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- EMDB-34546: State - I: Spike 2-up RBD with THSC20.HVTR04 (Fab4) -

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Basic information

Entry
Database: EMDB / ID: EMD-34546
TitleState - I: Spike 2-up RBD with THSC20.HVTR04 (Fab4)
Map dataState - I: Spike 2-up RBD with THSC20.HVTR04 (Fab4)
Sample
  • Complex: Wuhan SARS-CoV-2 Spike trimer complex with THSC20.HVTR04 (Fab4) [State I - 2-up RBD]
    • Complex: THSC20.HVTR04 (Fab4)
    • Complex: Wuhan SARS-CoV-2 Spike Protein
KeywordsMonoclonal antibodies / SARS-CoV-2 / Cryo-EM / IMMUNE SYSTEM
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / 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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 (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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Spike glycoprotein / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.54 Å
AuthorsRencilin CF / Ansari MY / Chatterjee A / Deshpande S / Mukherjee S / Singh R / Jayatheertha S / Reddy PM / Das P / Hingankar N ...Rencilin CF / Ansari MY / Chatterjee A / Deshpande S / Mukherjee S / Singh R / Jayatheertha S / Reddy PM / Das P / Hingankar N / Rathore D / Varadarajan R / Bhattacharya J / Dutta S
Funding support India, United States, 4 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/INF/22/SP22844/2017 India
Science and Engineering Research Board (SERB)SERB-EMR/2016/000608 and SERB-IPA/2020/000094 India
Bill & Melinda Gates FoundationINV-030592 United States
Department of Biotechnology (DBT, India)IA/TSG/19/1/600019 India
CitationJournal: RSC Adv / Year: 2025
Title: Cryo-EM reveals conformational variability in the SARS-CoV-2 spike protein RBD induced by two broadly neutralizing monoclonal antibodies.
Authors: Clayton Fernando Rencilin / Arnab Chatterjee / Mohammad Yousuf Ansari / Suprit Deshpande / Sohini Mukherjee / Randhir Singh / Sowrabha B Jayatheertha / Poorvi M Reddy / Nitin Hingankar / ...Authors: Clayton Fernando Rencilin / Arnab Chatterjee / Mohammad Yousuf Ansari / Suprit Deshpande / Sohini Mukherjee / Randhir Singh / Sowrabha B Jayatheertha / Poorvi M Reddy / Nitin Hingankar / Raghavan Varadarajan / Jayanta Bhattacharya / Somnath Dutta /
Abstract: SARS-CoV-2 spike proteins play a critical role in infection by interacting with the ACE2 receptors. Their receptor-binding domains and N-terminal domains exhibit remarkable flexibility and can adopt ...SARS-CoV-2 spike proteins play a critical role in infection by interacting with the ACE2 receptors. Their receptor-binding domains and N-terminal domains exhibit remarkable flexibility and can adopt various conformations that facilitate receptor engagement. Previous structural studies have reported the RBD of the spike protein in "up", "down", and various intermediate states, as well as its different conformational changes during ACE2 binding. This flexibility also influences its interactions with the neutralizing antibodies, yet its role in the antibody complexes remains understudied. In this study, we used cryo-electron microscopy to investigate the structural properties of two broadly neutralizing monoclonal antibodies, THSC20.HVTR04 and THSC20.HVTR26. These antibodies were isolated from an unvaccinated individual and demonstrated potent neutralization of multiple SARS-CoV-2 variants. Our analysis revealed distinct binding characteristics and conformational changes in the spike RBD upon binding with the monoclonal antibodies. The structural characterization of the spike protein-monoclonal antibody complexes provided valuable insights into the structural variability of the spike protein and the possible mechanisms for antibody-mediated neutralization.
History
DepositionOct 22, 2022-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_34546.png

Downloads & links

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Map

FileDownload / File: emd_34546.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationState - I: Spike 2-up RBD with THSC20.HVTR04 (Fab4)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.92 Å/pix.
x 336 pix.
= 309.12 Å		0.92 Å/pix.
x 336 pix.
= 309.12 Å		0.92 Å/pix.
x 336 pix.
= 309.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.29
Minimum - Maximum-14.274177999999999 - 26.441668
Average (Standard dev.)0.000000000003961 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 309.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: State - I: Spike 2-up RBD with THSC20.HVTR04 (Fab4): Half-map1

Fileemd_34546_half_map_1.map
AnnotationState - I: Spike 2-up RBD with THSC20.HVTR04 (Fab4): Half-map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: State - I: Spike 2-up RBD with THSC20.HVTR04 (Fab4): Half-map2

Fileemd_34546_half_map_2.map
AnnotationState - I: Spike 2-up RBD with THSC20.HVTR04 (Fab4): Half-map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Wuhan SARS-CoV-2 Spike trimer complex with THSC20.HVTR04 (Fab4) [...

EntireName: Wuhan SARS-CoV-2 Spike trimer complex with THSC20.HVTR04 (Fab4) [State I - 2-up RBD]
Components
  • Complex: Wuhan SARS-CoV-2 Spike trimer complex with THSC20.HVTR04 (Fab4) [State I - 2-up RBD]
    • Complex: THSC20.HVTR04 (Fab4)
    • Complex: Wuhan SARS-CoV-2 Spike Protein

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Supramolecule #1: Wuhan SARS-CoV-2 Spike trimer complex with THSC20.HVTR04 (Fab4) [...

SupramoleculeName: Wuhan SARS-CoV-2 Spike trimer complex with THSC20.HVTR04 (Fab4) [State I - 2-up RBD]
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #2: THSC20.HVTR04 (Fab4)

SupramoleculeName: THSC20.HVTR04 (Fab4) / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Wuhan SARS-CoV-2 Spike Protein

SupramoleculeName: Wuhan SARS-CoV-2 Spike Protein / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: Wuhan

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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 TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.75 µm / Nominal defocus min: 1.25 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

31100

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 163492
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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