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- EMDB-40007: Local map of SARS-Cov2 S protein structure in complex with neutra... -

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Basic information

Entry
Database: EMDB / ID: EMD-40007
TitleLocal map of SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-S21B10
Map dataLocal refinement map of SARS-CoV-2 spike glycoprotein bound to antibody 002-S21B10. Used in construction of composite map EMD-29950.
Sample
  • Complex: Antibody 002-S21B10 bound to spike glycoprotein trimer
    • Complex: Antibody 002-S21B10
    • Complex: Spike glycoprotein trimer
Keywordsantibody / spike / SARS-CoV-2 / viral protein-immune system complex / viral protein
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.85 Å
AuthorsPatel A / Ortlund EA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5U19 AI14237-04 (subaward 000520244-SP008-SC014) United States
CitationJournal: To Be Published
Title: Elucidating the mechanism of SARS-CoV-2 Omicron variant escape from a RBD class-3 human antibody
Authors: Patel A / Kumar S / Lai L / Chakravarthy C / Valanparambil R / Keen M / Laughlin ZT / Frank F / Cheedarla N / Verkerke HP / Neish AS / Roback JD / Davis CW / Wrammert J / Ahmed R / Suthar MS ...Authors: Patel A / Kumar S / Lai L / Chakravarthy C / Valanparambil R / Keen M / Laughlin ZT / Frank F / Cheedarla N / Verkerke HP / Neish AS / Roback JD / Davis CW / Wrammert J / Ahmed R / Suthar MS / Murali-Krishna K / Chandele A / Ortlund EA
History
DepositionMar 8, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40007.png

Downloads & links

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Map

FileDownload / File: emd_40007.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refinement map of SARS-CoV-2 spike glycoprotein bound to antibody 002-S21B10. Used in construction of composite map EMD-29950.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 416 pix.
= 440.211 Å		1.06 Å/pix.
x 416 pix.
= 440.211 Å		1.06 Å/pix.
x 416 pix.
= 440.211 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0582 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0992
Minimum - Maximum-1.1721083 - 1.7947717
Average (Standard dev.)-0.0004985869 (±0.015352613)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 440.2112 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of local refinement map of SARS-CoV-2...

Fileemd_40007_half_map_1.map
AnnotationHalf map of local refinement map of SARS-CoV-2 spike glycoprotein bound to antibody 002-S21B10.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of local refinement map of SARS-CoV-2...

Fileemd_40007_half_map_2.map
AnnotationHalf map of local refinement map of SARS-CoV-2 spike glycoprotein bound to antibody 002-S21B10.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Antibody 002-S21B10 bound to spike glycoprotein trimer

EntireName: Antibody 002-S21B10 bound to spike glycoprotein trimer
Components
  • Complex: Antibody 002-S21B10 bound to spike glycoprotein trimer
    • Complex: Antibody 002-S21B10
    • Complex: Spike glycoprotein trimer

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Supramolecule #1: Antibody 002-S21B10 bound to spike glycoprotein trimer

SupramoleculeName: Antibody 002-S21B10 bound to spike glycoprotein trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: Antibody 002-S21B10

SupramoleculeName: Antibody 002-S21B10 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Spike glycoprotein trimer

SupramoleculeName: Spike glycoprotein trimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
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

Concentration0.7 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClSodium Chloride
2.7 mMKClPotassium Chloride
8.0 mMNa2HPO4Sodium phosphate dibasic
2.0 mMKH2PO4Potassium phosphate monobasic
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 9054 / Average electron dose: 54.37 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1021598
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.85 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 326424
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 4 / Avg.num./class: 255399 / Software - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 100.25 / Target criteria: Correlation coefficient

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