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Yorodumi- EMDB-30983: Ultrapotent SARS-CoV-2 neutralizing antibodies with protective ef... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30983 | |||||||||
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Title | Ultrapotent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants | |||||||||
Map data | ||||||||||
Sample |
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Keywords | COVID-19 / spike glycoprotein / virus / VIRAL PROTEIN / antibody | |||||||||
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 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Guo H / Li T | |||||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Potent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants. Authors: Tingting Li / Xiaojian Han / Chenjian Gu / Hangtian Guo / Huajun Zhang / Yingming Wang / Chao Hu / Kai Wang / Fengjiang Liu / Feiyang Luo / Yanan Zhang / Jie Hu / Wang Wang / Shenglong Li / ...Authors: Tingting Li / Xiaojian Han / Chenjian Gu / Hangtian Guo / Huajun Zhang / Yingming Wang / Chao Hu / Kai Wang / Fengjiang Liu / Feiyang Luo / Yanan Zhang / Jie Hu / Wang Wang / Shenglong Li / Yanan Hao / Meiying Shen / Jingjing Huang / Yingyi Long / Shuyi Song / Ruixin Wu / Song Mu / Qian Chen / Fengxia Gao / Jianwei Wang / Shunhua Long / Luo Li / Yang Wu / Yan Gao / Wei Xu / Xia Cai / Di Qu / Zherui Zhang / Hongqing Zhang / Na Li / Qingzhu Gao / Guiji Zhang / Changlong He / Wei Wang / Xiaoyun Ji / Ni Tang / Zhenghong Yuan / Youhua Xie / Haitao Yang / Bo Zhang / Ailong Huang / Aishun Jin / Abstract: Accumulating mutations in the SARS-CoV-2 Spike (S) protein can increase the possibility of immune escape, challenging the present COVID-19 prophylaxis and clinical interventions. Here, 3 receptor ...Accumulating mutations in the SARS-CoV-2 Spike (S) protein can increase the possibility of immune escape, challenging the present COVID-19 prophylaxis and clinical interventions. Here, 3 receptor binding domain (RBD) specific monoclonal antibodies (mAbs), 58G6, 510A5 and 13G9, with high neutralizing potency blocking authentic SARS-CoV-2 virus display remarkable efficacy against authentic B.1.351 virus. Surprisingly, structural analysis has revealed that 58G6 and 13G9 both recognize the steric region S on the RBD, overlapping the E484K mutation presented in B.1.351. Also, 58G6 directly binds to another region S in the RBD. Significantly, 58G6 and 510A5 both demonstrate prophylactic efficacy against authentic SARS-CoV-2 and B.1.351 viruses in the transgenic mice expressing human ACE2 (hACE2), protecting weight loss and reducing virus loads. Together, we have evidenced 2 potent neutralizing Abs with unique mechanism targeting authentic SARS-CoV-2 mutants, which can be promising candidates to fulfill the urgent needs for the prolonged COVID-19 pandemic. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30983.map.gz | 483.9 MB | EMDB map data format | |
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Header (meta data) | emd-30983-v30.xml emd-30983.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
Images | emd_30983.png | 35.2 KB | ||
Filedesc metadata | emd-30983.cif.gz | 6.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30983 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30983 | HTTPS FTP |
-Validation report
Summary document | emd_30983_validation.pdf.gz | 522.9 KB | Display | EMDB validaton report |
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Full document | emd_30983_full_validation.pdf.gz | 522.5 KB | Display | |
Data in XML | emd_30983_validation.xml.gz | 8 KB | Display | |
Data in CIF | emd_30983_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30983 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30983 | HTTPS FTP |
-Related structure data
Related structure data | 7e3lMC 7e3kC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30983.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:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : SARS-CoV-2 Spike glycoprotein complex with 58G6 Fab
Entire | Name: SARS-CoV-2 Spike glycoprotein complex with 58G6 Fab |
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Components |
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-Supramolecule #1: SARS-CoV-2 Spike glycoprotein complex with 58G6 Fab
Supramolecule | Name: SARS-CoV-2 Spike glycoprotein complex with 58G6 Fab / type: complex / ID: 1 / 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 / Parent: 1 / Macromolecule list: #1 / Details: SARS-CoV-2 Spike protein ectodomain |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Fab
Supramolecule | Name: 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 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: 142.319219 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 KDGEWVFLST FLSGLEVLFQ GPGGWSHPQF EKGGGSGGGS GGSAWSHPQF EKGGS HHHH HHHH UniProtKB: Spike glycoprotein |
-Macromolecule #2: 58G6 heavy chain
Macromolecule | Name: 58G6 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.557422 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QMQLVQSGPE VKKPGTSVKV SCKASGFTFS SSAVQWVRQA RGQHLEWIGW IVVGSGNTNY AQKFQERVTL TRDMSTRTAY MELSSLRSE DTAVYYCAAP NCNSTTCHDG FDIWGQGTVV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String: QMQLVQSGPE VKKPGTSVKV SCKASGFTFS SSAVQWVRQA RGQHLEWIGW IVVGSGNTNY AQKFQERVTL TRDMSTRTAY MELSSLRSE DTAVYYCAAP NCNSTTCHDG FDIWGQGTVV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKV |
-Macromolecule #3: 58G6 light chain
Macromolecule | Name: 58G6 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.578066 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EIVLTQSPGT LSLSPGERAT LSCRASQSVR SSYLGWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE SEDFAVYYC QQYDNSPWTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String: EIVLTQSPGT LSLSPGERAT LSCRASQSVR SSYLGWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE SEDFAVYYC QQYDNSPWTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 20 / 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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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 108020 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |