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- EMDB-43139: SARS-CoV-2 Spike S2 bound to Fab 54043-5 -

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Basic information

Entry
Database: EMDB / ID: EMD-43139
TitleSARS-CoV-2 Spike S2 bound to Fab 54043-5
Map dataFinal refinement volume, DeepEMhancer sharpened. Used for model building.
Sample
  • Complex: Trimeric S2 bound to Fab 54043-5
    • Complex: S2
      • Protein or peptide: Spike protein S2
    • Complex: Fab 54043-5
      • Protein or peptide: 54043-5 Fab Heavy Chain
      • Protein or peptide: 54043-5 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 spike / S2 subunit / viral fusion / monoclonal antibody / VIRAL 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 / 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: 3.0 Å
AuthorsJohnson NV / McLellan JS
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2024
Title: Discovery and characterization of a pan-betacoronavirus S2-binding antibody.
Authors: Nicole V Johnson / Steven C Wall / Kevin J Kramer / Clinton M Holt / Sivakumar Periasamy / Simone I Richardson / Nelia P Manamela / Naveenchandra Suryadevara / Emanuele Andreano / Ida ...Authors: Nicole V Johnson / Steven C Wall / Kevin J Kramer / Clinton M Holt / Sivakumar Periasamy / Simone I Richardson / Nelia P Manamela / Naveenchandra Suryadevara / Emanuele Andreano / Ida Paciello / Giulio Pierleoni / Giulia Piccini / Ying Huang / Pan Ge / James D Allen / Naoko Uno / Andrea R Shiakolas / Kelsey A Pilewski / Rachel S Nargi / Rachel E Sutton / Alexandria A Abu-Shmais / Robert Parks / Barton F Haynes / Robert H Carnahan / James E Crowe / Emanuele Montomoli / Rino Rappuoli / Alexander Bukreyev / Ted M Ross / Giuseppe A Sautto / Jason S McLellan / Ivelin S Georgiev /
Abstract: The continued emergence of deadly human coronaviruses from animal reservoirs highlights the need for pan-coronavirus interventions for effective pandemic preparedness. Here, using linking B cell ...The continued emergence of deadly human coronaviruses from animal reservoirs highlights the need for pan-coronavirus interventions for effective pandemic preparedness. Here, using linking B cell receptor to antigen specificity through sequencing (LIBRA-seq), we report a panel of 50 coronavirus antibodies isolated from human B cells. Of these, 54043-5 was shown to bind the S2 subunit of spike proteins from alpha-, beta-, and deltacoronaviruses. A cryoelectron microscopy (cryo-EM) structure of 54043-5 bound to the prefusion S2 subunit of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike defined an epitope at the apex of S2 that is highly conserved among betacoronaviruses. Although non-neutralizing, 54043-5 induced Fc-dependent antiviral responses in vitro, including antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP). In murine SARS-CoV-2 challenge studies, protection against disease was observed after introduction of Leu234Ala, Leu235Ala, and Pro329Gly (LALA-PG) substitutions in the Fc region of 54043-5. Together, these data provide new insights into the protective mechanisms of non-neutralizing antibodies and define a broadly conserved epitope within the S2 subunit.
History
DepositionDec 14, 2023-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43139.png

Downloads & links

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Map

FileDownload / File: emd_43139.map.gz / Format: CCP4 / Size: 574.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal refinement volume, DeepEMhancer sharpened. Used for model building.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 532 pix.
= 500.08 Å		0.94 Å/pix.
x 532 pix.
= 500.08 Å		0.94 Å/pix.
x 532 pix.
= 500.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.03171633 - 1.7214057
Average (Standard dev.)0.00028469463 (±0.012144651)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions532532532
Spacing532532532
CellA=B=C: 500.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Final refinement volume, sharpened. Not DeepEMhancer sharpened.

Fileemd_43139_additional_1.map
AnnotationFinal refinement volume, sharpened. Not DeepEMhancer sharpened.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_43139_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_43139_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trimeric S2 bound to Fab 54043-5

EntireName: Trimeric S2 bound to Fab 54043-5
Components
  • Complex: Trimeric S2 bound to Fab 54043-5
    • Complex: S2
      • Protein or peptide: Spike protein S2
    • Complex: Fab 54043-5
      • Protein or peptide: 54043-5 Fab Heavy Chain
      • Protein or peptide: 54043-5 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Trimeric S2 bound to Fab 54043-5

SupramoleculeName: Trimeric S2 bound to Fab 54043-5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: S2

SupramoleculeName: S2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: Fab 54043-5

SupramoleculeName: Fab 54043-5 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Spike protein S2

MacromoleculeName: Spike protein S2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 65.948469 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRPTWAWWLF LVLLLALWAP ARGASQMSLG AENCVAYSNN SIAIPTNFTI SVTTEILPVS MTKTSVDCTM YICGDSTECS NLLLQYGSF CTQLNRALTG IAVEQDKNTQ EVFAQVKQIY CTPPIKDFGG FNFSQILPDP SKPSKRSPIE DLLFNKVTLA D AGFIKQYG ...String:
MRPTWAWWLF LVLLLALWAP ARGASQMSLG AENCVAYSNN SIAIPTNFTI SVTTEILPVS MTKTSVDCTM YICGDSTECS NLLLQYGSF CTQLNRALTG IAVEQDKNTQ EVFAQVKQIY CTPPIKDFGG FNFSQILPDP SKPSKRSPIE DLLFNKVTLA D AGFIKQYG DCLGDIAARD LICAQKFNGL TVLPPLLTDE MIAQYTSALL AGTITSGWTF GAGPALQIPF PMQMAYRFNG IG VTQNVLY ENQKLIANQF NSAIGKIQDS LSSTPSALGK LQDVVNQNAE ALNTLVKQLS SNFGAISSVL NDILSRLDPP EAE VQIDRL ITGRLQSLQT YVTQQLIRAA EIRASANLAA TKMSECVLGQ SKRVDFCGKG YHLMSFPQSA PHGVVFLHVT YVPA QEKNF TTAPAICHDG KAHFPREGVF VSNGTHWFVT QRNFYEPQII TTDNTFVSGN CDVVIGIVNN TVYDPLQPEL DSFKE ELDK YFKNHTSPDV DLGDISGINA SVVNIQKEID RLNEVAKNLN ESLIDLQELG KYEQGSGYIP EAPRDGQAYV RKDGEW VLL STFLGRSLEV LFQGPGHHHH HHHHSAWSHP QFEK

UniProtKB: Spike glycoprotein

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Macromolecule #2: 54043-5 Fab Heavy Chain

MacromoleculeName: 54043-5 Fab Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.130172 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVKPSQTLSL TCTVSGDSIS NSSYYWSWIR QYPSRRLEWI GYIYYNGRTY YNPSLNSRLS ISLDTSKNHF SLKLSSLTA ADTALYYCAR GFLGYCAGGS CFLNWLDPWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS ...String:
QVQLQESGPG LVKPSQTLSL TCTVSGDSIS NSSYYWSWIR QYPSRRLEWI GYIYYNGRTY YNPSLNSRLS ISLDTSKNHF SLKLSSLTA ADTALYYCAR GFLGYCAGGS CFLNWLDPWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSCDK

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Macromolecule #3: 54043-5 Fab Light Chain

MacromoleculeName: 54043-5 Fab Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.294916 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIIMTQSPAT LSVSPGGRAT LSCRASQSVS NNLAWYQQKP GQTPRLLIHG ASTRATGIPA RFSGSGSGTE FTLTISSLQS EDFAVYYCH QYHNWLLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
EIIMTQSPAT LSVSPGGRAT LSCRASQSVS NNLAWYQQKP GQTPRLLIHG ASTRATGIPA RFSGSGSGTE FTLTISSLQS EDFAVYYCH QYHNWLLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 15 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6xkl

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 126621
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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