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- EMDB-29794: SARS-CoV-2 spike/Nb2 complex with 1 RBD up (local refinement at 5.6 A) -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | SARS-CoV-2 spike/Nb2 complex with 1 RBD up (local refinement at 5.6 A) | |||||||||
![]() | local refinement of the Spike/Nb2 complex with 1 RBDs up sharpened map | |||||||||
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![]() | SARS-CoV-2 / VIRAL PROTEIN-IMMUNE SYSTEM complex / Nanobody | |||||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.6 Å | |||||||||
![]() | Ye G / Bu F / Liu B / Li F | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery of Nanosota-2, -3, and -4 as super potent and broad-spectrum therapeutic nanobody candidates against COVID-19. Authors: Gang Ye / Ruangang Pan / Fan Bu / Jian Zheng / Alise Mendoza / Wei Wen / Lanying Du / Benjamin Spiller / Brian E Wadzinski / Bin Liu / Stanley Perlman / Fang Li / ![]() Abstract: The COVID-19 pandemic exposed limitations of conventional antibodies as therapeutics, including high cost, limited potency, ineffectiveness against new viral variants, and primary reliance on ...The COVID-19 pandemic exposed limitations of conventional antibodies as therapeutics, including high cost, limited potency, ineffectiveness against new viral variants, and primary reliance on injection-only delivery. Nanobodies are single-domain antibodies with therapeutic potentials. We discovered three anti-SARS-CoV-2 nanobodies, named Nanosota-2, -3, and -4, from an immunized alpaca. Nanosota-2 is super potent against prototypic SARS-CoV-2, Nanosota-3 is highly potent against the omicron variant, and Nanosota-4 is effective against both SARS-CoV-1 and SARS-CoV-2. In addition to their super potency and combined broad antiviral spectrum, these nanobodies are cost-effective, can be easily adapted to new viral variants through phage display, and can potentially be administered as inhalers. The Nanosota series are powerful therapeutic candidates to combat circulating SARS-CoV-2 and prepare for possible future coronavirus pandemics. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 350.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.3 KB 21.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15.3 KB | Display | ![]() |
Images | ![]() | 62.1 KB | ||
Filedesc metadata | ![]() | 6.4 KB | ||
Others | ![]() ![]() ![]() | 181.4 MB 344.9 MB 344.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8g72MC ![]() 8g73C ![]() 8g74C ![]() 8g75C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | local refinement of the Spike/Nb2 complex with 1 RBDs up sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.73 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: local refinement of the Spike/Nb2 complex with 1...
File | emd_29794_additional_1.map | ||||||||||||
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Annotation | local refinement of the Spike/Nb2 complex with 1 RBDs up unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: local refinement of the Spike/Nb2 complex with 1 RBDs up map half A
File | emd_29794_half_map_1.map | ||||||||||||
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Annotation | local refinement of the Spike/Nb2 complex with 1 RBDs up map half_A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: local refinement of the Spike/Nb2 complex with 1 RBDs up map half B
File | emd_29794_half_map_2.map | ||||||||||||
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Annotation | local refinement of the Spike/Nb2 complex with 1 RBDs up map half_B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : SARS-CoV-2 spike/Nb2 complex with 1 RBD up
Entire | Name: SARS-CoV-2 spike/Nb2 complex with 1 RBD up |
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Components |
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-Supramolecule #1: SARS-CoV-2 spike/Nb2 complex with 1 RBD up
Supramolecule | Name: SARS-CoV-2 spike/Nb2 complex with 1 RBD up / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 425 KDa |
-Macromolecule #1: Nanosota-2
Macromolecule | Name: Nanosota-2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 16.750008 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MAQVQLQESG GGAVQPGGSL GLSCTASGFN FETSTVGWFR QAPGKENEGV SCINKGYEDT NYADSVKGRF TISRDAAKNT VYLQMDSLQ PEDTATYYCA AHNEPYFCDY SGRFRWNEYS YYGQGTQVTV SSGGQHHHHH HGAYPYDVPD YAS |
-Macromolecule #2: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 136.890484 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNPV LPFNDGVYFA STEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLG VYYHKNNKSW MESEFRVYSS ANNCTFEYVS Q PFLMDLEG ...String: QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNPV LPFNDGVYFA STEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLG VYYHKNNKSW MESEFRVYSS ANNCTFEYVS Q PFLMDLEG KQGNFKNLRE FVFKNIDGYF KIYSKHTPIN LVRDLPQGFS ALEPLVDLPI GINITRFQTL LALHRSYLTP GD SSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPTESIVRFP NIT NLCPFG EVFNATRFAS VYAWNRKRIS NCVADYSVLY NSASFSTFKC YGVSPTKLND LCFTNVYADS FVIRGDEVRQ IAPG QTGKI ADYNYKLPDD FTGCVIAWNS NNLDSKVGGN YNYLYRLFRK SNLKPFERDI STEIYQAGST PCNGVEGFNC YFPLQ SYGF QPTNGVGYQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CVNFNFNGLT GTGVLTESNK KFLPFQQFGR DIADTT DAV RDPQTLEILD ITPCSFGGVS VITPGTNTSN QVAVLYQDVN CTEVPVAIHA DQLTPTWRVY STGSNVFQTR AGCLIGA EH VNNSYECDIP IGAGICASYQ TQTNSPAGAR SVASQSIIAY TMSLGAENSV AYSNNSIAIP TNFTISVTTE ILPVSMTK T SVDCTMYICG DSTECSNLLL QYGSFCTQLN RALTGIAVEQ DKNTQEVFAQ VKQIYKTPPI KDFGGFNFSQ ILPDPSKPS KRSPIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFNGLTVLPP LLTDEMIAQY TSALLAGTIT SGWTFGAGPA LQIPFPMQM AYRFNGIGVT QNVLYENQKL IANQFNSAIG KIQDSLSSTP SALGKLQDVV NQNAQALNTL VKQLSSNFGA I SSVLNDIL SRLDPPEAEV QIDRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CVLGQSKRVD FCGKGYHLMS FP QSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVSGNCDVVI GIV NNTVYD PLQPELDSFK EELDKYFKNH TSPDVDLGDI SGINASVVNI QKEIDRLNEV AKNLNESLID LQELGKYEQY IKGS GYIPE APRDGQAYVR KDGEWVLLST FLGHHHHHH UniProtKB: Spike glycoprotein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |