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- PDB-22ea: Cryo-EM structure of MERS-CoV S protein bound with receptor DPP4 ... -

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Basic information

Entry
Database: PDB / ID: 22ea
TitleCryo-EM structure of MERS-CoV S protein bound with receptor DPP4 in the conformation 3 (3 up RBD and 3 DPP4 bound).
Components
  • Dipeptidyl peptidase 4 membrane form
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / MERS-CoV / S protein / Receptor / VIRAL PROTEIN-receptor complex
Function / homology
Function and homology information


glucagon processing / regulation of cell-cell adhesion mediated by integrin / negative regulation of neutrophil chemotaxis / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / dipeptidyl-peptidase IV / negative regulation of extracellular matrix disassembly / chemorepellent activity / intercellular canaliculus / dipeptidyl-peptidase activity / peptide hormone processing ...glucagon processing / regulation of cell-cell adhesion mediated by integrin / negative regulation of neutrophil chemotaxis / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / dipeptidyl-peptidase IV / negative regulation of extracellular matrix disassembly / chemorepellent activity / intercellular canaliculus / dipeptidyl-peptidase activity / peptide hormone processing / lamellipodium membrane / aminopeptidase activity / endothelial cell migration / endocytic vesicle / T cell costimulation / receptor-mediated endocytosis of virus by host cell / serine-type peptidase activity / T cell activation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / lamellipodium / virus receptor activity / protease binding / response to hypoxia / positive regulation of viral entry into host cell / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / cell adhesion / apical plasma membrane / endocytosis involved in viral entry into host cell / membrane raft / serine-type endopeptidase activity / fusion of virus membrane with host plasma membrane / signaling receptor binding / focal adhesion / lysosomal membrane / fusion of virus membrane with host endosome membrane / positive regulation of cell population proliferation / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / cell surface / protein homodimerization activity / proteolysis / extracellular exosome / extracellular region / membrane / identical protein binding / plasma 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 / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Peptidase S9, prolyl oligopeptidase, catalytic domain ...Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold / 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 glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 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
Spike glycoprotein / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Middle East respiratory syndrome-related coronavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsWang, Y.J. / Sun, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92469108 China
CitationJournal: To Be Published
Title: Cryo-EM structure of MERS-CoV S protein bound with receptor DPP4 in the conformation 3 (3 up RBD and 3 DPP4 bound).
Authors: Wang, Y.J. / Sun, L.
History
DepositionJan 7, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Dipeptidyl peptidase 4 membrane form
E: Dipeptidyl peptidase 4 membrane form
H: Spike glycoprotein
F: Dipeptidyl peptidase 4 membrane form
G: Dipeptidyl peptidase 4 membrane form
I: Spike glycoprotein
A: Dipeptidyl peptidase 4 membrane form
B: Dipeptidyl peptidase 4 membrane form
C: Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)991,0359
Polymers991,0359
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
Dipeptidyl peptidase 4 membrane form / Dipeptidyl peptidase IV membrane form


Mass: 91249.156 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP4, ADCP2, CD26 / Production host: Homo sapiens (human) / References: UniProt: P27487
#2: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 147846.609 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)
Gene: S, 3 / Production host: Homo sapiens (human) / References: UniProt: K9N5Q8
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: MERS-CoV S protein bound with receptor DPP4 in the conformation 3 (3 up RBD and 3 DPP4 bound).
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Tequatrovirus T4
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.17.1_3660model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44232 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00165469
ELECTRON MICROSCOPYf_angle_d0.32189070
ELECTRON MICROSCOPYf_dihedral_angle_d6.50423448
ELECTRON MICROSCOPYf_chiral_restr0.0399639
ELECTRON MICROSCOPYf_plane_restr0.00311454

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