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- EMDB-58663: Unbinned map of EMD-53938 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-58663
TitleUnbinned map of EMD-53938
Map dataReprocessed without binning of EMD-53938 and EMPIAR-12921. Zflipped
Sample
  • Complex: Trimeric RhGB07 Spike
KeywordsSpike protein of RhGB07 coronavirus / VIRAL PROTEIN
Biological speciesSarbecovirus sp. RhGB07
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsLau K / Dong CN / Ekundayo B
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: Understanding the future risk of bat coronavirus spillover into humans correlating sarbecovirus receptor usage, host range, and antigenicity
Authors: Thazuk N / Newman J
History
DepositionJun 24, 2026-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58663.png

Downloads & links

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Map

FileReleased
AnnotationReprocessed without binning of EMD-53938 and EMPIAR-12921. Zflipped
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 500 pix.
= 415. Å		0.83 Å/pix.
x 500 pix.
= 415. Å		0.83 Å/pix.
x 500 pix.
= 415. 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: 0.0706
Minimum - Maximum-0.33115384 - 0.4904758
Average (Standard dev.)0.00004067767 (±0.010733973)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 415.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Zflipped half map A

Fileemd_58663_half_map_1.map
AnnotationZflipped half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Zflipped half map B

Fileemd_58663_half_map_2.map
AnnotationZflipped half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trimeric RhGB07 Spike

EntireName: Trimeric RhGB07 Spike
Components
  • Complex: Trimeric RhGB07 Spike

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Supramolecule #1: Trimeric RhGB07 Spike

SupramoleculeName: Trimeric RhGB07 Spike / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Sarbecovirus sp. RhGB07

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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

Concentration2 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average exposure time: 5.04 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.2+220824) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7zss

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2+220824) / Number images used: 17685
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.3.2+220824)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.3.2+220824)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: PHENIX / Details: EMplace
DetailsModel was docked using Phenix EMPlace followed by manual building in Coot and phenix real space refine
RefinementSpace: REAL

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