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- EMDB-41158: CS2it1p2_F7K local refinement for HCMV Trimer in complex with CS2... -

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Basic information

Entry
Database: EMDB / ID: EMD-41158
TitleCS2it1p2_F7K local refinement for HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab
Map dataCS2it1p2_F7K local refinement map for HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab
Sample
  • Complex: HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab
    • Complex: HCMV Trimer
    • Complex: CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab
KeywordsVirus / glycoprotein / antibody / VIRAL PROTEIN
Biological speciesHuman betaherpesvirus 5 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsGoldsmith JA / McLellan JS
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Immunity / Year: 2023
Title: Single-cell analysis of memory B cells from top neutralizers reveals multiple sites of vulnerability within HCMV Trimer and Pentamer.
Authors: Matthias Zehner / Mira Alt / Artem Ashurov / Jory A Goldsmith / Rebecca Spies / Nina Weiler / Justin Lerma / Lutz Gieselmann / Dagmar Stöhr / Henning Gruell / Eric P Schultz / Christoph ...Authors: Matthias Zehner / Mira Alt / Artem Ashurov / Jory A Goldsmith / Rebecca Spies / Nina Weiler / Justin Lerma / Lutz Gieselmann / Dagmar Stöhr / Henning Gruell / Eric P Schultz / Christoph Kreer / Linda Schlachter / Hanna Janicki / Kerstin Laib Sampaio / Cora Stegmann / Michelle D Nemetchek / Sabrina Dähling / Leon Ullrich / Ulf Dittmer / Oliver Witzke / Manuel Koch / Brent J Ryckman / Ramin Lotfi / Jason S McLellan / Adalbert Krawczyk / Christian Sinzger / Florian Klein /
Abstract: Human cytomegalovirus (HCMV) can cause severe diseases in fetuses, newborns, and immunocompromised individuals. Currently, no vaccines are approved, and treatment options are limited. Here, we ...Human cytomegalovirus (HCMV) can cause severe diseases in fetuses, newborns, and immunocompromised individuals. Currently, no vaccines are approved, and treatment options are limited. Here, we analyzed the human B cell response of four HCMV top neutralizers from a cohort of 9,000 individuals. By single-cell analyses of memory B cells targeting the pentameric and trimeric HCMV surface complexes, we identified vulnerable sites on the shared gH/gL subunits as well as complex-specific subunits UL and gO. Using high-resolution cryogenic electron microscopy, we revealed the structural basis of the neutralization mechanisms of antibodies targeting various binding sites. Moreover, we identified highly potent antibodies that neutralized a broad spectrum of HCMV strains, including primary clinical isolates, that outperform known antibodies used in clinical trials. Our study provides a deep understanding of the mechanisms of HCMV neutralization and identifies promising antibody candidates to prevent and treat HCMV infection.
History
DepositionJul 2, 2023-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41158.png

Downloads & links

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Map

FileDownload / File: emd_41158.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCS2it1p2_F7K local refinement map for HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 360 pix.
= 338.4 Å		0.94 Å/pix.
x 360 pix.
= 338.4 Å		0.94 Å/pix.
x 360 pix.
= 338.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.414614 - 0.81932867
Average (Standard dev.)-0.00022596127 (±0.011060639)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 338.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: CS2it1p2 F7K local refinement sharpened map for HCMV Trimer...

Fileemd_41158_additional_1.map
AnnotationCS2it1p2_F7K local refinement sharpened map for HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CS2it1p2 F7K local refinement half map A for HCMV...

Fileemd_41158_half_map_1.map
AnnotationCS2it1p2_F7K local refinement half map A for HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CS2it1p2 F7K local refinement half map B for HCMV...

Fileemd_41158_half_map_2.map
AnnotationCS2it1p2_F7K local refinement half map B for HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab

EntireName: HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab
Components
  • Complex: HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab
    • Complex: HCMV Trimer
    • Complex: CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab

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Supramolecule #1: HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab

SupramoleculeName: HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: HCMV Trimer

SupramoleculeName: HCMV Trimer / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Human betaherpesvirus 5

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Supramolecule #3: CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab

SupramoleculeName: CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7lbe

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 376687
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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