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- EMDB-33551: Interface of SARS-CoV-2 WT Spike in complex with R15 Fab and P14 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-33551
TitleInterface of SARS-CoV-2 WT Spike in complex with R15 Fab and P14 Nanobody
Map data
Sample
  • Complex: Complex of SARS-CoV-2 Spike in complex with R15-F7 and P14-F18-35
    • Complex: SARS-CoV-2 Spike
      • Protein or peptide: Spike protein S1
    • Complex: R15
      • Protein or peptide: heavy chain of R15
      • Protein or peptide: light chain of R15
    • Complex: P14
      • Protein or peptide: P14 nanobody
  • Ligand: water
KeywordsSARS-CoV-2 / spike / bispecific antibody / SYZJ001 / R15-F7 / P14-F8-35 / STRUCTURAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / 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 / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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 (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human) / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsWang L / Zhu L
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: SARS-CoV-2 WT Spike in complex with R15 Fab and P14 Nanobody
Authors: Wang L
History
DepositionJun 5, 2022-
Header (metadata) releaseSep 6, 2023-
Map releaseSep 6, 2023-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33551.png

Downloads & links

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Map

FileDownload / File: emd_33551.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.)
1.07 Å/pix.
x 360 pix.
= 385.2 Å		1.07 Å/pix.
x 360 pix.
= 385.2 Å		1.07 Å/pix.
x 360 pix.
= 385.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 24.0
Minimum - Maximum-78.766814999999994 - 113.685005000000004
Average (Standard dev.)0.042347565 (±1.426402)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 385.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33551_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33551_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 : Complex of SARS-CoV-2 Spike in complex with R15-F7 and P14-F18-35

EntireName: Complex of SARS-CoV-2 Spike in complex with R15-F7 and P14-F18-35
Components
  • Complex: Complex of SARS-CoV-2 Spike in complex with R15-F7 and P14-F18-35
    • Complex: SARS-CoV-2 Spike
      • Protein or peptide: Spike protein S1
    • Complex: R15
      • Protein or peptide: heavy chain of R15
      • Protein or peptide: light chain of R15
    • Complex: P14
      • Protein or peptide: P14 nanobody
  • Ligand: water

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Supramolecule #1: Complex of SARS-CoV-2 Spike in complex with R15-F7 and P14-F18-35

SupramoleculeName: Complex of SARS-CoV-2 Spike in complex with R15-F7 and P14-F18-35
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #2: SARS-CoV-2 Spike

SupramoleculeName: SARS-CoV-2 Spike / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: R15

SupramoleculeName: R15 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Vicugna pacos (alpaca)

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Supramolecule #4: P14

SupramoleculeName: P14 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4

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Macromolecule #1: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 21.772391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NLCPFGEVFN ATRFASVYAW NRKRISNCVA DYSVLYNSAS FSTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGKIADYN YKLPDDFTGC VIAWNSNNLD SKVGGNYNYL YRLFRKSNLK PFERDISTEI YQAGSTPCNG VEGFNCYFPL Q SYGFQPTN ...String:
NLCPFGEVFN ATRFASVYAW NRKRISNCVA DYSVLYNSAS FSTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGKIADYN YKLPDDFTGC VIAWNSNNLD SKVGGNYNYL YRLFRKSNLK PFERDISTEI YQAGSTPCNG VEGFNCYFPL Q SYGFQPTN GVGYQPYRVV VLSFELLHAP ATVCGP

UniProtKB: Spike glycoprotein

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Macromolecule #2: heavy chain of R15

MacromoleculeName: heavy chain of R15 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.638069 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QMQLVQSGAE VKKPGASVKV SCKASGYTFT SYAISWVRQA PGQGLEWMGR IIPILGIANY AQKFQGRVTI TADESTSTAY MELSSRSED TAVYYCASGA FYYGSGSYPF DYWGQGT

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Macromolecule #3: light chain of R15

MacromoleculeName: light chain of R15 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.675858 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GDIQLTQSPS SLSASVGDRV TITCRASQDI SDYLNWYQQK PGKAPKLLIY AASSLQSGVP SRFSGSGSGT DFTLTISNLQ PEDFATYYC QQSYSAPRTF GQGTKVEIK

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Macromolecule #4: P14 nanobody

MacromoleculeName: P14 nanobody / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 13.461807 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EEQLVESGGG LVQPGGSLRL SCAASGFRFG SYYMSWVRQA PGKAPEWVSD INTRGETTRY SDSVKGRFTI ARDNANNTVF LFMNRLKPE DTAVYYCAVA ASGDTFEGRS DPDYWGQGTL VTVS

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 18 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 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: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 372940
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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