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- EMDB-61604: Cryo-EM structure of the GD-BatCoV (BtCoV/Ii/GD/2014-422) RBD in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-61604
TitleCryo-EM structure of the GD-BatCoV (BtCoV/Ii/GD/2014-422) RBD in complex with human DPP4
Map data
Sample
  • Complex: GD-BatCoV-RBD (BtCoV/Ii/GD/2014-422): human DPP4 complex
    • Protein or peptide: Dipeptidyl peptidase 4 soluble form,Isoform 1 of Immunoglobulin heavy constant gamma 1
    • Protein or peptide: Spike glycoprotein,Isoform 1 of Immunoglobulin heavy constant gamma 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordscomplex / VIRAL PROTEIN
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 speciesMiddle East respiratory syndrome-related coronavirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsYuan H / Xiong X
Funding support3 items
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, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61604.png

Downloads & links

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Map

FileDownload / File: emd_61604.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 320 pix.
= 422.4 Å		1.32 Å/pix.
x 320 pix.
= 422.4 Å		1.32 Å/pix.
x 320 pix.
= 422.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.021
Minimum - Maximum-0.10814377 - 0.19177765
Average (Standard dev.)-0.000006119179 (±0.005409809)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61604_half_map_1.map
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Half map: #1

Fileemd_61604_half_map_2.map
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Sample components

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Entire : GD-BatCoV-RBD (BtCoV/Ii/GD/2014-422): human DPP4 complex

EntireName: GD-BatCoV-RBD (BtCoV/Ii/GD/2014-422): human DPP4 complex
Components
  • Complex: GD-BatCoV-RBD (BtCoV/Ii/GD/2014-422): human DPP4 complex
    • Protein or peptide: Dipeptidyl peptidase 4 soluble form,Isoform 1 of Immunoglobulin heavy constant gamma 1
    • Protein or peptide: Spike glycoprotein,Isoform 1 of Immunoglobulin heavy constant gamma 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: GD-BatCoV-RBD (BtCoV/Ii/GD/2014-422): human DPP4 complex

SupramoleculeName: GD-BatCoV-RBD (BtCoV/Ii/GD/2014-422): human DPP4 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Middle East respiratory syndrome-related coronavirus

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Macromolecule #1: Dipeptidyl peptidase 4 soluble form,Isoform 1 of Immunoglobulin h...

MacromoleculeName: Dipeptidyl peptidase 4 soluble form,Isoform 1 of Immunoglobulin heavy constant gamma 1
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 114.306672 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLASRKTYT LTDYLKNTYR LKLYSLRWIS DHEYLYKQEN NILVFNAEYG NSSVFLENST FDEFGHSIN DYSISPDGQF ILLEYNYVKQ WRHSYTASYD IYDLNKRQLI TEERIPNNTQ WVTWSPVGHK LAYVWNNDIY V KIEPNLPS ...String:
MPMGSLQPLA TLYLLGMLVA SVLASRKTYT LTDYLKNTYR LKLYSLRWIS DHEYLYKQEN NILVFNAEYG NSSVFLENST FDEFGHSIN DYSISPDGQF ILLEYNYVKQ WRHSYTASYD IYDLNKRQLI TEERIPNNTQ WVTWSPVGHK LAYVWNNDIY V KIEPNLPS YRITWTGKED IIYNGITDWV YEEEVFSAYS ALWWSPNGTF LAYAQFNDTE VPLIEYSFYS DESLQYPKTV RV PYPKAGA VNPTVKFFVV NTDSLSSVTN ATSIQITAPA SMLIGDHYLC DVTWATQERI SLQWLRRIQN YSVMDICDYD ESS GRWNCL VARQHIEMST TGWVGRFRPS EPHFTLDGNS FYKIISNEEG YRHICYFQID KKDCTFITKG TWEVIGIEAL TSDY LYYIS NEYKGMPGGR NLYKIQLSDY TKVTCLSCEL NPERCQYYSV SFSKEAKYYQ LRCSGPGLPL YTLHSSVNDK GLRVL EDNS ALDKMLQNVQ MPSKKLDFII LNETKFWYQM ILPPHFDKSK KYPLLLDVYA GPCSQKADTV FRLNWATYLA STENII VAS FDGRGSGYQG DKIMHAINRR LGTFEVEDQI EAARQFSKMG FVDNKRIAIW GWSYGGYVTS MVLGSGSGVF KCGIAVA PV SRWEYYDSVY TERYMGLPTP EDNLDHYRNS TVMSRAENFK QVEYLLIHGT ADDNVHFQQS AQISKALVDV GVDFQAMW Y TDEDHGIASS TAHQHIYTHM SHFIKQCFSL PDPLVPRGSG GGGDPEPKSC DKTHTCPPCP APELLGGPSV FLFPPKPKD TLMISRTPEV TCVVVDVSHE DPEVKFNWYV DGVEVHNAKT KPREEQYNST YRVVSVLTVL HQDWLNGKEY KCKVSNKALP APIEKTISK AKGQPREPQV YTLPPSRDEL TKNQVSLTCL VKGFYPSDIA VEWESNGQPE NNYKTTPPVL DSDGSFFLYS K LTVDKSRW QQGNVFSCSV MHEALHNHYT QKSLSLSPGK

UniProtKB: Dipeptidyl peptidase 4, Immunoglobulin heavy constant gamma 1

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Macromolecule #2: Spike glycoprotein,Isoform 1 of Immunoglobulin heavy constant gamma 1

MacromoleculeName: Spike glycoprotein,Isoform 1 of Immunoglobulin heavy constant gamma 1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.544816 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRLSVCLLMF LLTPIKEVHS RGQFIEQPNS VECDFTKLLS GTPPQVYNFN RLVFTNCNYN LTKLLSLFMV NEFSCDGISP DAIARGCYS SLTVDYFAYP LSMKSYMQPG SAGVISQYNY KQSFANPTCR IFATAPANLT ITKPSSYSFI SKCSRLTGDN S HIETPIVI ...String:
MRLSVCLLMF LLTPIKEVHS RGQFIEQPNS VECDFTKLLS GTPPQVYNFN RLVFTNCNYN LTKLLSLFMV NEFSCDGISP DAIARGCYS SLTVDYFAYP LSMKSYMQPG SAGVISQYNY KQSFANPTCR IFATAPANLT ITKPSSYSFI SKCSRLTGDN S HIETPIVI NPGEYSICKN FAPNGFSQDG DYFTRQLSQL EGGGILVGVG SVTPMTDTLQ MGFIISVQYG TDTNSVCPMM DL GNSTTIT DKLGVCVEYD PLVPRGSGGG GDPEPKSCDK THTCPPCPAP ELLGGPSVFL FPPKPKDTLM ISRTPEVTCV VVD VSHEDP EVKFNWYVDG VEVHNAKTKP REEQYNSTYR VVSVLTVLHQ DWLNGKEYKC KVSNKALPAP IEKTISKAKG QPRE PQVYT LPPSRDELTK NQVSLTCLVK GFYPSDIAVE WESNGQPENN YKTTPPVLDS DGSFFLYSKL TVDKSRWQQG NVFSC SVMH EALHNHYTQK SLSLSPGK

UniProtKB: Spike glycoprotein, Immunoglobulin heavy constant gamma 1

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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: 8 / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4kr0

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 72715
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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