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- EMDB-34688: Local refinement of the SARS-CoV-2 Spike trimer in complex with R... -

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Entry
Database: EMDB / ID: EMD-34688
TitleLocal refinement of the SARS-CoV-2 Spike trimer in complex with RmAb 9H1 Fab
Map data
Sample
  • Complex: SARS-CoV-2 WT spike glycoprotein RBD complex with 9H1 Fabs
    • Complex: SARS-CoV-2 spike glycoprotein RBD
      • Protein or peptide: Spike protein S1
    • Complex: 9H1 Fab
      • Protein or peptide: rabbit antibody 9H1 light chain
      • Protein or peptide: rabbit antibody 9H1 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsVIRAL PROTEIN-IMMUNE SYSTEM COMPLEX
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
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsGuo H / Gao Y / Lu Y / Yang H / Ji X
Funding support China, 1 items
OrganizationGrant numberCountry
Other government China
CitationJournal: Biochem Biophys Res Commun / Year: 2023
Title: Mechanism of an RBM-targeted rabbit monoclonal antibody 9H1 neutralizing SARS-CoV-2.
Authors: Xiaoyu Chu / Xinyu Ding / Yixuan Yang / Yuchi Lu / Tinghan Li / Yan Gao / Le Zheng / Hang Xiao / Tingting Yang / Hao Cheng / Haibin Huang / Yang Liu / Yang Lou / Chao Wu / Yuxin Chen / ...Authors: Xiaoyu Chu / Xinyu Ding / Yixuan Yang / Yuchi Lu / Tinghan Li / Yan Gao / Le Zheng / Hang Xiao / Tingting Yang / Hao Cheng / Haibin Huang / Yang Liu / Yang Lou / Chao Wu / Yuxin Chen / Haitao Yang / Xiaoyun Ji / Hangtian Guo /
Abstract: The COVID-19 pandemic, caused by SARS-CoV-2, has led to over 750 million infections and 6.8 million deaths worldwide since late 2019. Due to the continuous evolution of SARS-CoV-2, many significant ...The COVID-19 pandemic, caused by SARS-CoV-2, has led to over 750 million infections and 6.8 million deaths worldwide since late 2019. Due to the continuous evolution of SARS-CoV-2, many significant variants have emerged, creating ongoing challenges to the prevention and treatment of the pandemic. Therefore, the study of antibody responses against SARS-CoV-2 is essential for the development of vaccines and therapeutics. Here we perform single particle cryo-electron microscopy (cryo-EM) structure determination of a rabbit monoclonal antibody (RmAb) 9H1 in complex with the SARS-CoV-2 wild-type (WT) spike trimer. Our structural analysis shows that 9H1 interacts with the receptor-binding motif (RBM) region of the receptor-binding domain (RBD) on the spike protein and by directly competing with angiotensin-converting enzyme 2 (ACE2), it blocks the binding of the virus to the receptor and achieves neutralization. Our findings suggest that utilizing rabbit-derived mAbs provides valuable insights into the molecular interactions between neutralizing antibodies and spike proteins and may also facilitate the development of therapeutic antibodies and expand the antibody library.
History
DepositionNov 8, 2022-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34688.png

Downloads & links

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Map

FileDownload / File: emd_34688.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.82 Å
Density
Contour LevelBy AUTHOR: 0.4026
Minimum - Maximum-0.80478984 - 2.3823907
Average (Standard dev.)-0.0022630235 (±0.021800168)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 419.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34688_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_34688_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 : SARS-CoV-2 WT spike glycoprotein RBD complex with 9H1 Fabs

EntireName: SARS-CoV-2 WT spike glycoprotein RBD complex with 9H1 Fabs
Components
  • Complex: SARS-CoV-2 WT spike glycoprotein RBD complex with 9H1 Fabs
    • Complex: SARS-CoV-2 spike glycoprotein RBD
      • Protein or peptide: Spike protein S1
    • Complex: 9H1 Fab
      • Protein or peptide: rabbit antibody 9H1 light chain
      • Protein or peptide: rabbit antibody 9H1 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV-2 WT spike glycoprotein RBD complex with 9H1 Fabs

SupramoleculeName: SARS-CoV-2 WT spike glycoprotein RBD complex with 9H1 Fabs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #2: SARS-CoV-2 spike glycoprotein RBD

SupramoleculeName: SARS-CoV-2 spike glycoprotein RBD / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Details: SARS-CoV-2 WT spike protein receptor-binding domain
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Supramolecule #3: 9H1 Fab

SupramoleculeName: 9H1 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Details: Fab fragment generated by proteolytic cleavage of IgG antibody

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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: 22.446193 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NITNLCPFGE VFNATRFASV YAWNRKRISN CVADYSVLYN SASFSTFKCY GVSPTKLNDL CFTNVYADSF VIRGDEVRQI APGQTGKIA DYNYKLPDDF TGCVIAWNSN NLDSKVGGNY NYLYRLFRKS NLKPFERDIS TEIYQAGSTP CNGVEGFNCY F PLQSYGFQ ...String:
NITNLCPFGE VFNATRFASV YAWNRKRISN CVADYSVLYN SASFSTFKCY GVSPTKLNDL CFTNVYADSF VIRGDEVRQI APGQTGKIA DYNYKLPDDF TGCVIAWNSN NLDSKVGGNY NYLYRLFRKS NLKPFERDIS TEIYQAGSTP CNGVEGFNCY F PLQSYGFQ PTNGVGYQPY RVVVLSFELL HAPATVCGPK KS

UniProtKB: Spike glycoprotein

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Macromolecule #2: rabbit antibody 9H1 light chain

MacromoleculeName: rabbit antibody 9H1 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 11.65484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVLTQTPSSV SAAVGGTVTI NCQASEDIYD NLVWYQQKPG QPPKLLIYDA STLAFGVSSR FRGSGSGTHF TLTMRDVQCD DAATYYCQG EFSCSSGDCT AFGGGTEVVV K

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Macromolecule #3: rabbit antibody 9H1 heavy chain

MacromoleculeName: rabbit antibody 9H1 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 12.556056 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVEESGGRL VTPGTPLTLT CTVSGFSLSR YAMSWVRQAP GKGLEWIGII VDSGHTAYAS WAKGRFTISR TSTTVDLKMT SLTTEDTAT YFCARETGGG AFYVFEFWGP GTVVTVSS

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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: 7.4
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: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 111153
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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