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- EMDB-40190: Local map of B3SB3L in complex with two-RBD-up state I of soluble... -

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Basic information

Entry
Database: EMDB / ID: EMD-40190
TitleLocal map of B3SB3L in complex with two-RBD-up state I of soluble SARS-CoV-2 Spike trimer
Map data
Sample
  • Complex: Local map of B3SB3L in complex with two-RBD-up state I of soluble SARS-CoV-2 Spike trimer
KeywordsVIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsLiu WP / Shokr A / Mabrouk M / Aly N / Zhang J / Aschauer P / Gao HL / Selvaraj G / Elzoghby A / Chen B ...Liu WP / Shokr A / Mabrouk M / Aly N / Zhang J / Aschauer P / Gao HL / Selvaraj G / Elzoghby A / Chen B / Kawano T / Nasr ML
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)4U54HL119145-08 United States
CitationJournal: To Be Published
Title: Luminescent biosensor platform for the rapid detection of viruses
Authors: Liu WP / Shokr A / Mabrouk M / Aly N / Zhang J / Aschauer P / Gao HL / Selvaraj G / Elzoghby A / Chen B / Kawano T / Nasr ML
History
DepositionMar 20, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40190.png

Downloads & links

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Map

FileDownload / File: emd_40190.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 600 pix.
= 498. Å		0.83 Å/pix.
x 600 pix.
= 498. Å		0.83 Å/pix.
x 600 pix.
= 498. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.015460592 - 1.8123035
Average (Standard dev.)0.0002814933 (±0.006404608)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 498.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_40190_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_40190_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Local map of B3SB3L in complex with two-RBD-up state I of soluble...

EntireName: Local map of B3SB3L in complex with two-RBD-up state I of soluble SARS-CoV-2 Spike trimer
Components
  • Complex: Local map of B3SB3L in complex with two-RBD-up state I of soluble SARS-CoV-2 Spike trimer

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Supramolecule #1: Local map of B3SB3L in complex with two-RBD-up state I of soluble...

SupramoleculeName: Local map of B3SB3L in complex with two-RBD-up state I of soluble SARS-CoV-2 Spike trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 600 KDa

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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

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
0.15 mol/LNaClsodium chloride
0.025 mol/LTris-HClTris hydrochloride
0.02 %DDMn-dodecyl-D-maltopyranoside
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.66 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 9451014
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7kj3

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION, cryoSPARC) / Number images used: 331406
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: RELION

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Atomic model buiding 1

Initial modelPDB ID:

7kj3


Chain - Chain ID: A / Chain - Residue range: 14-1211 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: AB INITIO MODEL

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