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- EMDB-45286: Cryo EM map of SARS-COV-2 (BQ 1.1) spike protein in complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-45286
TitleCryo EM map of SARS-COV-2 (BQ 1.1) spike protein in complex with Fab COV2-3891 (2 open 1 close)
Map data
Sample
  • Complex: SARS-COV-2 (BQ 1.1) spike protein in complex with Fab COV2-3891
    • Complex: SARS-COV-2 (BQ 1.1) spike
    • Complex: Fab COV-3891
KeywordsVIRAL-PROTEIN / Fab / IMMUNE-complex / SARS-CoV-2 / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBinshtein E / Crowe JE
Funding support United States, 1 items
OrganizationGrant numberCountry
Defense Advanced Research Projects Agency (DARPA)HR0011-18-2-0001 United States
CitationJournal: To Be Published
Title: Cryo EM map of SARS-COV-2 (BQ 1.1) spike protein in complex with Fab COV2-3891
Authors: Binshtein E / Crowe JE
History
DepositionJun 11, 2024-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45286.png

Downloads & links

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Map

FileDownload / File: emd_45286.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 400 pix.
= 388.2 Å		0.97 Å/pix.
x 400 pix.
= 388.2 Å		0.97 Å/pix.
x 400 pix.
= 388.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9705 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.032714613 - 0.08250044
Average (Standard dev.)0.00003672955 (±0.0024858734)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 388.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_45286_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_45286_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 : SARS-COV-2 (BQ 1.1) spike protein in complex with Fab COV2-3891

EntireName: SARS-COV-2 (BQ 1.1) spike protein in complex with Fab COV2-3891
Components
  • Complex: SARS-COV-2 (BQ 1.1) spike protein in complex with Fab COV2-3891
    • Complex: SARS-COV-2 (BQ 1.1) spike
    • Complex: Fab COV-3891

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Supramolecule #1: SARS-COV-2 (BQ 1.1) spike protein in complex with Fab COV2-3891

SupramoleculeName: SARS-COV-2 (BQ 1.1) spike protein in complex with Fab COV2-3891
type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 540 MDa

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Supramolecule #2: SARS-COV-2 (BQ 1.1) spike

SupramoleculeName: SARS-COV-2 (BQ 1.1) spike / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: Fab COV-3891

SupramoleculeName: Fab COV-3891 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50 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

Concentration0.2 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 14000 / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
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: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION, cryoSPARC) / Number images used: 167000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL

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