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- EMDB-23568: Cryo-EM map of SARS-CoV-2 Spike protein in complex with neutralis... -

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Basic information

Entry
Database: EMDB / ID: EMD-23568
TitleCryo-EM map of SARS-CoV-2 Spike protein in complex with neutralising nanobodies WNb2 and WNb10 (C1 symmetry)
Map dataPostProcessed map
Sample
  • Complex: Cryo-EM map of SARS-CoV-2 Spike protein in complex with neutralising nanobodies WNb2 and WNb10 (C1 symmetry)
    • Complex: neutralising nanobodies WNb2 and WNb10
      • Protein or peptide: WNb2
      • Protein or peptide: Wnb10
    • Complex: SARS-CoV-2 Spike proteinCoronavirus spike protein
      • Protein or peptide: SARS-CoV-2 Spike proteinCoronavirus spike protein
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
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesVicugna pacos (alpaca) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsPymm P / Tham W-H / Glukhova A
Funding support Australia, 2 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT2002073 Australia
Wellcome Trust208693/Z/17/Z Australia
CitationJournal: 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
DepositionMar 3, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateMay 5, 2021-
Current statusMay 5, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23568.png

Downloads & links

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Map

FileDownload / File: emd_23568.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostProcessed map
Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.017
Minimum - Maximum-0.045408927 - 0.09531523
Average (Standard dev.)8.319037e-05 (±0.0033905872)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 357.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z416416416
origin x/y/z0.0000.0000.000
length x/y/z357.760357.760357.760
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS416416416
D min/max/mean-0.0450.0950.000

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Supplemental data

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Additional map: refine3D map

Fileemd_23568_additional_1.map
Annotationrefine3D map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM map of SARS-CoV-2 Spike protein in complex with neutralis...

EntireName: Cryo-EM map of SARS-CoV-2 Spike protein in complex with neutralising nanobodies WNb2 and WNb10 (C1 symmetry)
Components
  • Complex: Cryo-EM map of SARS-CoV-2 Spike protein in complex with neutralising nanobodies WNb2 and WNb10 (C1 symmetry)
    • Complex: neutralising nanobodies WNb2 and WNb10
      • Protein or peptide: WNb2
      • Protein or peptide: Wnb10
    • Complex: SARS-CoV-2 Spike proteinCoronavirus spike protein
      • Protein or peptide: SARS-CoV-2 Spike proteinCoronavirus spike protein

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Supramolecule #1: Cryo-EM map of SARS-CoV-2 Spike protein in complex with neutralis...

SupramoleculeName: Cryo-EM map of SARS-CoV-2 Spike protein in complex with neutralising nanobodies WNb2 and WNb10 (C1 symmetry)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: neutralising nanobodies WNb2 and WNb10

SupramoleculeName: neutralising nanobodies WNb2 and WNb10 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Vicugna pacos (alpaca)

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Supramolecule #3: SARS-CoV-2 Spike protein

SupramoleculeName: SARS-CoV-2 Spike protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: SARS-CoV-2 Spike protein

MacromoleculeName: SARS-CoV-2 Spike protein / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
SequenceString: 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

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Macromolecule #2: WNb2

MacromoleculeName: WNb2 / type: protein_or_peptide / ID: 2 / Enantiomer: DEXTRO
Source (natural)Organism: Vicugna pacos (alpaca)
SequenceString:
QVQLQESGGG LVQPGGSLRL SCAVSGFTLD YYAIGWFRQA PGKEREGVSC ISSSGGNTKY ADSVKGRFTA SRDNAKNTFY LQMNSLKPED TAVYYCAAIA ATYYSGSYYF QCPHDGMDYW GKGTQVTVSS

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Macromolecule #3: Wnb10

MacromoleculeName: Wnb10 / type: protein_or_peptide / ID: 3 / Enantiomer: DEXTRO
Source (natural)Organism: Vicugna pacos (alpaca)
SequenceString:
QVQLQESGGG LVQPGGSLRL SCAASGFTFR RYLMGWARQV PGKGLEWVSG IYSDGSTYYA DSVKGRFTIS RDNAKNTVYL QMNSLKPEDT AVYYCAKDRM DGSTWPERDF GSWGQGTQVT VSS

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm 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

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22923
FSC plot (resolution estimation)

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