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Yorodumi- EMDB-22738: CryoEM reconstruction of SARS-CoV-2 receptor binding domain in co... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22738 | ||||||||||||||||||
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Title | CryoEM reconstruction of SARS-CoV-2 receptor binding domain in complex with the Fab fragment of neutralizing antibody 46 | ||||||||||||||||||
Map data | Fab 46 in complex with RBD domain of SARS-CoV-2 Spike protein. | ||||||||||||||||||
Sample |
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Biological species | Homo sapiens (human) / Severe acute respiratory syndrome coronavirus 2 | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | ||||||||||||||||||
Authors | Kucharska I / Tan YZ / Benlekbir S / Rubinstein JL / Julien JP | ||||||||||||||||||
Funding support | Canada, 5 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Multivalency transforms SARS-CoV-2 antibodies into ultrapotent neutralizers. Authors: Edurne Rujas / Iga Kucharska / Yong Zi Tan / Samir Benlekbir / Hong Cui / Tiantian Zhao / Gregory A Wasney / Patrick Budylowski / Furkan Guvenc / Jocelyn C Newton / Taylor Sicard / Anthony ...Authors: Edurne Rujas / Iga Kucharska / Yong Zi Tan / Samir Benlekbir / Hong Cui / Tiantian Zhao / Gregory A Wasney / Patrick Budylowski / Furkan Guvenc / Jocelyn C Newton / Taylor Sicard / Anthony Semesi / Krithika Muthuraman / Amy Nouanesengsy / Clare Burn Aschner / Katherine Prieto / Stephanie A Bueler / Sawsan Youssef / Sindy Liao-Chan / Jacob Glanville / Natasha Christie-Holmes / Samira Mubareka / Scott D Gray-Owen / John L Rubinstein / Bebhinn Treanor / Jean-Philippe Julien / Abstract: SARS-CoV-2, the virus responsible for COVID-19, has caused a global pandemic. Antibodies can be powerful biotherapeutics to fight viral infections. Here, we use the human apoferritin protomer as a ...SARS-CoV-2, the virus responsible for COVID-19, has caused a global pandemic. Antibodies can be powerful biotherapeutics to fight viral infections. Here, we use the human apoferritin protomer as a modular subunit to drive oligomerization of antibody fragments and transform antibodies targeting SARS-CoV-2 into exceptionally potent neutralizers. Using this platform, half-maximal inhibitory concentration (IC) values as low as 9 × 10 M are achieved as a result of up to 10,000-fold potency enhancements compared to corresponding IgGs. Combination of three different antibody specificities and the fragment crystallizable (Fc) domain on a single multivalent molecule conferred the ability to overcome viral sequence variability together with outstanding potency and IgG-like bioavailability. The MULTi-specific, multi-Affinity antiBODY (Multabody or MB) platform thus uniquely leverages binding avidity together with multi-specificity to deliver ultrapotent and broad neutralizers against SARS-CoV-2. The modularity of the platform also makes it relevant for rapid evaluation against other infectious diseases of global health importance. Neutralizing antibodies are a promising therapeutic for SARS-CoV-2. #1: Journal: Biorxiv / Year: 2020 Title: Multivalency transforms SARS-CoV-2 antibodies into broad and ultrapotent neutralizers Authors: Rujas E / Kucharska I / Tan YZ / Benlekbir S / Cui H / Zhao T / Wasney G / Budylowski P / Guvenc F / Newton J / Semesi A / Muthuraman K / Nouanesengsy A / Prieto K / Bueler S / Youssef S / ...Authors: Rujas E / Kucharska I / Tan YZ / Benlekbir S / Cui H / Zhao T / Wasney G / Budylowski P / Guvenc F / Newton J / Semesi A / Muthuraman K / Nouanesengsy A / Prieto K / Bueler S / Youssef S / Liao-Chan S / Glanville J / Christie-Holmes N / Mubareka S / Gray-Owen SD / Rubinstein JL / Treanor B / Julien JP | ||||||||||||||||||
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_22738.map.gz | 28.4 MB | EMDB map data format | |
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Header (meta data) | emd-22738-v30.xml emd-22738.xml | 19.4 KB 19.4 KB | Display Display | EMDB header |
Images | emd_22738.png | 178.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22738 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22738 | HTTPS FTP |
-Validation report
Summary document | emd_22738_validation.pdf.gz | 352.7 KB | Display | EMDB validaton report |
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Full document | emd_22738_full_validation.pdf.gz | 352.3 KB | Display | |
Data in XML | emd_22738_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | emd_22738_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22738 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22738 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_22738.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Fab 46 in complex with RBD domain of SARS-CoV-2 Spike protein. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 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 receptor binding domain in complex with the Fab fragme...
Entire | Name: SARS-CoV-2 receptor binding domain in complex with the Fab fragment of neutralizing antibody 46 |
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Components |
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-Supramolecule #1: SARS-CoV-2 receptor binding domain in complex with the Fab fragme...
Supramolecule | Name: SARS-CoV-2 receptor binding domain in complex with the Fab fragment of neutralizing antibody 46 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: Fab fragment of neutralizing antibody 46
Supramolecule | Name: Fab fragment of neutralizing antibody 46 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: SARS-CoV-2 receptor binding domain
Supramolecule | Name: SARS-CoV-2 receptor binding domain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Fab 46 heavy chain
Macromolecule | Name: Fab 46 heavy chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLLESGGG LVQPGRSLRL SCAASGFTFS SYAMSWVRQA PGKGLEWVST IYSGGSTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAED TAVYYCARGD S RDAFDIWG QGTMVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YF PEPVTVS WNSGALTSGV ...String: EVQLLESGGG LVQPGRSLRL SCAASGFTFS SYAMSWVRQA PGKGLEWVST IYSGGSTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAED TAVYYCARGD S RDAFDIWG QGTMVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YF PEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YIC NVNHKP SNTKVDKKVE PKSC |
-Macromolecule #2: Fab 46 light chain
Macromolecule | Name: Fab 46 light chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQSPSS LSASVGDRVT ITCRASQSIS SWLAWYQQKP GKAPKLLIYD ASNLETGVP SRFSGSGSGT DFTLTISSLQ PEDFATYYCQ QSYSTPFTFG P GTKVDIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KV DNALQSG NSQESVTEQD ...String: DIQMTQSPSS LSASVGDRVT ITCRASQSIS SWLAWYQQKP GKAPKLLIYD ASNLETGVP SRFSGSGSGT DFTLTISSLQ PEDFATYYCQ QSYSTPFTFG P GTKVDIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KV DNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQG LSSPVT KSFNRGEC |
-Macromolecule #3: Receptor Binding Domain of SARS-CoV-2 Spike
Macromolecule | Name: Receptor Binding Domain of SARS-CoV-2 Spike / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: RVQPTESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEVR QIAPGQTGKI ADYNYKLPDD FTGCVIAWNS NNLDSKVGGN YNYLYRLFRK SNLKPFERDI STEIYQAGST PCNGVEGFNC ...String: RVQPTESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEVR QIAPGQTGKI ADYNYKLPDD FTGCVIAWNS NNLDSKVGGN YNYLYRLFRK SNLKPFERDI STEIYQAGST PCNGVEGFNC YFPLQSYGFQ PTNGVGYQPY RVVVLSFELL HAPATVCGPK KSTNLVKNKC VNFHHHHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.0 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Homemade / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: glow discharged with PELCO easiGlow (Ted Pella) | ||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number real images: 4722 / Average exposure time: 9.6 sec. / Average electron dose: 45.0 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 magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |