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- EMDB-24255: SARS-CoV-2 S with NB21 nanobody -

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Basic information

Entry
Database: EMDB / ID: EMD-24255
TitleSARS-CoV-2 S with NB21 nanobody
Map dataCryo-EM Structure determination of COVS with Nb21
Sample
  • Complex: SARS Cov 2 Spike S with Nanobody Nb21
    • Complex: SARS Cov 2 Spike Protein
      • Protein or peptide: Spike glycoprotein
    • Complex: Nanobody Nb21
      • Protein or peptide: NB21 Nanobody
KeywordsCovS NB21 nanobody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / 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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / 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
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSun D / Zhang C
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R35 GM137905 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R35 GM128641 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)U24 GM129539 United States
CitationJournal: bioRxiv / Year: 2021
Title: Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting novel and conserved epitopes.
Authors: Dapeng Sun / Zhe Sang / Yong Joon Kim / Yufei Xiang / Tomer Cohen / Anna K Belford / Alexis Huet / James F Conway / Ji Sun / Derek J Taylor / Dina Schneidman-Duhovny / Cheng Zhang / Wei Huang / Yi Shi /
Abstract: There is an urgent need to develop effective interventions resistant to the evolving variants of SARS-CoV-2. Nanobodies (Nbs) are stable and cost-effective agents that can be delivered by novel ...There is an urgent need to develop effective interventions resistant to the evolving variants of SARS-CoV-2. Nanobodies (Nbs) are stable and cost-effective agents that can be delivered by novel aerosolization route to treat SARS-CoV-2 infections efficiently. However, it remains unknown if they possess broadly neutralizing activities against the prevalent circulating strains. We found that potent neutralizing Nbs are highly resistant to the convergent variants of concern that evade a large panel of neutralizing antibodies (Abs) and significantly reduce the activities of convalescent or vaccine-elicited sera. Subsequent determination of 9 high-resolution structures involving 6 potent neutralizing Nbs by cryoelectron microscopy reveals conserved and novel epitopes on virus spike inaccessible to Abs. Systematic structural comparison of neutralizing Abs and Nbs provides critical insights into how Nbs uniquely target the spike to achieve high-affinity and broadly neutralizing activity against the evolving virus. Our study will inform the rational design of novel pan-coronavirus vaccines and therapeutics.
History
DepositionJun 17, 2021-
Header (metadata) releaseAug 4, 2021-
Map releaseAug 4, 2021-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7n9b
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24255.png

Downloads & links

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Map

FileDownload / File: emd_24255.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM Structure determination of COVS with Nb21
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.018
Minimum - Maximum-0.07176648 - 0.13722354
Average (Standard dev.)0.00003715252 (±0.0035276196)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 424.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z424.960424.960424.960
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ232232232
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0720.1370.000

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Supplemental data

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Sample components

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Entire : SARS Cov 2 Spike S with Nanobody Nb21

EntireName: SARS Cov 2 Spike S with Nanobody Nb21
Components
  • Complex: SARS Cov 2 Spike S with Nanobody Nb21
    • Complex: SARS Cov 2 Spike Protein
      • Protein or peptide: Spike glycoprotein
    • Complex: Nanobody Nb21
      • Protein or peptide: NB21 Nanobody

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Supramolecule #1: SARS Cov 2 Spike S with Nanobody Nb21

SupramoleculeName: SARS Cov 2 Spike S with Nanobody Nb21 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: SARS Cov 2 Spike Protein

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

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Supramolecule #3: Nanobody Nb21

SupramoleculeName: Nanobody Nb21 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Lama glama (llama)

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1
Details: Pre-fusion stabilized HexaPro construct, including six proline substitutions and furin cleavage site RRAR 682-685 mutated to GSAS
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 152.31275 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGGEGLRASP RRRPLLPLQP RGCPRGDGCL RGGRGRAGFG FWRVTGGSSA SANHVHAFFF FLQLLGNVLV VVLSHHFGKE LRPSQAEFG TATMFVFLVL LPLVSSQCVN LTTRTQLPPA YTNSFTRGVY YPDKVFRSSV LHSTQDLFLP FFSNVTWFHA I HVSGTNGT ...String:
MGGEGLRASP RRRPLLPLQP RGCPRGDGCL RGGRGRAGFG FWRVTGGSSA SANHVHAFFF FLQLLGNVLV VVLSHHFGKE LRPSQAEFG TATMFVFLVL LPLVSSQCVN LTTRTQLPPA YTNSFTRGVY YPDKVFRSSV LHSTQDLFLP FFSNVTWFHA I HVSGTNGT KRFDNPVLPF NDGVYFASTE KSNIIRGWIF GTTLDSKTQS LLIVNNATNV VIKVCEFQFC NDPFLGVYYH KN NKSWMES EFRVYSSANN CTFEYVSQPF LMDLEGKQGN FKNLREFVFK NIDGYFKIYS KHTPINLVRD LPQGFSALEP LVD LPIGIN ITRFQTLLAL HRSYLTPGDS SSGWTAGAAA YYVGYLQPRT FLLKYNENGT ITDAVDCALD PLSETKCTLK SFTV EKGIY QTSNFRVQPT ESIVRFPNIT NLCPFGEVFN ATRFASVYAW NRKRISNCVA DYSVLYNSAS FSTFKCYGVS PTKLN DLCF TNVYADSFVI RGDEVRQIAP GQTGKIADYN YKLPDDFTGC VIAWNSNNLD SKVGGNYNYL YRLFRKSNLK PFERDI STE IYQAGSTPCN GVEGFNCYFP LQSYGFQPTN GVGYQPYRVV VLSFELLHAP ATVCGPKKST NLVKNKCVNF NFNGLTG TG VLTESNKKFL PFQQFGRDIA DTTDAVRDPQ TLEILDITPC SFGGVSVITP GTNTSNQVAV LYQDVNCTEV PVAIHADQ L TPTWRVYSTG SNVFQTRAGC LIGAEHVNNS YECDIPIGAG ICASYQTQTN SPGSASSVAS QSIIAYTMSL GAENSVAYS NNSIAIPTNF TISVTTEILP VSMTKTSVDC TMYICGDSTE CSNLLLQYGS FCTQLNRALT GIAVEQDKNT QEVFAQVKQI YKTPPIKDF GGFNFSQILP DPSKPSKRSP IEDLLFNKVT LADAGFIKQY GDCLGDIAAR DLICAQKFNG LTVLPPLLTD E MIAQYTSA LLAGTITSGW TFGAGPALQI PFPMQMAYRF NGIGVTQNVL YENQKLIANQ FNSAIGKIQD SLSSTPSALG KL QDVVNQN AQALNTLVKQ LSSNFGAISS VLNDILSRLD PPEAEVQIDR LITGRLQSLQ TYVTQQLIRA AEIRASANLA ATK MSECVL GQSKRVDFCG KGYHLMSFPQ SAPHGVVFLH VTYVPAQEKN FTTAPAICHD GKAHFPREGV FVSNGTHWFV TQRN FYEPQ IITTDNTFVS GNCDVVIGIV NNTVYDPLQP ELDSFKEELD KYFKNHTSPD VDLGDISGIN ASVVNIQKEI DRLNE VAKN LNESLIDLQE LGKYEQGSGY IPEAPRDGQA YVRKDGEWVL LSTFLGRSLE VLFQGPGHHH HHHHHSAWSH PQFEKG GGS GGGGSGGSAW SHPQFEK

UniProtKB: Spike glycoprotein

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Macromolecule #2: NB21 Nanobody

MacromoleculeName: NB21 Nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 15.770573 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MASMTGGQQM GRDPNSQVQL VESGGGLVQA GGSLRLSCAV SGLGAHRVGW FRRAPGKERE FVAAIGANGG NTNYLDSVKG RFTISRDNA KNTIYLQMNS LKPQDTAVYY CAARDIETAE YTYWGQGTQV TVSSKLAAAL EHHHHHH

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 91000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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