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- EMDB-60978: Cryo-EM structure of MERS-CoV S1-NTD bound with KNIH-88 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-60978
TitleCryo-EM structure of MERS-CoV S1-NTD bound with KNIH-88 Fab
Map data
Sample
  • Complex: Cryo-EM structure of MERS-CoV S1-NTD bound with KNIH-88 Fab
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Heavy chain from KNIH-88, monoclonal antibody
    • Protein or peptide: Light chain from KNIH-88, monoclonal antibody
Keywordsmonoclonal antibody / MERS-CoV S1-NTD / KNIH-88 / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX / VIRAL PROTEIN
Function / homology
Function and homology information


membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 / 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 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 speciesHomo sapiens (human) / Middle East respiratory syndrome-related coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsJeon H / Yoo Y / Park K / Choi K
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Infect Dis / Year: 2025
Title: A Novel Antibody Against the Non-RBD Region of Middle East Respiratory Syndrome Coronavirus Spike Protein.
Authors: So-Young Lee / Hye-Min Woo / Hyunbum Jeon / Na-Young Kim / Da Sol Kim / Chan Ki Park / Hyun-Joo Kim / Kyung-Chang Kim / Joo-Yeon Lee / Kunwoong Park / Youngki Yoo / Kiju Choi / Hansaem Lee /
Abstract: The Middle East respiratory syndrome coronavirus (MERS-CoV) was first identified in 2012 and has since spread worldwide. To date, no vaccines or therapeutics against MERS have been approved for ...The Middle East respiratory syndrome coronavirus (MERS-CoV) was first identified in 2012 and has since spread worldwide. To date, no vaccines or therapeutics against MERS have been approved for clinical use. The spike (S) protein of MERS-CoV facilitates attachment and fusion with target cell membranes. Therefore, inhibiting S protein attachment represents a key therapeutic strategy for treating early MERS-CoV infection. Herein, we present seven human neutralizing antibodies (KNIH-58, -68, -72, -78, -88, -90, and -95) against MERS-CoV. KNIH-58 and -68 bound to the receptor-binding subdomain (RBD) of the spike protein, while the other five monoclonal antibodies (mAbs) did not. KNIH-88, which targets the non-RBD region, exhibited potent neutralizing activities in vitro and in a transgenic mouse model, with similar results for KNIH-58. Structural analysis of KNIH-88 bound to the spike protein revealed novel epitopes in the non-RBD region. These findings may facilitate therapeutic and prophylactic antibody development against MERS-CoV.
History
DepositionJul 29, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60978.png

Downloads & links

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Map

FileDownload / File: emd_60978.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 400 pix.
= 298.04 Å		0.75 Å/pix.
x 400 pix.
= 298.04 Å		0.75 Å/pix.
x 400 pix.
= 298.04 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7451 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0547
Minimum - Maximum-0.47531694 - 0.6780739
Average (Standard dev.)0.00013574833 (±0.009418999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 298.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60978_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60978_half_map_1.map
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60978_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of MERS-CoV S1-NTD bound with KNIH-88 Fab

EntireName: Cryo-EM structure of MERS-CoV S1-NTD bound with KNIH-88 Fab
Components
  • Complex: Cryo-EM structure of MERS-CoV S1-NTD bound with KNIH-88 Fab
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Heavy chain from KNIH-88, monoclonal antibody
    • Protein or peptide: Light chain from KNIH-88, monoclonal antibody

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Supramolecule #1: Cryo-EM structure of MERS-CoV S1-NTD bound with KNIH-88 Fab

SupramoleculeName: Cryo-EM structure of MERS-CoV S1-NTD bound with KNIH-88 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Middle East respiratory syndrome-related coronavirus
Molecular weightTheoretical: 39.307207 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MIHSVFLLMF LLTPTESYVD VGPDSVKSAC IEVDIQQTFF DKTWPRPIDV SKADGIIYPQ GRTYSNITIT YQGLFPYQGD HGDMYVYSA GHATGTTPQK LFVANYSQDV KQFANGFVVR IGAAANSTGT VIISPSTSAT IRKIYPAFML GSSVGNFSDG K MGRFFNHT ...String:
MIHSVFLLMF LLTPTESYVD VGPDSVKSAC IEVDIQQTFF DKTWPRPIDV SKADGIIYPQ GRTYSNITIT YQGLFPYQGD HGDMYVYSA GHATGTTPQK LFVANYSQDV KQFANGFVVR IGAAANSTGT VIISPSTSAT IRKIYPAFML GSSVGNFSDG K MGRFFNHT LVLLPDGCGT LLRAFYCILE PRSGNHCPAG NSYTSFATYH TPATDCSDGN YNRNASLNSF KEYFNLRNCT FM YTYNITE DEILEWFGIT QTAQGVHLFS SRYVDLYGGN MFQFATLPVY DTIKYYSIIP HSIRSIQSDR KAWAAFYVYK LQP LTFLLD FSVDGYIRRA IDCGFNDLSQ LHCS

UniProtKB: Spike glycoprotein

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Macromolecule #2: Heavy chain from KNIH-88, monoclonal antibody

MacromoleculeName: Heavy chain from KNIH-88, monoclonal antibody / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.800584 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LIQPGGSLRL SCAASGFTVI DYYMTWVRQA PGKGLEWVSV IYAGGSTYYA DSVKGRFTVS RDYSRNTLYL QMNSLKAED TAVYYCTRDY LAAGGLWGQG ALVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT ...String:
EVQLVESGGG LIQPGGSLRL SCAASGFTVI DYYMTWVRQA PGKGLEWVSV IYAGGSTYYA DSVKGRFTVS RDYSRNTLYL QMNSLKAED TAVYYCTRDY LAAGGLWGQG ALVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEP

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Macromolecule #3: Light chain from KNIH-88, monoclonal antibody

MacromoleculeName: Light chain from KNIH-88, monoclonal antibody / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.218848 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPSS LSASVGDRVT ITCRASQGIR NNLAWYQQKP GQVPELLIYG ASNLKPGVPS RFSGSASGTD FTLTISSMQP EDVATYYCQ KYDSAPLTFG GGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
EIVLTQSPSS LSASVGDRVT ITCRASQGIR NNLAWYQQKP GQVPELLIYG ASNLKPGVPS RFSGSASGTD FTLTISSMQP EDVATYYCQ KYDSAPLTFG GGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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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: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / 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 / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.6 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1235152
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 150340
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5x4r

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9ixv:
Cryo-EM structure of MERS-CoV S1-NTD bound with KNIH-88 Fab

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