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- EMDB-12085: Cryo-EM map of the SARS-CoV-2 spike protein in complex with sybod... -

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Basic information

Entry
Database: EMDB / ID: EMD-12085
TitleCryo-EM map of the SARS-CoV-2 spike protein in complex with sybody#68 in a 2up/1flexible conformation.
Map data
SampleSARS-CoV-2 spike protein in complex with sybody#68:
(SARS-CoV-2 spike ...) x 2 / (sybody#68) x 2
Biological speciesSevere acute respiratory syndrome coronavirus 2 / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.76 Å
AuthorsWalter JD / Hutter CAJ / Garaeva AA / Scherer M / Zimmermann I / Wyss M / Rheinberger J / Ruedin Y / Earp JC / Egloff P ...Walter JD / Hutter CAJ / Garaeva AA / Scherer M / Zimmermann I / Wyss M / Rheinberger J / Ruedin Y / Earp JC / Egloff P / Sorgenfrei M / Huerlimann LM / Gonda I / Meier G / Remm S / Thavarasah S / Zimmer G / Slotboom DJ / Paulino C / Plattet P / Seeger MA
Funding support Netherlands, Switzerland, 3 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)722.017.001 Netherlands
Swiss National Science Foundation4078P0_198314 Switzerland
Netherlands Organisation for Scientific Research (NWO)740.018.016 Netherlands
CitationJournal: bioRxiv / Year: 2020
Title: Highly potent bispecific sybodies neutralize SARS-CoV-2
Authors: Walter JD / Hutter CAJ / Garaeva AA / Scherer M / Zimmermann I / Wyss M / Rheinberger J / Ruedin Y / Earp JC / Egloff P / Sorgenfrei M / Huerlimann LM / Gonda I / Meier G / Remm S / ...Authors: Walter JD / Hutter CAJ / Garaeva AA / Scherer M / Zimmermann I / Wyss M / Rheinberger J / Ruedin Y / Earp JC / Egloff P / Sorgenfrei M / Huerlimann LM / Gonda I / Meier G / Remm S / Thavarasah S / Zimmer G / Slotboom DJ / Paulino C / Plattet P / Seeger MA
Validation ReportSummary, Full report, XML, About validation report
History
DepositionDec 10, 2020-
Header (metadata) releaseDec 23, 2020-
Map releaseDec 23, 2020-
UpdateDec 23, 2020-
Current statusDec 23, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.024
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.024
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_12085.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.)
1.01 Å/pix.
x 400 pix.
= 404.8 Å
1.01 Å/pix.
x 400 pix.
= 404.8 Å
1.01 Å/pix.
x 400 pix.
= 404.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.012 Å
Density
Contour LevelBy AUTHOR: 0.024 / Movie #1: 0.024
Minimum - Maximum-0.038466237 - 0.08610039
Average (Standard dev.)-6.9298796e-05 (±0.0031536596)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 404.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0121.0121.012
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z404.800404.800404.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0380.086-0.000

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Supplemental data

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Segmentation: #1

Fileemd_12085_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: half-map 2 used for post processing step and...

Fileemd_12085_half_map_1.map
Annotationhalf-map 2 used for post processing step and FSC resolution calculation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: half-map 1 used for post processing step and...

Fileemd_12085_half_map_2.map
Annotationhalf-map 1 used for post processing step and FSC resolution calculation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire SARS-CoV-2 spike protein in complex with sybody#68

EntireName: SARS-CoV-2 spike protein in complex with sybody#68 / Number of components: 5

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Component #1: protein, SARS-CoV-2 spike protein in complex with sybody#68

ProteinName: SARS-CoV-2 spike protein in complex with sybody#68 / Recombinant expression: No

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Component #2: protein, SARS-CoV-2 spike protein

ProteinName: SARS-CoV-2 spike protein / Recombinant expression: No
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, sybody#68

ProteinName: sybody#68 / Recombinant expression: No
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: synthetic construct (others)

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Component #4: protein, SARS-CoV-2 spike protein

ProteinName: SARS-CoV-2 spike protein / Recombinant expression: No
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, sybody#68

ProteinName: sybody#68 / Recombinant expression: No
SourceSpecies: synthetic construct (others)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.75 mg/mL / Buffer solution: 2 mM Tris-HCl pH 8.0, 200 mM NaCl / pH: 8
Support filmat 5mA
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: OTHER / Temperature: 288 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 53 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 130000 X (nominal), 49407 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 300.0 - 2000.0 nm / Energy filter: GIF Bioquantum
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: (90.0 - 105.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 5109

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 24325
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 4.76 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 6X2B, 5M13

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