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Yorodumi- EMDB-34688: Local refinement of the SARS-CoV-2 Spike trimer in complex with R... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34688 | |||||||||
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Title | Local refinement of the SARS-CoV-2 Spike trimer in complex with RmAb 9H1 Fab | |||||||||
Map data | ||||||||||
Sample |
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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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / 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 / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 / Oryctolagus cuniculus (rabbit) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.59 Å | |||||||||
Authors | Guo H / Gao Y / Lu Y / Yang H / Ji X | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34688.map.gz | 483.6 MB | EMDB map data format | |
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Header (meta data) | emd-34688-v30.xml emd-34688.xml | 17.5 KB 17.5 KB | Display Display | EMDB header |
Images | emd_34688.png | 24.8 KB | ||
Others | emd_34688_half_map_1.map.gz emd_34688_half_map_2.map.gz | 475.7 MB 475.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34688 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34688 | HTTPS FTP |
-Related structure data
Related structure data | 8hedMC 8hebC 8hecC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34688.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34688_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34688_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 WT spike glycoprotein RBD complex with 9H1 Fabs
Entire | Name: SARS-CoV-2 WT spike glycoprotein RBD complex with 9H1 Fabs |
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Components |
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-Supramolecule #1: SARS-CoV-2 WT spike glycoprotein RBD complex with 9H1 Fabs
Supramolecule | Name: SARS-CoV-2 WT spike glycoprotein RBD complex with 9H1 Fabs type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #2: SARS-CoV-2 spike glycoprotein RBD
Supramolecule | Name: SARS-CoV-2 spike glycoprotein RBD / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1 Details: SARS-CoV-2 WT spike protein receptor-binding domain |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
-Supramolecule #3: 9H1 Fab
Supramolecule | Name: 9H1 Fab / type: complex / ID: 3 / Chimera: Yes / 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
Macromolecule | Name: Spike protein S1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 22.446193 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: rabbit antibody 9H1 light chain
Macromolecule | Name: rabbit antibody 9H1 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Molecular weight | Theoretical: 11.65484 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVLTQTPSSV SAAVGGTVTI NCQASEDIYD NLVWYQQKPG QPPKLLIYDA STLAFGVSSR FRGSGSGTHF TLTMRDVQCD DAATYYCQG EFSCSSGDCT AFGGGTEVVV K |
-Macromolecule #3: rabbit antibody 9H1 heavy chain
Macromolecule | Name: rabbit antibody 9H1 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Molecular weight | Theoretical: 12.556056 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QSVEESGGRL VTPGTPLTLT CTVSGFSLSR YAMSWVRQAP GKGLEWIGII VDSGHTAYAS WAKGRFTISR TSTTVDLKMT SLTTEDTAT YFCARETGGG AFYVFEFWGP GTVVTVSS |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 1 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: COMMON LINE |
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Final angle assignment | Type: COMMON LINE |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 111153 |