Neck channel of phage 812 after tail contraction (C1)

2026-01-21 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY citation citation_author em_admin pdbx_entry_details _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update PDBe PDBe 2023-08-31 2024-09-11 2024-09-11 2026-01-21 Ministry of Education, Youth and Sports of the Czech Republic Czech Republic Neck channel of phage 812 after tail contraction (C1) Cienikova Z Siborova M Fuzik T Plevka P phage, neck, A-form DNA, connector, VIRUS Cienikova Z Novacek J Siborova M Popelarova B Fuzik T Botka T Benesik M Bardy P Pantucek R Plevka P Genome anchoring, retention, and release by neck proteins of Staphylococcus phage 812. Commun Biol UK 2026 41507424 doi:10.1038/s42003-025-09477-8 2399-3642 8qem FULLOVERLAP PDB 8Q7D unspecified EMDB EMD-18372 associated EM volume

Staphylococcus phage 812 Staphylococcus phage 812 0 1 2 3 4

Purified phage virion was incubated in urea and LTA to induce tail contraction and genome ejection

Staphylococcus phage 812 K1-420 Staphylococcus aureus CCM 8428 1100.0 VIRION SPECIES false true Putative neck protein Staphylococcus phage 812 K1-420 0.034191703 12 LEVO MVNSMFGGDLDPYEKSLNYEYPYHPSGNPKHIDVSEIDNLTLADYGWSPDAVKAYMFGIVVQNPDTGQPMGDEFYNHILE RAVGKAERALDISILPDTQHEMRDYHETEFNSYMFVHAYRKPILQVENLQLQFNGRPIYKYPANWWKVEHLAGHVQLFPT ALMQTGQSMSYDAVFNGYPQLAGVYPPSGATFAPQMIRLEYVSGMLPRKKAGRNKPWEMPPELEQLVIKYALKEIYQVWG NLIIGAGIANKTLEVDGITETIGTTQSAMYGGASAQILQINEDIKELLDGLRAYFGYNMIGL A1YTN6 Portal protein Staphylococcus phage 812 K1-420 0.064155684 12 LEVO MADLFKQFRLGKDYGNNSTIAQVPIDEGLQANIKKIEQDNKEYQDLTKSLYGQQQAYAEPFIEMMDTNPEFRDKRSYMKN EHNLHDVLKKFGNNPILNAIILTRSNQVAMYCQPARYSEKGLGFEVRLRDLDAEPGRKEKEEMKRIEDFIVNTGKDKDVD RDSFQTFCKKIVRDTYIYDQVNFEKVFNKNNKTKLEKFIAVDPSTIFYATDKKGKIIKGGKRFVQVVDKRVVASFTSREL AMGIRNPRTELSSSGYGLSEVEIAMKEFIAYNNTESFNDRFFSHGGTTRGILQIRSDQQQSQHALENFKREWKSSLSGIN GSWQIPVVMADDIKFVNMTPTANDMQFEKWLNYLINIISALYGIDPAEIGFPNRGGATGSKGGSTLNEADPGKKQQQSQN KGLQPLLRFIEDLVNRHIISEYGDKYTFQFVGGDTKSATDKLNILKLETQIFKTVNEAREEQGKKPIEGGDIILDASFLQ GTAQLQQDKQYNDGKQKERLQMMMSLLEGDNDDSEEGQSTDSSNDDKEIGTDAQIKGDDNVYRTQTSNKGQGRKGEKSSD FKH A0A0U1WIV9 Channel DNA reverse strand (63-MER) Staphylococcus phage 812 K1-420 0.019439512 1 (DG)(DA)(DT)(DA)(DG)(DA)(DA)(DT)(DT)(DA)(DT)(DT)(DG)(DG)(DT)(DA)(DC)(DC)(DG)(DT) (DT)(DG)(DT)(DC)(DT)(DT)(DC)(DT)(DA)(DA)(DT)(DC)(DT)(DA)(DC)(DT)(DC)(DT)(DC)(DA) (DG)(DT)(DA)(DG)(DT)(DA)(DG)(DT)(DA)(DA)(DT)(DA)(DG)(DT)(DA)(DG)(DT)(DA)(DC)(DA) (DT)(DA)(DA) DNA Channel DNA forward strand (63-MER) Staphylococcus phage 812 K1-420 0.019386502 1 (DT)(DT)(DA)(DT)(DG)(DT)(DA)(DC)(DT)(DA)(DC)(DT)(DA)(DT)(DT)(DA)(DC)(DT)(DA)(DC) (DT)(DA)(DC)(DT)(DG)(DA)(DG)(DA)(DG)(DT)(DA)(DG)(DA)(DT)(DT)(DA)(DG)(DA)(DA)(DG) (DA)(DC)(DA)(DA)(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DA)(DA)(DT)(DA)(DA)(DT)(DT)(DC)(DT) (DA)(DT)(DC) DNA singleParticle particle 8.0 50.0 C4H11NO3 Tris 10.0 NaCl sodium chloride 10.0 CaCl calcium chloride Quantifoil R2/1 COPPER 200 CARBON HOLEY GLOW DISCHARGE 30 ETHANE-PROPANE 100 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.1 2.4 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 20 GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 4000 4000 1 15371 7.0 42.0 1

Frame alignment and dose-weighting with MotionCor2, then contrast inversion and normalization

32222

Particle selection using cross-correlation against capsid template

Gctf 1.0.6 PHASE FLIPPING AND AMPLITUDE CORRECTION EMD-8209 1 C1 FOURIER SPACE 3.96 FSC 0.143 CUT-OFF RELION 3.1 13296 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 6 17304.0 RELION 3.1

Neck aligned in C6 was symmetry-expanded to C1 and classified with a mask on the channel DNA without orientation search

emd_18372.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 416 416 416 0 0 0 416 416 416 439.712 439.712 439.712 90.0 90.0 90.0 X Y Z -0.01860386 0.041595794 0.0003767884 0.002027256 1.057 1.057 1.057 0.011 AUTHOR ::::EMDATABANK.org::::D_1292133051:::: Neck channel of phage 812 after tail contraction (C1) 8Q7D PDB experimental model Other in silico model

Web 3DNA 2.0

FLEXIBLE FIT

B-A-B-form dsDNA model was generated with Web 3DNA 2.0. Portal and neck dodecamers were sourced from models refined in C12 symmetry. All input models were fitted into the asymmetric map. Tunnel loops of the portal were extended into the asymmetric density.

cross-correlation coefficient REAL emd_18372_msk_1.map emd_18372_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 416 416 416 0 0 0 416 416 416 439.712 439.712 439.712 90.0 90.0 90.0 X Y Z -0.05014635 0.06707033 0.00019411217 0.0061656856 1.057 1.057 1.057 AUTHOR ::::EMDATABANK.org::::D_1292133051:::: Half-map 2 emd_18372_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 416 416 416 0 0 0 416 416 416 439.712 439.712 439.712 90.0 90.0 90.0 X Y Z -0.054083623 0.07005056 0.00019807905 0.00617697 1.057 1.057 1.057 AUTHOR ::::EMDATABANK.org::::D_1292133051:::: Half-map 1