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- EMDB-25574: SARS-CoV-2 S-RBD + Fab 54042-4 -

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Basic information

Entry
Database: EMDB / ID: EMD-25574
TitleSARS-CoV-2 S-RBD + Fab 54042-4
Map dataLocal refinement. SARS-CoV-2 S RBD bound to 54042-4 Fab
Sample
  • Complex: Complex of SARS-CoV-2 S-ECD with 54042-4 Fab
    • Protein or peptide: Spike protein S1
    • Protein or peptide: 54042-4 Fab - Heavy Chain
    • Protein or peptide: 54042-4 Fab - Light Chain
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 / 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 speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsJohnson NV / Mclellan JS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI127521 United States
CitationJournal: Cell Rep / Year: 2021
Title: Potent neutralization of SARS-CoV-2 variants of concern by an antibody with an uncommon genetic signature and structural mode of spike recognition.
Authors: Kevin J Kramer / Nicole V Johnson / Andrea R Shiakolas / Naveenchandra Suryadevara / Sivakumar Periasamy / Nagarajan Raju / Jazmean K Williams / Daniel Wrapp / Seth J Zost / Lauren M Walker ...Authors: Kevin J Kramer / Nicole V Johnson / Andrea R Shiakolas / Naveenchandra Suryadevara / Sivakumar Periasamy / Nagarajan Raju / Jazmean K Williams / Daniel Wrapp / Seth J Zost / Lauren M Walker / Steven C Wall / Clinton M Holt / Ching-Lin Hsieh / Rachel E Sutton / Ariana Paulo / Rachel S Nargi / Edgar Davidson / Benjamin J Doranz / James E Crowe / Alexander Bukreyev / Robert H Carnahan / Jason S McLellan / Ivelin S Georgiev /
Abstract: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages that are more transmissible and resistant to currently approved antibody therapies poses a considerable ...The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages that are more transmissible and resistant to currently approved antibody therapies poses a considerable challenge to the clinical treatment of coronavirus disease (COVID-19). Therefore, the need for ongoing discovery efforts to identify broadly reactive monoclonal antibodies to SARS-CoV-2 is of utmost importance. Here, we report a panel of SARS-CoV-2 antibodies isolated using the linking B cell receptor to antigen specificity through sequencing (LIBRA-seq) technology from an individual who recovered from COVID-19. Of these antibodies, 54042-4 shows potent neutralization against authentic SARS-CoV-2 viruses, including variants of concern (VOCs). A cryoelectron microscopy (cryo-EM) structure of 54042-4 in complex with the SARS-CoV-2 spike reveals an epitope composed of residues that are highly conserved in currently circulating SARS-CoV-2 lineages. Further, 54042-4 possesses uncommon genetic and structural characteristics that distinguish it from other potently neutralizing SARS-CoV-2 antibodies. Together, these findings provide motivation for the development of 54042-4 as a lead candidate to counteract current and future SARS-CoV-2 VOCs.
History
DepositionNov 29, 2021-
Header (metadata) releaseApr 13, 2022-
Map releaseApr 13, 2022-
UpdateApr 13, 2022-
Current statusApr 13, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25574.png

Downloads & links

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Map

FileDownload / File: emd_25574.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refinement. SARS-CoV-2 S RBD bound to 54042-4 Fab
Voxel sizeX=Y=Z: 0.81 Å
Density
Contour LevelBy AUTHOR: 0.362
Minimum - Maximum-0.001046848 - 2.042425
Average (Standard dev.)0.00039080522 (±0.015275543)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 414.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Full SARS-CoV-2 spike trimer with 3 copies of 54042-4 bound

Fileemd_25574_additional_1.map
AnnotationFull SARS-CoV-2 spike trimer with 3 copies of 54042-4 bound
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map

Fileemd_25574_half_map_1.map
AnnotationHalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map

Fileemd_25574_half_map_2.map
AnnotationHalf 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 : Complex of SARS-CoV-2 S-ECD with 54042-4 Fab

EntireName: Complex of SARS-CoV-2 S-ECD with 54042-4 Fab
Components
  • Complex: Complex of SARS-CoV-2 S-ECD with 54042-4 Fab
    • Protein or peptide: Spike protein S1
    • Protein or peptide: 54042-4 Fab - Heavy Chain
    • Protein or peptide: 54042-4 Fab - Light Chain

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Supramolecule #1: Complex of SARS-CoV-2 S-ECD with 54042-4 Fab

SupramoleculeName: Complex of SARS-CoV-2 S-ECD with 54042-4 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 22.603408 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEVR QIAPGQTGK IADYNYKLPD DFTGCVIAWN SNNLDSKVGG NYNYLYRLFR KSNLKPFERD ISTEIYQAGS TPCNGVEGFN C YFPLQSYG ...String:
FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEVR QIAPGQTGK IADYNYKLPD DFTGCVIAWN SNNLDSKVGG NYNYLYRLFR KSNLKPFERD ISTEIYQAGS TPCNGVEGFN C YFPLQSYG FQPTNGVGYQ PYRVVVLSFE LLHAPATVCG PKK

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Macromolecule #2: 54042-4 Fab - Heavy Chain

MacromoleculeName: 54042-4 Fab - Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.145856 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QITLKESGPT LVKPTQTLTL TCTFSGFSLS TIGVGVSWIR QPPGKALDWL ALIYWDDDKR YSPSLKSRLT VTMDTSKNQV VLTLTNMDP VDTATYFCAH GLFSSSDWGG LDVWGQGTTV T

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Macromolecule #3: 54042-4 Fab - Light Chain

MacromoleculeName: 54042-4 Fab - Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.734157 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DMQMTQSPSS LSASVGDRVT ITCRASQSVF TYLNWYQQKP GKAPKLLIYA ASRLQSGVPS RFRGSGSGTD FTLTISSLQP EDFATYYCQ QSHSTPFIFG PGTKVDIK

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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

Concentration0.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
2.0 mMTris-Cltris base
200.0 mMNaClSodium chloridesodium chloride
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: -4 force, 3 s blot.
DetailsSample was monodisperse. All S proteins had 3 Fabs bound.

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 0.0025 µm / Nominal defocus min: 0.0015 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 478385
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6vsb

Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 214408
FSC plot (resolution estimation)

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