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- EMDB-30919: SARS-CoV2 spike protein with Fab fragment of enhancing antibody (... -

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Basic information

Entry
Database: EMDB / ID: EMD-30919
TitleSARS-CoV2 spike protein with Fab fragment of enhancing antibody (8D2)-3
Map dataSARS-CoV2 spike protein with Fab fragment of enhancing antibody 3
Sample
  • Complex: Apo spike protein trimer of SARS-CoV2 with Fab fragment of enhancing antibody (8D2)-3
    • Complex: SARS-CoV2 spike protein
    • Complex: Fab fragment of enhancing antibody 8D2
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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / 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 / 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 speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.16 Å
AuthorsLiu Y / Soh WT / Kishikawa J / Hirose M / Kato T / Okada M / Arase H
Funding support Japan, 7 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP19fk0108161 Japan
Japan Agency for Medical Research and Development (AMED)JP20nf0101623 Japan
Japan Agency for Medical Research and Development (AMED)JP20nk0101602 Japan
Japan Agency for Medical Research and Development (AMED)JP17am0101108 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP19H04808 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05279 Japan
Japan Society for the Promotion of Science (JSPS)JP19H03478 Japan
CitationJournal: Cell / Year: 2021
Title: An infectivity-enhancing site on the SARS-CoV-2 spike protein targeted by antibodies.
Authors: Yafei Liu / Wai Tuck Soh / Jun-Ichi Kishikawa / Mika Hirose / Emi E Nakayama / Songling Li / Miwa Sasai / Tatsuya Suzuki / Asa Tada / Akemi Arakawa / Sumiko Matsuoka / Kanako Akamatsu / ...Authors: Yafei Liu / Wai Tuck Soh / Jun-Ichi Kishikawa / Mika Hirose / Emi E Nakayama / Songling Li / Miwa Sasai / Tatsuya Suzuki / Asa Tada / Akemi Arakawa / Sumiko Matsuoka / Kanako Akamatsu / Makoto Matsuda / Chikako Ono / Shiho Torii / Kazuki Kishida / Hui Jin / Wataru Nakai / Noriko Arase / Atsushi Nakagawa / Maki Matsumoto / Yukoh Nakazaki / Yasuhiro Shindo / Masako Kohyama / Keisuke Tomii / Koichiro Ohmura / Shiro Ohshima / Toru Okamoto / Masahiro Yamamoto / Hironori Nakagami / Yoshiharu Matsuura / Atsushi Nakagawa / Takayuki Kato / Masato Okada / Daron M Standley / Tatsuo Shioda / Hisashi Arase /
Abstract: Antibodies against the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein prevent SARS-CoV-2 infection. However, the effects of antibodies against other spike protein domains are largely ...Antibodies against the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein prevent SARS-CoV-2 infection. However, the effects of antibodies against other spike protein domains are largely unknown. Here, we screened a series of anti-spike monoclonal antibodies from coronavirus disease 2019 (COVID-19) patients and found that some of antibodies against the N-terminal domain (NTD) induced the open conformation of RBD and thus enhanced the binding capacity of the spike protein to ACE2 and infectivity of SARS-CoV-2. Mutational analysis revealed that all of the infectivity-enhancing antibodies recognized a specific site on the NTD. Structural analysis demonstrated that all infectivity-enhancing antibodies bound to NTD in a similar manner. The antibodies against this infectivity-enhancing site were detected at high levels in severe patients. Moreover, we identified antibodies against the infectivity-enhancing site in uninfected donors, albeit at a lower frequency. These findings demonstrate that not only neutralizing antibodies but also enhancing antibodies are produced during SARS-CoV-2 infection.
History
DepositionJan 22, 2021-
Header (metadata) releaseJun 2, 2021-
Map releaseJun 2, 2021-
UpdateJul 7, 2021-
Current statusJul 7, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30919.png

Downloads & links

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Map

FileDownload / File: emd_30919.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSARS-CoV2 spike protein with Fab fragment of enhancing antibody 3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 440 pix.
= 387.2 Å		0.88 Å/pix.
x 440 pix.
= 387.2 Å		0.88 Å/pix.
x 440 pix.
= 387.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15 / Movie #1: 0.15
Minimum - Maximum-0.26240432 - 0.82380575
Average (Standard dev.)-0.0011632999 (±0.023856591)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 387.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.880.880.88
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z387.200387.200387.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-210-210-210
NX/NY/NZ420420420
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.2620.824-0.001

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Supplemental data

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Mask #1

Fileemd_30919_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: SARS-CoV2 spike protein with Fab fragment of enhancing...

Fileemd_30919_half_map_1.map
AnnotationSARS-CoV2 spike protein with Fab fragment of enhancing antibody 3 half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: SARS-CoV2 spike protein with Fab fragment of enhancing...

Fileemd_30919_half_map_2.map
AnnotationSARS-CoV2 spike protein with Fab fragment of enhancing antibody 3 half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Apo spike protein trimer of SARS-CoV2 with Fab fragment of enhanc...

EntireName: Apo spike protein trimer of SARS-CoV2 with Fab fragment of enhancing antibody (8D2)-3
Components
  • Complex: Apo spike protein trimer of SARS-CoV2 with Fab fragment of enhancing antibody (8D2)-3
    • Complex: SARS-CoV2 spike protein
    • Complex: Fab fragment of enhancing antibody 8D2

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Supramolecule #1: Apo spike protein trimer of SARS-CoV2 with Fab fragment of enhanc...

SupramoleculeName: Apo spike protein trimer of SARS-CoV2 with Fab fragment of enhancing antibody (8D2)-3
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: Expi293F

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Supramolecule #2: SARS-CoV2 spike protein

SupramoleculeName: SARS-CoV2 spike protein / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: Expi293F

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Supramolecule #3: Fab fragment of enhancing antibody 8D2

SupramoleculeName: Fab fragment of enhancing antibody 8D2 / type: complex / ID: 3 / Parent: 1

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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: 8
GridMaterial: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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: BRIGHT FIELD / Cs: 0.059 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2135
CTF correctionSoftware - Name: cryoSPARC (ver. 3.0.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0.1) / Number images used: 74399
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.0.1)
FSC plot (resolution estimation)

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