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- PDB-9jmj: Cryo-EM structure of the GD-BatCoV (BtCoV/Ii/GD/2014-422) RBD in ... -

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Basic information

Entry
Database: PDB / ID: 9jmj
TitleCryo-EM structure of the GD-BatCoV (BtCoV/Ii/GD/2014-422) RBD in complex with human DPP4
Components
  • Dipeptidyl peptidase 4 soluble form,Isoform 1 of Immunoglobulin heavy constant gamma 1
  • Spike glycoprotein,Isoform 1 of Immunoglobulin heavy constant gamma 1
KeywordsVIRAL PROTEIN / complex
Function / homology
Function and homology information


glucagon processing / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / Fc-gamma receptor I complex binding / chemorepellent activity / psychomotor behavior / intercellular canaliculus ...glucagon processing / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / Fc-gamma receptor I complex binding / chemorepellent activity / psychomotor behavior / intercellular canaliculus / complement-dependent cytotoxicity / IgG immunoglobulin complex / dipeptidyl-peptidase activity / antibody-dependent cellular cytotoxicity / peptide hormone processing / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / locomotory exploration behavior / lamellipodium membrane / FCGR activation / endocytic vesicle / complement activation, classical pathway / Role of phospholipids in phagocytosis / aminopeptidase activity / endothelial cell migration / behavioral fear response / antigen binding / T cell costimulation / receptor-mediated endocytosis of virus by host cell / serine-type peptidase activity / FCGR3A-mediated IL10 synthesis / T cell activation / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / antibacterial humoral response / lamellipodium / virus receptor activity / protease binding / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / response to hypoxia / receptor-mediated virion attachment to host cell / cell adhesion / apical plasma membrane / membrane raft / endocytosis involved in viral entry into host cell / signaling receptor binding / lysosomal membrane / fusion of virus membrane with host plasma membrane / serine-type endopeptidase activity / focal adhesion / 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 space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, HKU4-like / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Prolyl endopeptidase family serine active site. / : / Peptidase S9, serine active site / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Spike glycoprotein S2, coronavirus, C-terminal ...Spike (S) protein S1 subunit, receptor-binding domain, HKU4-like / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Prolyl endopeptidase family serine active site. / : / Peptidase S9, serine active site / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Alpha/Beta hydrolase fold / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Spike glycoprotein / Immunoglobulin heavy constant gamma 1 / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Middle East respiratory syndrome-related coronavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsYuan, H. / Xiong, X.
Funding support3items
OrganizationGrant numberCountry
Other governmentSRPG22-002
Other government2021YFA1300903
Other government2022A1515110495
CitationJournal: Sci Adv / Year: 2025
Title: Structures and receptor binding activities of merbecovirus spike proteins reveal key signatures for human DPP4 adaptation.
Authors: Hang Yuan / Jingjing Wang / Yong Ma / Zimu Li / Xijie Gao / Gul Habib / Banghui Liu / Jing Chen / Jun He / Peng Zhou / Zheng-Li Shi / Xinwen Chen / Xiaoli Xiong /
Abstract: Merbecoviruses from bats, pangolins, and hedgehogs pose significant zoonotic threats, with a limited understanding of receptor binding by their spike (S) proteins. Here, we report cryo-EM structures ...Merbecoviruses from bats, pangolins, and hedgehogs pose significant zoonotic threats, with a limited understanding of receptor binding by their spike (S) proteins. Here, we report cryo-EM structures of GD-BatCoV (BtCoV-422) and SE-PangolinCoV (MjHKU4r-CoV-1) RBDs in complex with human DPP4 (hDPP4). These structures exhibit a substantial offset in their hDPP4 interaction interfaces, revealing a conserved hydrophobic cluster as a convergent signature of DPP4 binding within the MERS-HKU4 clade of merbecoviruses. Structure-guided mutagenesis demonstrates that favorable interactions are distributed across multiple receptor binding motif (RBM) regions, working synergistically to confer high-affinity hDPP4 binding. Swapping of the merbecovirus RBM regions indicate limited plasticity and interchangeability among these regions. In addition, we report cryo-EM structures of six merbecovirus S-trimers. Structure-based phylogenetics suggests that hDPP4-binding merbecoviruses undergo convergent evolution, while ACE2-binding merbecoviruses exhibit diversification in their binding mechanisms. These findings offer critical insights into merbecovirus receptor utilization, providing a structural understanding for future surveillance.
History
DepositionSep 20, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data 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
A: Dipeptidyl peptidase 4 soluble form,Isoform 1 of Immunoglobulin heavy constant gamma 1
C: Dipeptidyl peptidase 4 soluble form,Isoform 1 of Immunoglobulin heavy constant gamma 1
B: Spike glycoprotein,Isoform 1 of Immunoglobulin heavy constant gamma 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,48519
Polymers284,1583
Non-polymers5,32716
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Dipeptidyl peptidase 4 soluble form,Isoform 1 of Immunoglobulin heavy constant gamma 1 / Dipeptidyl peptidase IV soluble form / Ig gamma-1 chain C region / Ig gamma-1 chain C region EU / ...Dipeptidyl peptidase IV soluble form / Ig gamma-1 chain C region / Ig gamma-1 chain C region EU / Ig gamma-1 chain C region KOL / Ig gamma-1 chain C region NIE


Mass: 114306.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP4, ADCP2, CD26, IGHG1 / Production host: Homo sapiens (human) / References: UniProt: P27487, UniProt: P01857
#2: Protein Spike glycoprotein,Isoform 1 of Immunoglobulin heavy constant gamma 1 / GD-BatCoV / S glycoprotein / E2 / Peplomer protein / Ig gamma-1 chain C region / Ig gamma-1 chain C ...GD-BatCoV / S glycoprotein / E2 / Peplomer protein / Ig gamma-1 chain C region / Ig gamma-1 chain C region EU / Ig gamma-1 chain C region KOL / Ig gamma-1 chain C region NIE


Mass: 55544.816 Da / Num. of mol.: 1 / Fragment: RBD,RBD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus, (gene. exp.) Homo sapiens (human)
Gene: IGHG1 / Production host: Homo sapiens (human) / References: UniProt: A0A2R4KP93, UniProt: P01857
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 7 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
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: GD-BatCoV-RBD (BtCoV/Ii/GD/2014-422): human DPP4 complex
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Middle East respiratory syndrome-related coronavirus1335626
31Homo sapiens (human)9606
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72715 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314195
ELECTRON MICROSCOPYf_angle_d0.59619304
ELECTRON MICROSCOPYf_dihedral_angle_d4.7321996
ELECTRON MICROSCOPYf_chiral_restr0.0472123
ELECTRON MICROSCOPYf_plane_restr0.0052427

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