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- EMDB-41181: CS3pt1p4_C1L local refinement for HCMV Pentamer in complex with C... -

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Basic information

Entry
Database: EMDB / ID: EMD-41181
TitleCS3pt1p4_C1L local refinement for HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab
Map dataCS3pt1p4_C1L local refinement map for HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab
Sample
  • Complex: HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab
    • Complex: HCMV Pentamer
    • Complex: CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab
KeywordsVirus / glycoprotein / antibody / VIRAL PROTEIN
Biological speciesHuman betaherpesvirus 5 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGoldsmith JG / McLellan JS
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: HCMV neutralization by broad antibody targeting
Authors: Zehner M / Goldsmith JG / McLellan JS / Klein F
History
DepositionJul 5, 2023-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateAug 9, 2023-
Current statusAug 9, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41181.png

Downloads & links

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Map

FileDownload / File: emd_41181.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCS3pt1p4_C1L local refinement map for HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 400 pix.
= 376. Å		0.94 Å/pix.
x 400 pix.
= 376. Å		0.94 Å/pix.
x 400 pix.
= 376. 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: 0.22
Minimum - Maximum-0.32493314 - 0.7187663
Average (Standard dev.)0.0003283368 (±0.006605911)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 376.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: CS3pt1p4 C1L local refinement sharpened map for HCMV Pentamer...

Fileemd_41181_additional_1.map
AnnotationCS3pt1p4_C1L local refinement sharpened map for HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CS3pt1p4 C1L local refinement half map A for HCMV...

Fileemd_41181_half_map_1.map
AnnotationCS3pt1p4_C1L local refinement half map A for HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CS3pt1p4 C1L local refinement half map B for HCMV...

Fileemd_41181_half_map_2.map
AnnotationCS3pt1p4_C1L local refinement half map B for HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L 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 Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab

EntireName: HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab
Components
  • Complex: HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab
    • Complex: HCMV Pentamer
    • Complex: CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab

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Supramolecule #1: HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab

SupramoleculeName: HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: HCMV Pentamer

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

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Supramolecule #3: CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab

SupramoleculeName: CS2pt1p2_A10L Fab and CS3pt1p4_C1L 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71677
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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