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- EMDB-33656: Local map of the interface of ACE2 and BA.5 RBD -

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Basic information

Entry
Database: EMDB / ID: EMD-33656
TitleLocal map of the interface of ACE2 and BA.5 RBD
Map data
Sample
  • Complex: SIT1-ACE2-BA.5 RBD complex
    • Complex: SIT1
    • Complex: ACE2 FL
    • Complex: RBD of BA.5 spike
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsShen YP / Li YN / Zhang YY / Yan RH
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0509301 China
CitationJournal: Cell Discovery / Year: 2022
Title: Structures of ACE2-SIT1 recognized by Omicron variants of SARS-CoV-2
Authors: Shen YP / Li Y / Zhang Y / Yan R
History
DepositionJun 21, 2022-
Header (metadata) releaseJan 4, 2023-
Map releaseJan 4, 2023-
UpdateJan 4, 2023-
Current statusJan 4, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33656.png

Downloads & links

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Map

FileDownload / File: emd_33656.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 288 pix.
= 313.056 Å		1.09 Å/pix.
x 288 pix.
= 313.056 Å		1.09 Å/pix.
x 288 pix.
= 313.056 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.08578622 - 0.14630608
Average (Standard dev.)0.00016792487 (±0.002745923)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 313.056 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33656_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_33656_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 : SIT1-ACE2-BA.5 RBD complex

EntireName: SIT1-ACE2-BA.5 RBD complex
Components
  • Complex: SIT1-ACE2-BA.5 RBD complex
    • Complex: SIT1
    • Complex: ACE2 FL
    • Complex: RBD of BA.5 spike

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Supramolecule #1: SIT1-ACE2-BA.5 RBD complex

SupramoleculeName: SIT1-ACE2-BA.5 RBD complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: SIT1

SupramoleculeName: SIT1 / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: ACE2 FL

SupramoleculeName: ACE2 FL / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #4: RBD of BA.5 spike

SupramoleculeName: RBD of BA.5 spike / type: complex / ID: 4 / Chimera: Yes / Parent: 1 / Macromolecule list: #3

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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: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm
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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 766786
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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