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- EMDB-62194: Cryo-EM structure of MjHKU4r-CoV-1 receptor-binding domain comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-62194
TitleCryo-EM structure of MjHKU4r-CoV-1 receptor-binding domain complexed with human CD26
Map data
Sample
  • Complex: Cryo-EM structure of MjHKU4r-CoV-1 receptor-binding domain complexed with human CD26
    • Protein or peptide: Dipeptidyl peptidase 4 soluble form
    • Protein or peptide: Spike protein S1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsComplex / VIRAL PROTEIN/HYDROLASE / VIRAL PROTEIN-HYDROLASE 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 / chemorepellent activity / psychomotor behavior / intercellular canaliculus / dipeptidyl-peptidase activity ...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 / chemorepellent activity / psychomotor behavior / intercellular canaliculus / dipeptidyl-peptidase activity / peptide hormone processing / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / aminopeptidase activity / endothelial cell migration / behavioral fear response / 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 / 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 exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
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 ...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 / 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
Similarity search - Domain/homology
Spike glycoprotein / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesMammalia (mammals) / Homo sapiens (human) / Tylonycteris bat coronavirus HKU4
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsSun JQ / Han P
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29010202 China
CitationJournal: Hlife / Year: 2025
Title: Rational design of human CD26 receptor for a strong neutralizing ability against MjHKU4r-CoV-1 and MERS-CoV
Authors: Zhang Y / Tian M / Han Y / Sun J / Li W / Bai C / Su C / Han P
History
DepositionOct 27, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62194.png

Downloads & links

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Map

FileDownload / File: emd_62194.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 440 pix.
= 303.6 Å		0.69 Å/pix.
x 440 pix.
= 303.6 Å		0.69 Å/pix.
x 440 pix.
= 303.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.101
Minimum - Maximum-0.27722237 - 0.8024277
Average (Standard dev.)-0.0016097032 (±0.023236003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 303.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62194_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62194_half_map_2.map
Projections & Slices
AxesZYX

Projections

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of MjHKU4r-CoV-1 receptor-binding domain comple...

EntireName: Cryo-EM structure of MjHKU4r-CoV-1 receptor-binding domain complexed with human CD26
Components
  • Complex: Cryo-EM structure of MjHKU4r-CoV-1 receptor-binding domain complexed with human CD26
    • Protein or peptide: Dipeptidyl peptidase 4 soluble form
    • Protein or peptide: Spike protein S1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of MjHKU4r-CoV-1 receptor-binding domain comple...

SupramoleculeName: Cryo-EM structure of MjHKU4r-CoV-1 receptor-binding domain complexed with human CD26
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mammalia (mammals)

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Macromolecule #1: Dipeptidyl peptidase 4 soluble form

MacromoleculeName: Dipeptidyl peptidase 4 soluble form / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.445375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTSRKTYTLT DYLKNTYRLK LYSLRWISDH EYLYKQENNI LVFNAEYGNS SVFLENSTF DEFGHSINDY SISPDGQFIL LEYNYVKQWR HSYTASYDIY DLNKRQLITE ERIPNNTQWV TWSPVGHKLA Y VWNNDIYV ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTSRKTYTLT DYLKNTYRLK LYSLRWISDH EYLYKQENNI LVFNAEYGNS SVFLENSTF DEFGHSINDY SISPDGQFIL LEYNYVKQWR HSYTASYDIY DLNKRQLITE ERIPNNTQWV TWSPVGHKLA Y VWNNDIYV KIEPNLPSYR ITWTGKEDII YNGITDWVYE EEVFSAYSAL WWSPNGTFLA YAQFNDTEVP LIEYSFYSDE SL QYPKTVR VPYPKAGAVN PTVKFFVVNT DSLSSVTNAT SIQITAPASM LIGDHYLCDV TWATQERISL QWLRRIQNYS VMD ICDYDE SSGRWNCLVA RQHIEMSTTG WVGRFRPSEP HFTLDGNSFY KIISNEEGYR HICYFQIDKK DCTFITKGTW EVIG IEALT SDYLYYISNE YKGMPGGRNL YKIQLSDYTK VTCLSCELNP ERCQYYSVSF SKEAKYYQLR CSGPGLPLYT LHSSV NDKG LRVLEDNSAL DKMLQNVQMP SKKLDFIILN ETKFWYQMIL PPHFDKSKKY PLLLDVYAGP CSQKADTVFR LNWATY LAS TENIIVASFD GRGSGYQGDK IMHAINRRLG TFEVEDQIEA ARQFSKMGFV DNKRIAIWGW SYGGYVTSMV LGSGSGV FK CGIAVAPVSR WEYYDSVYTE RYMGLPTPED NLDHYRNSTV MSRAENFKQV EYLLIHGTAD DNVHFQQSAQ ISKALVDV G VDFQAMWYTD EDHGIASSTA HQHIYTHMSH FIKQCFSLPH HHHHH

UniProtKB: Dipeptidyl peptidase 4

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Macromolecule #2: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 2
Details: Sequence reference for strain 'Tylonycteris bat coronavirus HKU4' is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0AAE8ZFM2.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tylonycteris bat coronavirus HKU4
Molecular weightTheoretical: 25.60725 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHSSALLCCL VLLTGVRAKE CDFTPMLVGV PPQVYNFKRL VFTNCNYNLT KLLSLFMVNE FSCNGISPDA IARGCYSSLT VDYFAYPLS MRSYIQPGSA GDISLYNYKQ SFANPTCRVL ATAPANLTLT KPSAYGYFQK CSRVSGEHNS VETPLYINPG E YSICRSFS ...String:
MHSSALLCCL VLLTGVRAKE CDFTPMLVGV PPQVYNFKRL VFTNCNYNLT KLLSLFMVNE FSCNGISPDA IARGCYSSLT VDYFAYPLS MRSYIQPGSA GDISLYNYKQ SFANPTCRVL ATAPANLTLT KPSAYGYFQK CSRVSGEHNS VETPLYINPG E YSICRSFS PYGFSEDGEV FRRQLTQYEG GGILVGVGAK LAMTDKLEMG FIISVQYGTD TNSVCPMHHH HHH

UniProtKB: Spike glycoprotein

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 10 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 237919
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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