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

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Basic information

Entry
Database: PDB / ID: 9ixv
TitleCryo-EM structure of MERS-CoV S1-NTD bound with KNIH-88 Fab
Components
  • Heavy chain from KNIH-88, monoclonal antibody
  • Light chain from KNIH-88, monoclonal antibody
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / monoclonal antibody / MERS-CoV S1-NTD / KNIH-88 / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX
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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) 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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesMiddle East respiratory syndrome-related coronavirus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsJeon, H. / Yoo, Y. / Park, K. / Choi, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Infect Dis / Year: 2025
Title: A Novel Antibody Against the Non-Receptor-Binding Domain Region of Middle East Respiratory Syndrome Coronavirus Spike Protein.
Authors: So-Young Lee / Hye-Min Woo / Hyunbum Jeon / Nayoung 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-CoV 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-CoV have been approved for clinical use. The spike 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 7 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 5 monoclonal antibodies 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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike glycoprotein
H: Heavy chain from KNIH-88, monoclonal antibody
L: Light chain from KNIH-88, monoclonal antibody


Theoretical massNumber of molelcules
Total (without water)85,3273
Polymers85,3273
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 39307.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus
Gene: S, 3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: K9N5Q8
#2: Antibody Heavy chain from KNIH-88, monoclonal antibody


Mass: 22800.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#3: Antibody Light chain from KNIH-88, monoclonal antibody


Mass: 23218.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of MERS-CoV S1-NTD bound with KNIH-88 Fab
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 600 nm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7PHENIX1.20.1model fitting
19PHENIX1.20.1model refinement
20Coot0.9.8.92model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 1235152
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150340 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
15X4R

5x4r

15X4R1PDBexperimental model
21AlphaFoldin silico model
RefinementCross valid method: NONE

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