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- EMDB-25685: CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in... -
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Open data
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Basic information
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Title | CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with neutralizing fabs 2C12, 7I13 and 13H11 | |||||||||
![]() | Composite map generated by combining focused refined maps. Map used for model refinements | |||||||||
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Function / homology | ![]() host cell endosome / host cell Golgi apparatus / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Kschonsak M / Johnson MC / Schelling R / Green EM / Rouge L / Ho H / Patel N / Kilic C / Kraft E / Arthur CP ...Kschonsak M / Johnson MC / Schelling R / Green EM / Rouge L / Ho H / Patel N / Kilic C / Kraft E / Arthur CP / Rohou AL / Comps-Agrar L / Martinez-Martin N / Perez L / Payandeh J / Ciferri C | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Structural basis for HCMV Pentamer receptor recognition and antibody neutralization. Authors: Marc Kschonsak / Matthew C Johnson / Rachel Schelling / Evan M Green / Lionel Rougé / Hoangdung Ho / Nidhi Patel / Cem Kilic / Edward Kraft / Christopher P Arthur / Alexis L Rohou / ...Authors: Marc Kschonsak / Matthew C Johnson / Rachel Schelling / Evan M Green / Lionel Rougé / Hoangdung Ho / Nidhi Patel / Cem Kilic / Edward Kraft / Christopher P Arthur / Alexis L Rohou / Laetitia Comps-Agrar / Nadia Martinez-Martin / Laurent Perez / Jian Payandeh / Claudio Ciferri / ![]() ![]() Abstract: Human cytomegalovirus (HCMV) represents the viral leading cause of congenital birth defects and uses the gH/gL/UL128-130-131A complex (Pentamer) to enter different cell types, including epithelial ...Human cytomegalovirus (HCMV) represents the viral leading cause of congenital birth defects and uses the gH/gL/UL128-130-131A complex (Pentamer) to enter different cell types, including epithelial and endothelial cells. Upon infection, Pentamer elicits the most potent neutralizing response against HCMV, representing a key vaccine candidate. Despite its relevance, the structural basis for Pentamer receptor recognition and antibody neutralization is largely unknown. Here, we determine the structures of Pentamer bound to neuropilin 2 (NRP2) and a set of potent neutralizing antibodies against HCMV. Moreover, we identify thrombomodulin (THBD) as a functional HCMV receptor and determine the structures of the Pentamer-THBD complex. Unexpectedly, both NRP2 and THBD also promote dimerization of Pentamer. Our results provide a framework for understanding HCMV receptor engagement, cell entry, antibody neutralization, and outline strategies for antiviral therapies against HCMV. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 116 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 55.8 KB 55.8 KB | Display Display | ![]() |
Images | ![]() | 57.5 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 32.5 MB 116.1 MB 115.7 MB 32.5 MB 32.5 MB 116 MB 32.5 MB 116.2 MB 115.4 MB 115.5 MB 32.5 MB 115.7 MB 32.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7t4qMC ![]() 7t4rC ![]() 7t4sC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Composite map generated by combining focused refined maps. Map used for model refinements | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1948 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
+Additional map: Half map 2 of focused refinement on 2C12, 7I13, UL region.
+Additional map: Sharpened map of focused refinement on gH and...
+Additional map: Non-sharpened map of focused refinement on gH and 13H11 region.
+Additional map: Half map 2 of focused refinement on gH and 13H11 region.
+Additional map: Half map 1 of focused refinement on gH and 13H11 region.
+Additional map: Sharpened map of focused refinement on gL region....
+Additional map: Half map 2 of focused refinement on gL region.
+Additional map: Sharpened map of focused refinement on 2C12, 7I13,...
+Additional map: Non-sharpened map of focused refinement on gL region.
+Additional map: Non-sharpened map of overall (non-focused) refinement.
+Additional map: Half map 1 of focused refinement on gL region.
+Additional map: Non-sharpened map of focused refinement on 2C12, 7I13, UL region.
+Additional map: Half map 1 of focused refinement on 2C12, 7I13, UL region.
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Sample components
+Entire : Pentameric complex of HCMV proteins gH, gL, UL128, UL130, UL131A ...
+Supramolecule #1: Pentameric complex of HCMV proteins gH, gL, UL128, UL130, UL131A ...
+Macromolecule #1: Envelope glycoprotein H
+Macromolecule #2: Envelope glycoprotein L
+Macromolecule #3: Envelope protein UL128
+Macromolecule #4: Envelope glycoprotein UL130
+Macromolecule #5: Envelope protein UL131A
+Macromolecule #6: Fab 2C12 heavy chain
+Macromolecule #7: Fab 2C12 light chain
+Macromolecule #8: Fab 7I13 light chain
+Macromolecule #9: Fab 7I13 heavy chain
+Macromolecule #10: Fab 13H11 heavy chain
+Macromolecule #11: Fab 13H11 light chain
+Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 1.77 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: UltrAuFoil R0.6/1 / Material: GOLD / Mesh: 300 Details: The grid was incubated with a thiol reactive self-assembling reaction mixture of 4mM monothiolalkane(C11)PEG6-OH (11-mercaptoundecyl) hexaethyleneglycol, (SPT-0011P6, SensoPath Technologies, ...Details: The grid was incubated with a thiol reactive self-assembling reaction mixture of 4mM monothiolalkane(C11)PEG6-OH (11-mercaptoundecyl) hexaethyleneglycol, (SPT-0011P6, SensoPath Technologies, Inc., Bozeman, MT)[23]. Grids were incubated with this self-assembled, monolayer (SAM) solution for 24 hours. Prior to grid freezing, grids were removed from the SAM solution and rinsed with EtOH. | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: LEICA EM GP / Details: blot for 3.5s before plunging. | |||||||||
Details | The sample was monodisperse. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 18326 / Average exposure time: 10.0 sec. / Average electron dose: 58.0 e/Å2 Details: Images were collected in movie-mode at 5 frames/second. |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Particle selection | Number selected: 5128264 / Details: template-matching particle picking |
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CTF correction | Software - Name: CTFFIND (ver. 4.1.13) |
Startup model | Type of model: OTHER Details: ab-initio 3D model generation from select particles within cisTEM |
Initial angle assignment | Type: OTHER / Software - Name: cisTEM (ver. 1.02) / Details: Auto-refine in cisTEM |
Final 3D classification | Number classes: 100 / Software - Name: RELION (ver. 3.1) |
Final angle assignment | Type: OTHER / Software - Name: cisTEM (ver. 1.02) Details: Manual refine in cisTEM. Map was divided in 3 sections to refine map with focused refinements. |
Final reconstruction | Number classes used: 39 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.02) Details: A composite map was generated from the three individual focused 3D maps using phenix combine_focused_maps Number images used: 4792984 |
Details | Movie frames were corrected for motion and aligned. Images with a CTF fit resolution of 8.0 A or better were selected for particle picking. |