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Yorodumi- EMDB-34687: SARS-CoV-2 Spike trimer in complex with RmAb 9H1 Fab in the class... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34687 | |||||||||
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Title | SARS-CoV-2 Spike trimer in complex with RmAb 9H1 Fab in the class 2 conformation | |||||||||
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 / 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 / symbiont-mediated suppression of host innate immune response / 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 / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 / Oryctolagus cuniculus (rabbit) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 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_34687.map.gz | 483.9 MB | EMDB map data format | |
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Header (meta data) | emd-34687-v30.xml emd-34687.xml | 18.5 KB 18.5 KB | Display Display | EMDB header |
Images | emd_34687.png | 34.5 KB | ||
Others | emd_34687_half_map_1.map.gz emd_34687_half_map_2.map.gz | 475.7 MB 475.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34687 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34687 | HTTPS FTP |
-Validation report
Summary document | emd_34687_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_34687_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_34687_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | emd_34687_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34687 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34687 | HTTPS FTP |
-Related structure data
Related structure data | 8hecMC 8hebC 8hedC 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_34687.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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_34687_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34687_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 complex with RmAb 9H1 Fabs
Entire | Name: SARS-CoV-2 WT spike glycoprotein complex with RmAb 9H1 Fabs |
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Components |
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-Supramolecule #1: SARS-CoV-2 WT spike glycoprotein complex with RmAb 9H1 Fabs
Supramolecule | Name: SARS-CoV-2 WT spike glycoprotein complex with RmAb 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: spike glycoprotein
Supramolecule | Name: spike glycoprotein / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1 / Details: SARS-CoV-2 WT spike protein ectodomain |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-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 glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 133.75325 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF ...String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRDLPQ GFSALEPLVD LPIGINITRF QT LLALHRS YLTPGDSSSG WTAGAAAYYV GYLQPRTFLL KYNENGTITD AVDCALDPLS ETKCTLKSFT VEKGIYQTSN FRV QPTESI VRFPNITNLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNVY ADSF VIRGD EVRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYLYRL FRKSNLKPFE RDISTEIYQA GSTPC NGVE GFNCYFPLQS YGFQPTNGVG YQPYRVVVLS FELLHAPATV CGPKKSTNLV KNKCVNFNFN GLTGTGVLTE SNKKFL PFQ QFGRDIADTT DAVRDPQTLE ILDITPCSFG GVSVITPGTN TSNQVAVLYQ DVNCTEVPVA IHADQLTPTW RVYSTGS NV FQTRAGCLIG AEHVNNSYEC DIPIGAGICA SYQTQTNSPG SASSVASQSI IAYTMSLGAE NSVAYSNNSI AIPTNFTI S VTTEILPVSM TKTSVDCTMY ICGDSTECSN LLLQYGSFCT QLNRALTGIA VEQDKNTQEV FAQVKQIYKT PPIKDFGGF NFSQILPDPS KPSKRSFIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFG AGAALQIPFA MQMAYRFNGI GVTQNVLYEN QKLIANQFNS AIGKIQDSLS STASALGKLQ DVVNQNAQAL N TLVKQLSS NFGAISSVLN DILSRLDPPE AEVQIDRLIT GRLQSLQTYV TQQLIRAAEI RASANLAATK MSECVLGQSK RV DFCGKGY HLMSFPQSAP HGVVFLHVTY VPAQEKNFTT APAICHDGKA HFPREGVFVS NGTHWFVTQR NFYEPQIITT DNT FVSGNC DVVIGIVNNT VYDPLQPELD SFKEELDKYF KNHTSPDVDL GDISGINASV VNIQKEIDRL NEVAKNLNES LIDL QELGK YEQ |
-Macromolecule #2: rabbit antibody 9H1 light chain
Macromolecule | Name: rabbit antibody 9H1 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / 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: 3 / 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: 27 / 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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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 119309 |
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Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |