 1.0 AUTHOR em-half-volume_P1