[English] 日本語
Yorodumi- EMDB-30635: S-3C1-F3b structure, all the three RBDs are in the up conformatio... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30635 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | S-3C1-F3b structure, all the three RBDs are in the up conformation and each of them associates with a 3C1 Fab | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | VIRAL PROTEIN | |||||||||
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 | Mus musculus (house mouse) / Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
Authors | Cong Y / Liu CX | |||||||||
Funding support | China, 1 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Development and structural basis of a two-MAb cocktail for treating SARS-CoV-2 infections. Authors: Chao Zhang / Yifan Wang / Yuanfei Zhu / Caixuan Liu / Chenjian Gu / Shiqi Xu / Yalei Wang / Yu Zhou / Yanxing Wang / Wenyu Han / Xiaoyu Hong / Yong Yang / Xueyang Zhang / Tingfeng Wang / ...Authors: Chao Zhang / Yifan Wang / Yuanfei Zhu / Caixuan Liu / Chenjian Gu / Shiqi Xu / Yalei Wang / Yu Zhou / Yanxing Wang / Wenyu Han / Xiaoyu Hong / Yong Yang / Xueyang Zhang / Tingfeng Wang / Cong Xu / Qin Hong / Shutian Wang / Qiaoyu Zhao / Weihua Qiao / Jinkai Zang / Liangliang Kong / Fangfang Wang / Haikun Wang / Di Qu / Dimitri Lavillette / Hong Tang / Qiang Deng / Youhua Xie / Yao Cong / Zhong Huang / Abstract: The ongoing pandemic of coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Neutralizing antibodies against SARS-CoV-2 are an option for ...The ongoing pandemic of coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Neutralizing antibodies against SARS-CoV-2 are an option for drug development for treating COVID-19. Here, we report the identification and characterization of two groups of mouse neutralizing monoclonal antibodies (MAbs) targeting the receptor-binding domain (RBD) on the SARS-CoV-2 spike (S) protein. MAbs 2H2 and 3C1, representing the two antibody groups, respectively, bind distinct epitopes and are compatible in formulating a noncompeting antibody cocktail. A humanized version of the 2H2/3C1 cocktail is found to potently neutralize authentic SARS-CoV-2 infection in vitro with half inhibitory concentration (IC50) of 12 ng/mL and effectively treat SARS-CoV-2-infected mice even when administered at as late as 24 h post-infection. We determine an ensemble of cryo-EM structures of 2H2 or 3C1 Fab in complex with the S trimer up to 3.8 Å resolution, revealing the conformational space of the antigen-antibody complexes and MAb-triggered stepwise allosteric rearrangements of the S trimer, delineating a previously uncharacterized dynamic process of coordinated binding of neutralizing antibodies to the trimeric S protein. Our findings provide important information for the development of MAb-based drugs for preventing and treating SARS-CoV-2 infections. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30635.map.gz | 26.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-30635-v30.xml emd-30635.xml | 16.1 KB 16.1 KB | Display Display | EMDB header |
Images | emd_30635.png | 112.4 KB | ||
Filedesc metadata | emd-30635.cif.gz | 6.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30635 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30635 | HTTPS FTP |
-Validation report
Summary document | emd_30635_validation.pdf.gz | 357.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_30635_full_validation.pdf.gz | 356.7 KB | Display | |
Data in XML | emd_30635_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | emd_30635_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30635 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30635 | HTTPS FTP |
-Related structure data
Related structure data | 7dccMC 7dcxC 7dd2C 7dd8C 7dddC 7ddnC 7dk4C 7dk5C 7dk6C 7dk7C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_30635.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.02 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Complex of SARC-CoV2-S protein with 3C1 fab, all the three RBDs a...
Entire | Name: Complex of SARC-CoV2-S protein with 3C1 fab, all the three RBDs are in the up conformation and each of them associates with a 3C1 Fab |
---|---|
Components |
|
-Supramolecule #1: Complex of SARC-CoV2-S protein with 3C1 fab, all the three RBDs a...
Supramolecule | Name: Complex of SARC-CoV2-S protein with 3C1 fab, all the three RBDs are in the up conformation and each of them associates with a 3C1 Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) |
-Supramolecule #2: 3C1 fab with a heavy chain and a light chain
Supramolecule | Name: 3C1 fab with a heavy chain and a light chain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #3 |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #3: SARC-CoV2-S protein
Supramolecule | Name: SARC-CoV2-S protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
---|
-Macromolecule #1: The heavy chain of 3C1 fab
Macromolecule | Name: The heavy chain of 3C1 fab / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) / Strain: Balb/c |
Molecular weight | Theoretical: 24.151785 KDa |
Sequence | String: EVQLQESGPS LVKPSQTLSL TCSVTGDSIT NGYWNWIRKF PGNKLEYMGY ISYSGSTYYS PSLKSRISIT RDTSKNQHYL QLNSVTSED TATYYCASDY HGSKYYFDYW GQGTTLTVSS AKTTPPSVYP LAPGSAAQTN SMVTLGCLVK GYFPEPVTVT W NSGSLSSG ...String: EVQLQESGPS LVKPSQTLSL TCSVTGDSIT NGYWNWIRKF PGNKLEYMGY ISYSGSTYYS PSLKSRISIT RDTSKNQHYL QLNSVTSED TATYYCASDY HGSKYYFDYW GQGTTLTVSS AKTTPPSVYP LAPGSAAQTN SMVTLGCLVK GYFPEPVTVT W NSGSLSSG VHTFPAVLQS DLYTLSSSVT VPSSTWPSET VTCNVAHPAS STKVDKKIVP RDCG |
-Macromolecule #2: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 140.055906 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 YEQGSGYIPE APRDGQAYVR KDGEWVLLST FLENLYFQGD YKDDDDKHHH HHHHHH UniProtKB: Spike glycoprotein |
-Macromolecule #3: The light chain of 3C1 fab
Macromolecule | Name: The light chain of 3C1 fab / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) / Strain: Balb/c |
Molecular weight | Theoretical: 23.89133 KDa |
Sequence | String: DIVMTQSHKF MSTSVGHRVS ITCKASQDVG NDVAWYQQKP GQSPKLLIYW ASTRHTGVPD RFTGSGSGTD FTLTISNVQS EDLADYFCQ QYNRYPYTFG GGTKLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String: DIVMTQSHKF MSTSVGHRVS ITCKASQDVG NDVAWYQQKP GQSPKLLIYW ASTRHTGVPD RFTGSGSGTD FTLTISNVQS EDLADYFCQ QYNRYPYTFG GGTKLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNEC |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Grid | Model: Quantifoil / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. Details: To handle the potential preferred orientation problem, for sample frozen using holey carbon grid, 0.05% Octyl beta-D-glucopyranoside (Sigma) or 0.1% polylysine (Polysciences) was added into ...Details: To handle the potential preferred orientation problem, for sample frozen using holey carbon grid, 0.05% Octyl beta-D-glucopyranoside (Sigma) or 0.1% polylysine (Polysciences) was added into the sample or applied on grid before freezing, respectively. | ||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 6.45 sec. / Average electron dose: 49.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: RANDOM CONICAL TILT |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71057 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |