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- EMDB-33655: TM domain of SIT1 -

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Basic information

Entry
Database: EMDB / ID: EMD-33655
TitleTM domain of SIT1
Map data
Sample
  • Complex: SIT1-ACE2-BA.2 RBD complex
    • Complex: SIT1
    • Complex: ACE2 FL
    • Complex: RBD of BA.2 spike
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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 Discov / Year: 2022
Title: Structures of ACE2-SIT1 recognized by Omicron variants of SARS-CoV-2.
Authors: Yaping Shen / Jianhui Wang / Yaning Li / Yuanyuan Zhang / Ruilin Tian / Renhong Yan /
History
DepositionJun 21, 2022-
Header (metadata) releaseNov 30, 2022-
Map releaseNov 30, 2022-
UpdateNov 30, 2022-
Current statusNov 30, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33655.png

Downloads & links

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Map

FileDownload / File: emd_33655.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.087 Å
Density
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.322186 - 0.3203389
Average (Standard dev.)-2.1438478e-05 (±0.004619917)
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_33655_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_33655_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.2 RBD complex

EntireName: SIT1-ACE2-BA.2 RBD complex
Components
  • Complex: SIT1-ACE2-BA.2 RBD complex
    • Complex: SIT1
    • Complex: ACE2 FL
    • Complex: RBD of BA.2 spike

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Supramolecule #1: SIT1-ACE2-BA.2 RBD complex

SupramoleculeName: SIT1-ACE2-BA.2 RBD complex / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: SIT1

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

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Supramolecule #3: ACE2 FL

SupramoleculeName: ACE2 FL / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #2

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Supramolecule #4: RBD of BA.2 spike

SupramoleculeName: RBD of BA.2 spike / type: complex / Chimera: Yes / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 254426

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