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Yorodumi- EMDB-26509: SARS-CoV-2 spike in complex with multivalent miniprotein inhibito... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26509 | |||||||||
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Title | SARS-CoV-2 spike in complex with multivalent miniprotein inhibitor FUS31-G10 (2RBDs open) | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Severe acute respiratory syndrome coronavirus 2 / Synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.57 Å | |||||||||
Authors | Park YJ / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Veesler D | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Sci Transl Med / Year: 2022 Title: Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice. Authors: Andrew C Hunt / James Brett Case / Young-Jun Park / Longxing Cao / Kejia Wu / Alexandra C Walls / Zhuoming Liu / John E Bowen / Hsien-Wei Yeh / Shally Saini / Louisa Helms / Yan Ting Zhao / ...Authors: Andrew C Hunt / James Brett Case / Young-Jun Park / Longxing Cao / Kejia Wu / Alexandra C Walls / Zhuoming Liu / John E Bowen / Hsien-Wei Yeh / Shally Saini / Louisa Helms / Yan Ting Zhao / Tien-Ying Hsiang / Tyler N Starr / Inna Goreshnik / Lisa Kozodoy / Lauren Carter / Rashmi Ravichandran / Lydia B Green / Wadim L Matochko / Christy A Thomson / Bastian Vögeli / Antje Krüger / Laura A VanBlargan / Rita E Chen / Baoling Ying / Adam L Bailey / Natasha M Kafai / Scott E Boyken / Ajasja Ljubetič / Natasha Edman / George Ueda / Cameron M Chow / Max Johnson / Amin Addetia / Mary-Jane Navarro / Nuttada Panpradist / Michael Gale / Benjamin S Freedman / Jesse D Bloom / Hannele Ruohola-Baker / Sean P J Whelan / Lance Stewart / Michael S Diamond / David Veesler / Michael C Jewett / David Baker / Abstract: New variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to arise and prolong the coronavirus disease 2019 (COVID-19) pandemic. Here, we used a cell-free expression ...New variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to arise and prolong the coronavirus disease 2019 (COVID-19) pandemic. Here, we used a cell-free expression workflow to rapidly screen and optimize constructs containing multiple computationally designed miniprotein inhibitors of SARS-CoV-2. We found the broadest efficacy was achieved with a homotrimeric version of the 75-residue angiotensin-converting enzyme 2 (ACE2) mimic AHB2 (TRI2-2) designed to geometrically match the trimeric spike architecture. Consistent with the design model, in the cryo-electron microscopy structure TRI2-2 forms a tripod at the apex of the spike protein that engaged all three receptor binding domains simultaneously. TRI2-2 neutralized Omicron (B.1.1.529), Delta (B.1.617.2), and all other variants tested with greater potency than the monoclonal antibodies used clinically for the treatment of COVID-19. TRI2-2 also conferred prophylactic and therapeutic protection against SARS-CoV-2 challenge when administered intranasally in mice. Designed miniprotein receptor mimics geometrically arrayed to match pathogen receptor binding sites could be a widely applicable antiviral therapeutic strategy with advantages over antibodies in greater resistance to viral escape and antigenic drift, and advantages over native receptor traps in lower chances of autoimmune responses. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26509.map.gz | 230 MB | EMDB map data format | |
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Header (meta data) | emd-26509-v30.xml emd-26509.xml | 22.3 KB 22.3 KB | Display Display | EMDB header |
Images | emd_26509.png | 45.1 KB | ||
Others | emd_26509_additional_1.map.gz emd_26509_half_map_1.map.gz emd_26509_half_map_2.map.gz | 121.6 MB 226.3 MB 226.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26509 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26509 | HTTPS FTP |
-Related 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_26509.map.gz / Format: CCP4 / Size: 244.1 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: 1.05 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_26509_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_26509_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_26509_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 spike in complex with multivalent miniprotein inhibito...
Entire | Name: SARS-CoV-2 spike in complex with multivalent miniprotein inhibitor FUS31-G10 (2RBDs open) |
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Components |
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-Supramolecule #1: SARS-CoV-2 spike in complex with multivalent miniprotein inhibito...
Supramolecule | Name: SARS-CoV-2 spike in complex with multivalent miniprotein inhibitor FUS31-G10 (2RBDs open) type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #2: SARS-CoV-2 spike
Supramolecule | Name: SARS-CoV-2 spike / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: Multivalent miniprotein inhibitor FUS31-G10
Supramolecule | Name: Multivalent miniprotein inhibitor FUS31-G10 / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Synthetic construct (others) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: SARS-CoV-2 Spike
Macromolecule | Name: SARS-CoV-2 Spike / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
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 |
-Macromolecule #2: Multivalent miniprotein inhibitor FUS31-G10
Macromolecule | Name: Multivalent miniprotein inhibitor FUS31-G10 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Synthetic construct (others) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MEKKI SAWS HPQFEK GGG SGGGSGGSAW SHPQFEKGGS GSSG NLDEL HMQMTDLVYE ALHFAKDEEF QKHVFQLFEK ATKAYKNKDR QKLEKVVEEL KELLERLLS GGGSGGGSGG DKENVLQKI YEIMKELERL GHAEASMQVS DLIYEFMKTK DENLLEEAER LLEEVKR |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 70.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: cryoSPARC ab initio |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 9733 |