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Yorodumi- EMDB-23567: Cryo-EM map of SARS-CoV-2 Spike protein bound to neutralising nan... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23567 | |||||||||
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Title | Cryo-EM map of SARS-CoV-2 Spike protein bound to neutralising nanobodies WNb2 and WNb10 (C3 symmetry) | |||||||||
Map data | Postprocessed map | |||||||||
Sample |
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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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / 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 / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Vicugna pacos (alpaca) / evere acute respiratory syndrome coronavirus 2 / Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Pymm P / Tham W-H / Glukhova A | |||||||||
Funding support | Australia, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. Authors: Phillip Pymm / Amy Adair / Li-Jin Chan / James P Cooney / Francesca L Mordant / Cody C Allison / Ester Lopez / Ebene R Haycroft / Matthew T O'Neill / Li Lynn Tan / Melanie H Dietrich / ...Authors: Phillip Pymm / Amy Adair / Li-Jin Chan / James P Cooney / Francesca L Mordant / Cody C Allison / Ester Lopez / Ebene R Haycroft / Matthew T O'Neill / Li Lynn Tan / Melanie H Dietrich / Damien Drew / Marcel Doerflinger / Michael A Dengler / Nichollas E Scott / Adam K Wheatley / Nicholas A Gherardin / Hariprasad Venugopal / Deborah Cromer / Miles P Davenport / Raelene Pickering / Dale I Godfrey / Damian F J Purcell / Stephen J Kent / Amy W Chung / Kanta Subbarao / Marc Pellegrini / Alisa Glukhova / Wai-Hong Tham / Abstract: Neutralizing antibodies are important for immunity against SARS-CoV-2 and as therapeutics for the prevention and treatment of COVID-19. Here, we identified high-affinity nanobodies from alpacas ...Neutralizing antibodies are important for immunity against SARS-CoV-2 and as therapeutics for the prevention and treatment of COVID-19. Here, we identified high-affinity nanobodies from alpacas immunized with coronavirus spike and receptor-binding domains (RBD) that disrupted RBD engagement with the human receptor angiotensin-converting enzyme 2 (ACE2) and potently neutralized SARS-CoV-2. Epitope mapping, X-ray crystallography, and cryo-electron microscopy revealed two distinct antigenic sites and showed two neutralizing nanobodies from different epitope classes bound simultaneously to the spike trimer. Nanobody-Fc fusions of the four most potent nanobodies blocked ACE2 engagement with RBD variants present in human populations and potently neutralized both wild-type SARS-CoV-2 and the N501Y D614G variant at concentrations as low as 0.1 nM. Prophylactic administration of either single nanobody-Fc or as mixtures reduced viral loads by up to 10-fold in mice infected with the N501Y D614G SARS-CoV-2 virus. These results suggest a role for nanobody-Fc fusions as prophylactic agents against SARS-CoV-2. | |||||||||
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_23567.map.gz | 257.3 MB | EMDB map data format | |
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Header (meta data) | emd-23567-v30.xml emd-23567.xml | 19.8 KB 19.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23567_fsc.xml | 14.7 KB | Display | FSC data file |
Images | emd_23567.png | 155.1 KB | ||
Others | emd_23567_additional_1.map.gz emd_23567_half_map_1.map.gz emd_23567_half_map_2.map.gz | 218.4 MB 218.9 MB 219.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23567 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23567 | 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_23567.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Postprocessed map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: map after Refine3D
File | emd_23567_additional_1.map | ||||||||||||
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Annotation | map after Refine3D | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-volume 1
File | emd_23567_half_map_1.map | ||||||||||||
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Annotation | half-volume 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-volume 2
File | emd_23567_half_map_2.map | ||||||||||||
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Annotation | half-volume 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM map of SARS-CoV-2 Spike protein bound to neutralising nan...
Entire | Name: Cryo-EM map of SARS-CoV-2 Spike protein bound to neutralising nanobodies WNb2 and WNb10 (C3 symmetry) |
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Components |
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-Supramolecule #1: Cryo-EM map of SARS-CoV-2 Spike protein bound to neutralising nan...
Supramolecule | Name: Cryo-EM map of SARS-CoV-2 Spike protein bound to neutralising nanobodies WNb2 and WNb10 (C3 symmetry) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: neutralising nanobodies WNb2 and WNb10
Supramolecule | Name: neutralising nanobodies WNb2 and WNb10 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Vicugna pacos (alpaca) |
-Supramolecule #3: SARS-CoV-2 Spike protein
Supramolecule | Name: SARS-CoV-2 Spike protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: evere acute respiratory syndrome coronavirus 2 |
-Macromolecule #1: SARS-CoV-2 Spike protein
Macromolecule | Name: SARS-CoV-2 Spike protein / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Sequence | String: MGGEGLRASP RRRPLLPLQP RGCPRGDGCL RGGRGRAGFG FWRVTGGSSA SANHVHAFFF FLQLLGNVLV VVLSHHFGKE LRPSQAEFGT ATMFVFLVLL PLVSSQCVNL TTRTQLPPAY TNSFTRGVYY PDKVFRSSVL HSTQDLFLPF FSNVTWFHAI HVSGTNGTKR ...String: MGGEGLRASP RRRPLLPLQP RGCPRGDGCL RGGRGRAGFG FWRVTGGSSA SANHVHAFFF FLQLLGNVLV VVLSHHFGKE LRPSQAEFGT ATMFVFLVLL PLVSSQCVNL TTRTQLPPAY TNSFTRGVYY PDKVFRSSVL HSTQDLFLPF FSNVTWFHAI HVSGTNGTKR FDNPVLPFND GVYFASTEKS NIIRGWIFGT TLDSKTQSLL IVNNATNVVI KVCEFQFCND PFLGVYYHKN NKSWMESEFR VYSSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRDLPQ GFSALEPLVD LPIGINITRF QTLLALHRSY LTPGDSSSGW TAGAAAYYVG YLQPRTFLLK YNENGTITDA VDCALDPLSE TKCTLKSFTV EKGIYQTSNF RVQPTESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEVR QIAPGQTGKI ADYNYKLPDD FTGCVIAWNS NNLDSKVGGN YNYLYRLFRK SNLKPFERDI STEIYQAGST PCNGVEGFNC YFPLQSYGFQ PTNGVGYQPY RVVVLSFELL HAPATVCGPK KSTNLVKNKC VNFNFNGLTG TGVLTESNKK FLPFQQFGRD IADTTDAVRD PQTLEILDIT PCSFGGVSVI TPGTNTSNQV AVLYQDVNCT EVPVAIHADQ LTPTWRVYST GSNVFQTRAG CLIGAEHVNN SYECDIPIGA GICASYQTQT NSPGSASSVA SQSIIAYTMS LGAENSVAYS NNSIAIPTNF TISVTTEILP VSMTKTSVDC TMYICGDSTE CSNLLLQYGS FCTQLNRALT GIAVEQDKNT QEVFAQVKQI YKTPPIKDFG GFNFSQILPD PSKPSKRSPI EDLLFNKVTL ADAGFIKQYG DCLGDIAARD LICAQKFNGL TVLPPLLTDE MIAQYTSALL AGTITSGWTF GAGPALQIPF PMQMAYRFNG IGVTQNVLYE NQKLIANQFN SAIGKIQDSL SSTPSALGKL QDVVNQNAQA LNTLVKQLSS NFGAISSVLN DILSRLDPPE AEVQIDRLIT GRLQSLQTYV TQQLIRAAEI RASANLAATK MSECVLGQSK RVDFCGKGYH LMSFPQSAPH GVVFLHVTYV PAQEKNFTTA PAICHDGKAH FPREGVFVSN GTHWFVTQRN FYEPQIITTD NTFVSGNCDV VIGIVNNTVY DPLQPELDSF KEELDKYFKN HTSPDVDLGD ISGINASVVN IQKEIDRLNE VAKNLNESLI DLQELGKYEQ GSGYIPEAPR DGQAYVRKDG EWVLLSTFLG RSLEVLFQGP GHHHHHHHHS AWSHPQFEKG GGSGGGGSGG SAWSHPQFEK |
-Macromolecule #2: Wnb2
Macromolecule | Name: Wnb2 / type: protein_or_peptide / ID: 2 / Enantiomer: DEXTRO |
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Source (natural) | Organism: Vicugna pacos (alpaca) |
Sequence | String: QVQLQESGGG LVQPGGSLRL SCAVSGFTLD YYAIGWFRQA PGKEREGVSC ISSSGGNTKY ADSVKGRFTA SRDNAKNTFY LQMNSLKPED TAVYYCAAIA ATYYSGSYYF QCPHDGMDYW GKGTQVTVSS |
-Macromolecule #3: Wnb10
Macromolecule | Name: Wnb10 / type: protein_or_peptide / ID: 3 / Enantiomer: DEXTRO |
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Source (natural) | Organism: Vicugna pacos (alpaca) |
Sequence | String: QVQLQESGGG LVQPGGSLRL SCAASGFTFR RYLMGWARQV PGKGLEWVSG IYSDGSTYYA DSVKGRFTIS RDNAKNTVYL QMNSLKPEDT AVYYCAKDRM DGSTWPERDF GSWGQGTQVT VSS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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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 |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 55.9 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |