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- EMDB-27750: Cryo-EM structure of SARS-CoV-2 RBD in complex with anti-SARS-CoV... -

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Entry
Database: EMDB / ID: EMD-27750
TitleCryo-EM structure of SARS-CoV-2 RBD in complex with anti-SARS-CoV-2 DARPin,SR16m, and two antibody Fabs, S309 and CR3022
Map dataSARS-CoV-2 RBD structure in complex with DARPin, SR16m, and antibody Fabs, S309 and CR3022
Sample
  • Complex: DARPin SR16m in complex with SARS-CoV-2 RBD and antibody Fabs, S309 and CR3022
    • Protein or peptide: Anti-SARS-CoV-2 DARPin SR16m
    • Protein or peptide: Spike protein S1
    • Protein or peptide: Antibody S309 light chain
    • Protein or peptide: antibody S309 heavy chain
    • Protein or peptide: antibody CR3022 heavy chain
    • Protein or peptide: antibody CR3022 light chain
KeywordsDARPins / Anti-SARS-CoV-2 / therapeutics / COVID-19 / 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 / receptor-mediated endocytosis of virus by host cell / membrane fusion / 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 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.26 Å
AuthorsKwon YD / Gorman J / Kwong PD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)HSSN261200800001E United States
CitationJournal: Nat Chem Biol / Year: 2023
Title: A potent and broad neutralization of SARS-CoV-2 variants of concern by DARPins.
Authors: Vikas Chonira / Young D Kwon / Jason Gorman / James Brett Case / Zhiqiang Ku / Rudo Simeon / Ryan G Casner / Darcy R Harris / Adam S Olia / Tyler Stephens / Lawrence Shapiro / Michael F ...Authors: Vikas Chonira / Young D Kwon / Jason Gorman / James Brett Case / Zhiqiang Ku / Rudo Simeon / Ryan G Casner / Darcy R Harris / Adam S Olia / Tyler Stephens / Lawrence Shapiro / Michael F Bender / Hannah Boyd / I-Ting Teng / Yaroslav Tsybovsky / Florian Krammer / Ningyan Zhang / Michael S Diamond / Peter D Kwong / Zhiqiang An / Zhilei Chen /
Abstract: We report the engineering and selection of two synthetic proteins-FSR16m and FSR22-for the possible treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. FSR16m and ...We report the engineering and selection of two synthetic proteins-FSR16m and FSR22-for the possible treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. FSR16m and FSR22 are trimeric proteins composed of DARPin SR16m or SR22 fused with a T4 foldon. Despite selection by a spike protein from a now historical SARS-CoV-2 strain, FSR16m and FSR22 exhibit broad-spectrum neutralization of SARS-CoV-2 strains, inhibiting authentic B.1.351, B.1.617.2 and BA.1.1 viruses, with respective IC values of 3.4, 2.2 and 7.4 ng ml for FSR16m. Cryo-EM structures revealed that these DARPins recognize a region of the receptor-binding domain (residues 456, 475, 486, 487 and 489) overlapping a critical portion of the angiotensin-converting enzyme 2 (ACE2)-binding surface. K18-hACE2 transgenic mice inoculated with B.1.617.2 and receiving intranasally administered FSR16m showed less weight loss and 10-100-fold lower viral burden in upper and lower respiratory tracts. The strong and broad neutralization potency makes FSR16m and FSR22 promising candidates for the prevention and treatment of infection by SARS-CoV-2.
History
DepositionJul 30, 2022-
Header (metadata) releaseDec 7, 2022-
Map releaseDec 7, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27750.png

Downloads & links

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Map

FileDownload / File: emd_27750.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSARS-CoV-2 RBD structure in complex with DARPin, SR16m, and antibody Fabs, S309 and CR3022
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 256 pix.
= 223.488 Å		0.87 Å/pix.
x 256 pix.
= 223.488 Å		0.87 Å/pix.
x 256 pix.
= 223.488 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.873 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.21079898 - 0.40346062
Average (Standard dev.)0.0015653295 (±0.019272504)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 223.488 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: SARS-CoV-2 RBD structure in complex with DARPin, SR16m,...

Fileemd_27750_half_map_1.map
AnnotationSARS-CoV-2 RBD structure in complex with DARPin, SR16m, and antibody Fabs, S309 and CR3022
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: SARS-CoV-2 RBD structure in complex with DARPin, SR16m,...

Fileemd_27750_half_map_2.map
AnnotationSARS-CoV-2 RBD structure in complex with DARPin, SR16m, and antibody Fabs, S309 and CR3022
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DARPin SR16m in complex with SARS-CoV-2 RBD and antibody Fabs, S3...

EntireName: DARPin SR16m in complex with SARS-CoV-2 RBD and antibody Fabs, S309 and CR3022
Components
  • Complex: DARPin SR16m in complex with SARS-CoV-2 RBD and antibody Fabs, S309 and CR3022
    • Protein or peptide: Anti-SARS-CoV-2 DARPin SR16m
    • Protein or peptide: Spike protein S1
    • Protein or peptide: Antibody S309 light chain
    • Protein or peptide: antibody S309 heavy chain
    • Protein or peptide: antibody CR3022 heavy chain
    • Protein or peptide: antibody CR3022 light chain

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Supramolecule #1: DARPin SR16m in complex with SARS-CoV-2 RBD and antibody Fabs, S3...

SupramoleculeName: DARPin SR16m in complex with SARS-CoV-2 RBD and antibody Fabs, S309 and CR3022
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: DARPin SR16m in complex with SARS-CoV-2 RBD and antibody Fabs, S309 and CR3022
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Anti-SARS-CoV-2 DARPin SR16m

MacromoleculeName: Anti-SARS-CoV-2 DARPin SR16m / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.793023 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GKKLLEAARA GQDDEVRILM ANGADVNALD LFGVTPLHLA AERGHLEIVE VLLKNGADVN AGDAFGRTPL HLAALGGHLE IVEVLLKNG ADVNACDLYG VTPLHLAAGL GHLEIVEVLL KNGADVNAQD KFGKTAFDIS IDNGNEDLAE ILQSSSKLAA A L

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Macromolecule #2: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 22.100758 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PNITNLCPFG EVFNATRFAS VYAWNRKRIS NCVADYSVLY NSASFSTFKC YGVSPTKLND LCFTNVYADS FVIRGDEVRQ IAPGQTGKI ADYNYKLPDD FTGCVIAWNS NNLDSKVGGN YNYLYRLFRK SNLKPFERDI STEIYQAGST PCNGVEGFNC Y FPLQSYGF ...String:
PNITNLCPFG EVFNATRFAS VYAWNRKRIS NCVADYSVLY NSASFSTFKC YGVSPTKLND LCFTNVYADS FVIRGDEVRQ IAPGQTGKI ADYNYKLPDD FTGCVIAWNS NNLDSKVGGN YNYLYRLFRK SNLKPFERDI STEIYQAGST PCNGVEGFNC Y FPLQSYGF QPTNGVGYQP YRVVVLSFEL LHAPATVCG

UniProtKB: Spike glycoprotein

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Macromolecule #3: Antibody S309 light chain

MacromoleculeName: Antibody S309 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.204697 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPGT LSLSPGERAT LSCRASQTVS STSLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQHDTSLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
EIVLTQSPGT LSLSPGERAT LSCRASQTVS STSLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQHDTSLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #4: antibody S309 heavy chain

MacromoleculeName: antibody S309 heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.573471 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGASVKV SCKASGYPFT SYGISWVRQA PGQGLEWMGW ISTYNGNTNY AQKFQGRVTM TTDTSTTTGY MELRRLRSD DTAVYYCARD YTRGAWFGES LIGGFDNWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
QVQLVQSGAE VKKPGASVKV SCKASGYPFT SYGISWVRQA PGQGLEWMGW ISTYNGNTNY AQKFQGRVTM TTDTSTTTGY MELRRLRSD DTAVYYCARD YTRGAWFGES LIGGFDNWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SC

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Macromolecule #5: antibody CR3022 heavy chain

MacromoleculeName: antibody CR3022 heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.382369 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TQMQLVQSGT EVKKPGESLK ISCKGSGYGF ITYWIGWVRQ MPGKGLEWMG IIYPGDSETR YSPSFQGQVT ISADKSINTA YLQWSSLKA SDTAIYYCAG GSGISTPMDV WGQGTTVTVA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String:
TQMQLVQSGT EVKKPGESLK ISCKGSGYGF ITYWIGWVRQ MPGKGLEWMG IIYPGDSETR YSPSFQGQVT ISADKSINTA YLQWSSLKA SDTAIYYCAG GSGISTPMDV WGQGTTVTVA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSC

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Macromolecule #6: antibody CR3022 light chain

MacromoleculeName: antibody CR3022 light chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.289885 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQLTQSPDS LAVSLGERAT INCKSSQSVL YSSINKNYLA WYQQKPGQPP KLLIYWASTR ESGVPDRFSG SGSGTDFTLT ISSLQAEDV AVYYCQQYYS TPYTFGQGTK VEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES ...String:
DIQLTQSPDS LAVSLGERAT INCKSSQSVL YSSINKNYLA WYQQKPGQPP KLLIYWASTR ESGVPDRFSG SGSGTDFTLT ISSLQAEDV AVYYCQQYYS TPYTFGQGTK VEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES VTEQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNRG EC

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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

Concentration1 mg/mL
BufferpH: 7.4 / Details: 10 mM HEPES, 7.4, 150 mM NaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.25 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4115887
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7bno


Details: 7BNO for RBD 7TN0 for antibody S309 6YLA for antibody CR3022
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 37197
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7bno


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 134 / Target criteria: CC
Output model

PDB-8dw3:
Cryo-EM structure of SARS-CoV-2 RBD in complex with anti-SARS-CoV-2 DARPin,SR16m, and two antibody Fabs, S309 and CR3022

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