2024-11-06 REL RCSB RCSB RCSB 2021-03-15 2021-08-11 2021-08-11 2024-11-06 Cryo-EM structure of the HCMV pentamer bound by human neuropilin 2 Wrapp D McLellan JS HCMV pentamer, NRP2, cytomegalovirus, host receptor, VIRAL PROTEIN, VIRAL PROTEIN-HOST RECEPTOR complex Wrapp D Ye X Ku Z Su H Jones HG Wang N Mishra AK Freed DC Li F Tang A Li L Jaijyan DK Zhu H Wang D Fu TM Zhang N An Z McLellan JS Structural basis for HCMV Pentamer recognition by neuropilin 2 and neutralizing antibodies. Sci Adv US 8 eabm2546 eabm2546 2022 35275718 doi:10.1126/sciadv.abm2546 2375-2548 7m22 FULLOVERLAP The ectodomain of the HCMV pentamer bound by domains a1a2b1b2 of human neuropilin 2 The ectodomain of the HCMV pentamer bound by domains a1a2b1b2 of human neuropilin 2 0 1 2 3 4
The primary map is the result of a focused refinement that encompasses the HCMV UL proteins (UL128, UL130, UL131) and NRP2 domains a2b1b2. The included additional map is the non-focused refinement in which the entire HCMV pentamer ectodomain and the entirety of NRP2 a1a2b1b2 can be observed.
0.23 The ectodomain of the HCMV pentamer 1 1 2 3 Human betaherpesvirus 5 Domains a1a2b1b2 of human neuropilin 2 1 4 Homo sapiens Envelope protein UL128 Human cytomegalovirus 0.016684299 1 Homo sapiens LEVO EECCEFINVNHPPERCYDFKMCNRFTVALRCPDGEVCYSPEKTAEIRGIVTTMTHSLTRQVVHNKLTSCNYNPLYLEADG RIRCGKVNDKAQYLLGAAGSVPYRWINLEYDKITRIVGLDQYLESVKKHKRLDVCRAKMGYMLQ C8BLJ3 Envelope glycoprotein UL130 Human cytomegalovirus 0.021761678 1 Homo sapiens LEVO SPWSTLTANQNPSPPWSKLTYSKPHDAATFYCPFLYPSPPRSPLQFSGFQQVSTGPECRNETLYLLYNREGQTLVERSST WVKKVIWYLSGRNQTILQRMPQTASKPSDGNVQISVEDAKIFGAHMVPKQTKLLRFVVNDGTRYQMCVMKLESWAHVFRD YSVSFQVRLTFTEANNQTYTFCTHPNLIV A0A0G2TB82 UL131A Human cytomegalovirus 0.013005457 1 Homo sapiens LEVO QCQRETAEKNDYYRVPHYWDACSRALPDQTRYKYVEQLVDLTLNYHYDASHGLDNFDVLKRINVTEVSLLISDFRRQNRR GGTNKRTTFNAAGSLAPHARSLEFSVRLFAN Q38M21 Neuropilin-2 Homo sapiens 0.065430434 1 Homo sapiens LEVO QPDPPCGGRLNSKDAGYITSPGYPQDYPSHQNCEWIVYAPEPNQKIVLNFNPHFEIEKHDCKYDFIEIRDGDSESADLLG KHCGNIAPPTIISSGSMLYIKFTSDYARQGAGFSLRYEIFKTGSEDCSKNFTSPNGTIESPGFPEKYPHNLDCTFTILAK PKMEIILQFLIFDLEHDPLQVGEGDCKYDWLDIWDGIPHVGPLIGKYCGTKTPSELRSSTGILSLTFHTDMAVAKDGFSA RYYLVHQEPLENFQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNLDSNKEYLQVDLRFLTMLTAI ATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHKVFQANNDATEVVLNKLHAPLLTRFVRIRPQTWHSGIALRL ELFGCRVTDAPCSNMLGMLSGLIADSQISASSTQEYLWSPSAARLVSSRSGWFPRIPQAQPGEEWLQVDLGTPKTVKGVI IQGARGGDSITAVEARAFVRKFKVSYSLNGKDWEYIQDPRTQQPKLFEGNMHYDTPDIRRFDPIPAQYVRVYPERWSPAG IGMRLEVLGCDWTGSLEVLFQ O60462 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 2 NAG CALCIUM ION 4.0078e-05 1 CA singleParticle particle 0.4 8.0 2.0 C4H11NO3 Tris 200.0 NaCl sodium chloride 2.0 CaCl2 calcium chloride 0.02 NaN3 sodium azide 0.1 (C6.2H10.3O1.35N0.65Na0.35)~72 amphipol A8-35 UltrAuFoil R1.2/1.3 GOLD GOLD HOLEY ARRAY PLASMA CLEANING ETHANE 100 277.15 FEI VITROBOT MARK IV
Grid was blotted with a force of -6 for 3 seconds.
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN
Collected from a single grid at -30 degrees tilt
GATAN K3 (6k x 4k) 80.0 1 745025 C1 3.65 FSC 0.143 CUT-OFF cryoSPARC 203130 COMMON LINE cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC cryoSPARC emd_23629.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 412.03198 412.03198 412.03198 90.0 90.0 90.0 X Y Z -0.0433535 2.5595467 0.00009640274 0.011446471 1.073 1.073 1.073 0.17 AUTHOR Focused refinement map, calculated in cryoSPARC and sharpened using DeepEMhancer. 5VOB PDB experimental model 2QQK PDB experimental model emd_23629_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 412.03198 412.03198 412.03198 90.0 90.0 90.0 X Y Z -0.0006072221 2.2017572 0.0020776996 0.03616376 1.073 1.073 1.073 AUTHOR Full map that was subsequently subjected to focused refinement. Calculated in cryoSPARC and sharpened using DeepEMhancer. emd_23629_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 412.03198 412.03198 412.03198 90.0 90.0 90.0 X Y Z -3.5510054 4.861504 0.0011249847 0.096499994 1.073 1.073 1.073 AUTHOR Half-map A for focused refinement. emd_23629_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 412.03198 412.03198 412.03198 90.0 90.0 90.0 X Y Z -3.2443447 3.6698818 0.001135073 0.09660333 1.073 1.073 1.073 AUTHOR Half-map B for focused refinement.