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- EMDB-50427: SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein in complex w... -

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Basic information

Entry
Database: EMDB / ID: EMD-50427
TitleSARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein in complex with the single chain fragment scFv76-77
Map dataunsharped map
Sample
  • Complex: SARS-CoV-2 Spike protein in complex with the single chain fragment scFv76-77
    • Complex: SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein
      • Protein or peptide: SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein
    • Complex: scFv76-77 single chain fragment
      • Protein or peptide: scFv76-77 single chain fragment
KeywordsSARS-CoV-2 / Spike / single chain fragment / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBerlinguer M / Chaves-Sanjuan A / Milazzo FM / Minenkova O / De Santis R / Bolognesi M
Funding support Italy, 1 items
OrganizationGrant numberCountry
Other private Italy
CitationJournal: To Be Published
Title: Structure of scFv76-77 in complex with SARS-CoV-2 Omicron Spike protein
Authors: Chaves-Sanjuan A / Bolognesi M
History
DepositionMay 25, 2024-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50427.png

Downloads & links

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Map

FileDownload / File: emd_50427.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharped map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 400 pix.
= 355.6 Å		0.89 Å/pix.
x 400 pix.
= 355.6 Å		0.89 Å/pix.
x 400 pix.
= 355.6 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.889 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.35793203 - 1.4877242
Average (Standard dev.)0.00036511672 (±0.061862353)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 355.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50427_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Additional map: sharped map

Fileemd_50427_additional_1.map
Annotationsharped map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50427_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50427_half_map_2.map
Projections & Slices
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Sample components

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Entire : SARS-CoV-2 Spike protein in complex with the single chain fragmen...

EntireName: SARS-CoV-2 Spike protein in complex with the single chain fragment scFv76-77
Components
  • Complex: SARS-CoV-2 Spike protein in complex with the single chain fragment scFv76-77
    • Complex: SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein
      • Protein or peptide: SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein
    • Complex: scFv76-77 single chain fragment
      • Protein or peptide: scFv76-77 single chain fragment

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Supramolecule #1: SARS-CoV-2 Spike protein in complex with the single chain fragmen...

SupramoleculeName: SARS-CoV-2 Spike protein in complex with the single chain fragment scFv76-77
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 510 KDa

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Supramolecule #2: SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein

SupramoleculeName: SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: scFv76-77 single chain fragment

SupramoleculeName: scFv76-77 single chain fragment / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein

MacromoleculeName: SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
SequenceString: QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHVISRFDN PVLPFNDGVY FASIEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL DVYYHKNNKS WMESEFRVYS SANNCTFEYV SQPFLMDLEG KQGNFKNLRE ...String:
QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHVISRFDN PVLPFNDGVY FASIEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL DVYYHKNNKS WMESEFRVYS SANNCTFEYV SQPFLMDLEG KQGNFKNLRE FVFKNIDGYF KIYSKHTPII VPEDLPQGFS ALEPLVDLPI GINITRFQTL LALHRSSSGW TAGAAAYYVG YLQPRTFLLK YNENGTITDA VDCALDPLSE TKCTLKSFTV EKGIYQTSNF RVQPTESIVR FPNITNLCPF DEVFNATRFA SVYAWNRKRI SNCVADYSVL YNLAPFFTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEVR QIAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDSKVSGN YNYLYRLFRK SNLKPFERDI STEIYQAGNK PCNGVAGFNC YFPLRSYSFR PTYGVGHQPY RVVVLSFELL HAPATV(NAG)CGP KKSTNLVKNK CVNFNFNGLK GTGVLTESNK KFLPFQQFGR DIADTTDAVR DPQTLEILDI TPCSFGGVSV ITPGTNTSNQ VAVLYQGVNC TEVNVFQTRA GCLIGAEYVN NSYECDIPIG AGICASYQTS QSIIAYTMSL GAENSVAYSN NSIAIPTNFT ISVTTEILPV SMTKTSVDCT MYICGDSTEC SNLLLQYGSF CTQLKRALTG IAVEQDKNTQ EVFAQVKQIY KTPPIKYFGG FNFSQILPDP SKSKRSFIED LLFNKVTKFK GLTVLPPLLT DEMIAQYTSA LLAGTITSGW TFGAGAALQI PFAMQMAYRF NGIGVTQNVL YENQKLIANQ FNSAIGKIQD SLSSTASALG KLQDVVNHNA QALNTLVKQL SSKFGAISSV LNDIFSRLDP PEAEVQIDRL ITGRLQSLQT YVTQQLIRAA EIRASANLAA TKMSECVLGQ SKRVDFCGKG YHLMSFPQSA PHGVVFLHVT YVPAQEKNFT TAPAICHDGK AHFPREGVFV SNGTHWFVTQ RNFYEPQIIT TDNTFVSGNC DVVIGIVNNT VYDPLQPELD S

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Macromolecule #2: scFv76-77 single chain fragment

MacromoleculeName: scFv76-77 single chain fragment / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: RTMEEVQLLQ SAGGLVQPG G SLRLSCAA SG FTVSANY MSW VRQAPG KGLE WVSVI YPGGS TFYA DSVKGR FTI SKDNSKN TL YLQMNSLR V EDTAVYYCA RDLSVAGAFD IWGQGTLVT V SSGGGGSG GG GSGGGGS EIV LTQSPG TLSL SPGEK ...String:
RTMEEVQLLQ SAGGLVQPG G SLRLSCAA SG FTVSANY MSW VRQAPG KGLE WVSVI YPGGS TFYA DSVKGR FTI SKDNSKN TL YLQMNSLR V EDTAVYYCA RDLSVAGAFD IWGQGTLVT V SSGGGGSG GG GSGGGGS EIV LTQSPG TLSL SPGEK ATLFC RASQ TFSSNY LAW YQQKPGQ AP SLLIYGGS T RAAGIPDRF SGSGSGTDFT LTINRLEPE D FAIYYCQE YG SSPRVTF GQG TRLEIK RAAA GDYKD DDDKH HHHH H

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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

Concentration0.6 mg/mL
BufferpH: 7 / Details: PBS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4132 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 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: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 615030
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 45441
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC (ver. 3.3.1)

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Atomic model buiding 1

Initial modelPDB ID:

7zce


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: FLEXIBLE FIT

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