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- EMDB-32719: Local CryoEM structure of the SARS-CoV S2P in complex with BD55-3... -

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Basic information

Entry
Database: EMDB / ID: EMD-32719
TitleLocal CryoEM structure of the SARS-CoV S2P in complex with BD55-3152 Fab
Map data
Sample
  • Complex: the SARS-CoV S2P in complex with BD55-3152 Fab
    • Protein or peptide: BD55-3152H
    • Protein or peptide: BD55-3152L
    • Protein or peptide: Spike protein S1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsantibody / complex / VIRAL PROTEIN
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / identical protein binding / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsDu S / Xiao JY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Local CryoEM structure of the SARS-CoV S2P in complex with BD55-3152 Fab
Authors: Du S / Xiao JY
History
DepositionJan 26, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32719.png

Downloads & links

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Map

FileDownload / File: emd_32719.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 360 pix.
= 374.4 Å		1.04 Å/pix.
x 360 pix.
= 374.4 Å		1.04 Å/pix.
x 360 pix.
= 374.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.246
Minimum - Maximum-1.5020455 - 2.2522805
Average (Standard dev.)0.00013212 (±0.032151084)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 374.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : the SARS-CoV S2P in complex with BD55-3152 Fab

EntireName: the SARS-CoV S2P in complex with BD55-3152 Fab
Components
  • Complex: the SARS-CoV S2P in complex with BD55-3152 Fab
    • Protein or peptide: BD55-3152H
    • Protein or peptide: BD55-3152L
    • Protein or peptide: Spike protein S1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: the SARS-CoV S2P in complex with BD55-3152 Fab

SupramoleculeName: the SARS-CoV S2P in complex with BD55-3152 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: BD55-3152H

MacromoleculeName: BD55-3152H / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.819539 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSLILLFL VAVATRVLSQ VQLVQSGAEV KKPGASVIVS CKASGYRFIS HYIHWVRQAP GQGLEWMGKI DPSGRGTTYA QKLQGRVSV TRDTSTSSVY MALSGLRSDD TAVYYCARDR FPLSDPYVWG SPLGGLDVWG QGTTVIVSSA STKGPSVFPL A PSSKSTSG ...String:
MGWSLILLFL VAVATRVLSQ VQLVQSGAEV KKPGASVIVS CKASGYRFIS HYIHWVRQAP GQGLEWMGKI DPSGRGTTYA QKLQGRVSV TRDTSTSSVY MALSGLRSDD TAVYYCARDR FPLSDPYVWG SPLGGLDVWG QGTTVIVSSA STKGPSVFPL A PSSKSTSG GTAALGCLVK DYFPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NT KVDKKVE PKSCDKTHHH HHH

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Macromolecule #2: BD55-3152L

MacromoleculeName: BD55-3152L / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.830543 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSS YDLTQPPSVS VSPGQTARIT CSGDALPSQY VYWYQQRPGQ APVLVMYKDS ERPPGIPERF SGSTSGTTA TLTITGVQAE DEADYYCQSA DASTTYHVFG GGTKVTVVGQ PKAAPSVTLF PPSSEELQAN KATLVCLISD F YPGAVTVA ...String:
MGWSCIILFL VATATGVHSS YDLTQPPSVS VSPGQTARIT CSGDALPSQY VYWYQQRPGQ APVLVMYKDS ERPPGIPERF SGSTSGTTA TLTITGVQAE DEADYYCQSA DASTTYHVFG GGTKVTVVGQ PKAAPSVTLF PPSSEELQAN KATLVCLISD F YPGAVTVA WKADSSPVKA GVETTTPSKQ SNNKYAASSY LSLTPEQWKS HRSYSCQVTH EGSTVEKTVA PTECS

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Macromolecule #3: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus
Molecular weightTheoretical: 20.523072 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
CPFGEVFNAT KFPSVYAWER KKISNCVADY SVLYNSTFFS TFKCYGVSAT KLNDLCFSNV YADSFVVKGD DVRQIAPGQT GVIADYNYK LPDDFMGCVL AWNTRNIDAT STGNYNYKYR YLRHGKLRPF ERDISNVPFS PDGKPCTPPA LNCYWPLNDY G FYTTTGIG YQPYRVVVLS FE

UniProtKB: Spike glycoprotein

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k 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: DARK FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 222513
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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