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Yorodumi- EMDB-34742: SARS-CoV-2 spike in complex with neutralizing antibody NIV-11 foc... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34742 | |||||||||||||||||||||||||||||||||
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Title | SARS-CoV-2 spike in complex with neutralizing antibody NIV-11 focused on RBD and NIV-11 interface | |||||||||||||||||||||||||||||||||
Map data | 0.16 | |||||||||||||||||||||||||||||||||
Sample |
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Keywords | Complex / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||||||||||||||||||||||||||
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 / 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 / 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: 3.4 Å | |||||||||||||||||||||||||||||||||
Authors | Moriyama S / Anraku Y / Muranishi S / Adachi Y / Kuroda D / Higuchi Y / Kotaki R / Tonouchi K / Yumoto K / Suzuki T ...Moriyama S / Anraku Y / Muranishi S / Adachi Y / Kuroda D / Higuchi Y / Kotaki R / Tonouchi K / Yumoto K / Suzuki T / Kita S / Someya T / Fukuhara H / Kuroda Y / Yamamoto T / Onodera T / Fukushi S / Maeda K / Nakamura-Uchiyama F / Hashiguchi T / Hoshino A / Maenaka K / Takahashi Y | |||||||||||||||||||||||||||||||||
Funding support | Japan, 10 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants. Authors: Saya Moriyama / Yuki Anraku / Shunta Taminishi / Yu Adachi / Daisuke Kuroda / Shunsuke Kita / Yusuke Higuchi / Yuhei Kirita / Ryutaro Kotaki / Keisuke Tonouchi / Kohei Yumoto / Tateki Suzuki ...Authors: Saya Moriyama / Yuki Anraku / Shunta Taminishi / Yu Adachi / Daisuke Kuroda / Shunsuke Kita / Yusuke Higuchi / Yuhei Kirita / Ryutaro Kotaki / Keisuke Tonouchi / Kohei Yumoto / Tateki Suzuki / Taiyou Someya / Hideo Fukuhara / Yudai Kuroda / Tsukasa Yamamoto / Taishi Onodera / Shuetsu Fukushi / Ken Maeda / Fukumi Nakamura-Uchiyama / Takao Hashiguchi / Atsushi Hoshino / Katsumi Maenaka / Yoshimasa Takahashi / Abstract: SARS-CoV-2 Omicron subvariants have evolved to evade receptor-binding site (RBS) antibodies that exist in diverse individuals as public antibody clones. We rationally selected RBS antibodies ...SARS-CoV-2 Omicron subvariants have evolved to evade receptor-binding site (RBS) antibodies that exist in diverse individuals as public antibody clones. We rationally selected RBS antibodies resilient to mutations in emerging Omicron subvariants. Y489 was identified as a site of virus vulnerability and a common footprint of broadly neutralizing antibodies against the subvariants. Multiple Y489-binding antibodies were encoded by public clonotypes and additionally recognized F486, potentially accounting for the emergence of Omicron subvariants harboring the F486V mutation. However, a subclass of antibodies broadly neutralized BA.4/BA.5 variants via hydrophobic binding sites of rare clonotypes along with high mutation-resilience under escape mutation screening. A computationally designed antibody based on one of the Y489-binding antibodies, NIV-10/FD03, was able to bind XBB with any 486 mutation and neutralized XBB.1.5. The structural basis for the mutation-resilience of this Y489-binding antibody group may provide important insights into the design of therapeutics resistant to viral escape. | |||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34742.map.gz | 108.3 MB | EMDB map data format | |
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Header (meta data) | emd-34742-v30.xml emd-34742.xml | 26.7 KB 26.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34742_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_34742.png | 51.9 KB | ||
Masks | emd_34742_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-34742.cif.gz | 8.2 KB | ||
Others | emd_34742_half_map_1.map.gz emd_34742_half_map_2.map.gz | 200.2 MB 200.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34742 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34742 | HTTPS FTP |
-Related structure data
Related structure data | 8hgmMC 7yh6C 7yh7C 8hesC 8hglC 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_34742.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | 0.16 | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.173 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_34742_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: 0.433
File | emd_34742_half_map_1.map | ||||||||||||
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Annotation | 0.433 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: 0.433
File | emd_34742_half_map_2.map | ||||||||||||
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Annotation | 0.433 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-COV-2 spike glycoprotein in complex with NIV-11
Entire | Name: SARS-COV-2 spike glycoprotein in complex with NIV-11 |
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Components |
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-Supramolecule #1: SARS-COV-2 spike glycoprotein in complex with NIV-11
Supramolecule | Name: SARS-COV-2 spike glycoprotein in complex with NIV-11 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 570 KDa |
-Supramolecule #2: SARS-CoV-2 spike glycoprotein
Supramolecule | Name: SARS-CoV-2 spike glycoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 420 KDa |
-Supramolecule #3: NIV-11 Fab
Supramolecule | Name: NIV-11 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 50 KDa |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / 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: 142.427438 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 KPSKRSPIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFG AGPALQIPFP MQMAYRFNGI GVTQNVLYEN QKLIANQFNS AIGKIQDSLS STPSALGKLQ 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 FLGRSLEVLF QGPGHHHHHH HHSAWSHPQF EKGGGSGGGG SGGSA WSHP QFEK UniProtKB: Spike glycoprotein |
-Macromolecule #2: NIV-11 Fab heavy chain
Macromolecule | Name: NIV-11 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.753709 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QLVQSGPEVK KPGTSVKVSC KASGFTFYYS AVQWVRQARG QRLEWLGWMA VGSGKANYAQ KFQERLTLTR DMSTSTAYME LSSLRSEDT AVYYCAAPNC TGGSCYDGFN LWGQGTVVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String: QLVQSGPEVK KPGTSVKVSC KASGFTFYYS AVQWVRQARG QRLEWLGWMA VGSGKANYAQ KFQERLTLTR DMSTSTAYME LSSLRSEDT AVYYCAAPNC TGGSCYDGFN LWGQGTVVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPKS |
-Macromolecule #3: NIV-11 Fab light chain
Macromolecule | Name: NIV-11 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.555137 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EIVLTQSPGT LSLSPGDRAI LSCRASQTVN SNYLAWYQQK PGQAPRLLIY GTSSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYGSSPWLF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String: EIVLTQSPGT LSLSPGDRAI LSCRASQTVN SNYLAWYQQK PGQAPRLLIY GTSSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYGSSPWLF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL |
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Buffer | pH: 7.4 Details: octyl-maltoside, fluorinated solution was added to PBS solution to a final concentration of 0.03% |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV / Details: blotting time 5 s and blotting force 5.. |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 5170 / Average exposure time: 1.5 sec. / Average electron dose: 51.41 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |