2025-12-10 REL PDBe INITIAL_RELEASE REPOSITORY PDBe PDBe 2025-06-25 2025-12-10 2025-12-10 2025-12-10 Medical Research Council (MRC, United Kingdom) U-016275 IAA-CiC United Kingdom Other private Cryo-EM structure of Shigella flexneri LptDE dimer: closed-state unbound and open-state bound by Oekolampad phage RBP Dunbar E Basle A van den Berg B lipopolysaccharide transport, receptor-binding protein, outer membrane protein complex, beta-barrel, bacteriophage, MEMBRANE PROTEIN Dunbar E Clark R Basle A Allyjaun S Newman H Hubbard J Khalid S van den Berg B Small siphophage binding to an open state of the LptDE outer membrane lipopolysaccharide translocon. Proc.Natl.Acad.Sci.USA US 122 e2516650122 e2516650122 2025 41296721 doi:10.1073/pnas.2516650122 1091-6490 0040 PNASA6 9rpw FULLOVERLAP EMDB EMD-54173 associated EM volume
Cryo-EM structure of Shigella flexneri LptDE dimer: closed-state unbound and open-state bound by Oekolampad phage RBP
 LptDE-RBP complex LptDE-RBP complex 0 1 2 3 Shigella flexneri 0.0203 LptDE 1 1 2 Shigella flexneri RBP 1 3 Escherichia phage Oekolampad LPS-assembly protein LptD Shigella flexneri 0.08974060199999999 2 Escherichia coli LEVO MEKRIPTLLATMIATALYSQQGLAADLASQCMLGVPSYDRPLVQGDTNDLPVTINADHAKGDYPDDAVFTGSVDIMQGNS RLQADEVQLHQKEAPGQPEPVRTVDALGNVHYDDNQVILKGPKGWANLNTKDTNVWEGDYQMVGRQGRGKADLMKQRGEN RYTILDNGSFTSCLPGSDTWSVVGSEIIHDREEQVAEIWNARFKVGPVPIFYSPYLQLPVGDKRRSGFLIPNAKYTTTNY FEFYLPYYWNIAPNMDATITPHYMHRRGNIMWENEFRYLSQAGAGLMELDYLPSDKVYEDEHPNDDSSRRWLFYWNHSGV MDQVWRFNVDYTKVSDPSYFNDFDNKYGSSTDGYATQKFSVGYAVQNFNATVSTKQFQVFSEQNTSSYSAEPQLDVNYYQ NDVGPFDTRIYGQAVHFVNTRDDMPEATRVHLEPTINLPLSNNWGSINTEAKFLATHYQQTNLDWYNSRNTTKLDESVNR VMPQFKVDGKMVFERDMEMLAPGYTQTLEPRAQYLYVPYRDQSDIYNYDSSLLQSDYSGLFRDRTYGGLDRIASANQVTT GVTSRIYDDAAVERFNISVGQIYYFTESRTGDDNITWENDDKTGSLVWAGDTYWRISERWGLRGGIQYDTRLDNVATSNS SIEYRRDEDRLVQLNYHYASPEYIQATLPKYYSTAEQYKNGISQVGAVASRPIADRWSIVGAYYYDTNANKQADSMLGVQ YSSCCYAIRVGYERKLNGWDNDKQHAVYDNAIGFNIELRGLSSNYGLGTQEMLRSNILPYQNTL Q83SQ0 LPS-assembly lipoprotein LptE Shigella flexneri 0.022206471000000002 2 Escherichia coli LEVO MRYLATLLLSLAVLITAGCGWHLRDTTQVPSTMKVMILDSGDPNGPLSRAVRNQLRLNGVELLDKETTRKDVPSLRLGKV SIAKDTASVFRNGQTAEYQMIMTVNATVLIPGRDIYPISAKVFRSFFDNPQMALAKDNEQDMIVKEMYDRAAEQLIRKLP SIRAADIRSDEEQTSTTTDTPATPARVSTMLGNENLYFQ Q83LX4 Tail fiber protein Escherichia phage Oekolampad 0.035347891 1 Escherichia coli LEVO MGAGILIDYNDGRPRMEITAGLRAPSYCTSFNQRAQSNKTLTINTPLTAGSQVVVALTRPVEVIEVFDQTLVIPDPFYVT SVTRNGNSGITLRGDDAYGAYSGLPQWAGVIMEVLPVGSRNAGLLVANSTDFTAISNVAKLMTCRYAKRVRVNGSMALPV SGVPFARWDDGNVSVGFDGGSIIVRNASYGGIDDVAASVDMDLVIFNNTPPTPGTGITMTNNQNQVTFSTVNKPFVYDRT INIGTSDQNIGNSLIQLSYTGALIQNNGGYNHVRMNGIRMAGNNVRVAKNRVIGNYSRQQFQMPGKNIAVPTPLLVIPNM YHHHHHH A0AAE8B389 singleParticle particle 7.5 10.0 C8H18N2O4S HEPES 100.0 NaCl sodium chloride 0.05 C24H46O11 DDM
10mM HEPES, pH7.5, 100mM NaCl, 0.05% (w/v) DDM
 Quantifoil R1.2/1.3 COPPER 200 GLOW DISCHARGE ETHANE 100 277.15 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.8 2.0 165000.0 FEI FALCON IV (4k x 4k) 1 10744 35.6 1 1902801 cryoSPARC NONE 3.2 FSC 0.143 CUT-OFF cryoSPARC 55494 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_54173.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 576 576 576 0 0 0 576 576 576 426.24 426.24 426.24 90.0 90.0 90.0 X Y Z -0.24664672 0.4837809 0.0003376322 0.008688047 0.74 0.74 0.74 0.09 AUTHOR AlphaFold in silico model RIGID BODY FIT emd_54173_msk_1.map emd_54173_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 576 576 576 0 0 0 576 576 576 426.24 426.24 426.24 90.0 90.0 90.0 X Y Z -0.62781894 0.9216628 0.00032607102 0.06505388 0.74 0.74 0.74 AUTHOR emd_54173_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 576 576 576 0 0 0 576 576 576 426.24 426.24 426.24 90.0 90.0 90.0 X Y Z -0.6455254 0.8078099 0.0003269286 0.0654551 0.74 0.74 0.74 AUTHOR