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- EMDB-68192: MERS-CoV RBD in complex with receptor DPP4 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-68192
TitleMERS-CoV RBD in complex with receptor DPP4
Map data
Sample
  • Complex: Cryo-EM structure of MERS-CoV RBD in complex with receptor DPP4
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Dipeptidyl peptidase 4 membrane form
KeywordsMERS-CoV / DPP4 / VIRAL PROTEIN / 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 speciesTequatrovirus T4 / Middle East respiratory syndrome-related coronavirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsWang YJ / Sun L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92469108 China
CitationJournal: To Be Published
Title: Structure of MERS-CoV RBD in complex with receptor DPP4.
Authors: Wang YJ / Sun L
History
DepositionJan 7, 2026-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68192.png

Downloads & links

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Map

FileDownload / File: emd_68192.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 300 pix.
= 279.6 Å		0.93 Å/pix.
x 300 pix.
= 279.6 Å		0.93 Å/pix.
x 300 pix.
= 279.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.5102747 - 1.2406596
Average (Standard dev.)0.00324736 (±0.044174932)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 279.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_68192_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_68192_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of MERS-CoV RBD in complex with receptor DPP4

EntireName: Cryo-EM structure of MERS-CoV RBD in complex with receptor DPP4
Components
  • Complex: Cryo-EM structure of MERS-CoV RBD in complex with receptor DPP4
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Dipeptidyl peptidase 4 membrane form

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Supramolecule #1: Cryo-EM structure of MERS-CoV RBD in complex with receptor DPP4

SupramoleculeName: Cryo-EM structure of MERS-CoV RBD in complex with receptor DPP4
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Tequatrovirus T4

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Middle East respiratory syndrome-related coronavirus
Molecular weightTheoretical: 147.846609 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MIHSVFLLMF LLTPTESYVD VGPDSVKSAC IEVDIQQTFF DKTWPRPIDV SKADGIIYPQ GRTYSNITIT YQGLFPYQGD HGDMYVYSA GHATGTTPQK LFVANYSQDV KQFANGFVVR IGAAANSTGT VIISPSTSAT IRKIYPAFML GSSVGNFSDG K MGRFFNHT ...String:
MIHSVFLLMF LLTPTESYVD VGPDSVKSAC IEVDIQQTFF DKTWPRPIDV SKADGIIYPQ GRTYSNITIT YQGLFPYQGD HGDMYVYSA GHATGTTPQK LFVANYSQDV KQFANGFVVR IGAAANSTGT VIISPSTSAT IRKIYPAFML GSSVGNFSDG K MGRFFNHT LVLLPDGCGT LLRAFYCILE PRSGNHCPAG NSYTSFATYH TPATDCSDGN YNRNASLNSF KEYFNLRNCT FM YTYNITE DEILEWFGIT QTAQGVHLFS SRYVDLYGGN MFQFATLPVY DTIKYYSIIP HSIRSIQSDR KAWAAFYVYK LQP LTFLLD FSVDGYIRRA IDCGFNDLSQ LHCSYESFDV ESGVYSVSSF EAKPSGSVVE QAEGVECDFS PLLSGTPPQV YNFK RLVFT NCNYNLTKLL SLFSVNDFTC SQISPAAIAS NCYSSLILDY FSYPLSMKSD LSVSSAGPIS QFNYKQSFSN PTCLI LATV PHNLTTITKP LKYSYINKCS RFLSDDRTEV PQLVNANQYS PCVSIVPSTV WEDGDYYRKQ LSPLEGGGWL VASGST VAM TEQLQMGFGI TVQYGTDTNS VCPKLEFAND TKIASQLGNC VEYSLYGVSG RGVFQNCTAV GVRQQRFVYD AYQNLVG YY SDDGNYYCLR ACVSVPVSVI YDKETKTHAT LFGSVACEHI SSTMSQYSRS TRSMLKRRDS TYGPLQTPVG CVLGLVNS S LFVEDCKLPL GQSLCALPDT PSTLTPRSVR SVPGEMRLAS IAFNHPIQVD QLNSSYFKLS IPTNFSFGVT QEYIQTTIQ KVTVDCKQYV CNGFQKCEQL LREYGQFCSK INQALHGANL RQDDSVRNLF ASVKSSQSSP IIPGFGGDFN LTLLEPVSIS TGSRSARSA IEDLLFDKVT IADPGYMQGY DDCMQQGPAS ARDLICAQYV AGYKVLPPLM DVNMEAAYTS SLLGSIAGVG W TAGLSSFA AIPFAQSIFY RLNGVGITQQ VLSENQKLIA NKFNQALGAM QTGFTTTNEA FHKVQDAVNN NAQALSKLAS EL SNTFGAI SASIGDIIQR LDVLEQDAQI DRLINGRLTT LNAFVAQQLV RSESAALSAQ LAKDKVNECV KAQSKRSGFC GQG THIVSF VVNAPNGLYF MHVGYYPSNH IEVVSAYGLC DAANPTNCIA PVNGYFIKTN NTRIVDEWSY TGSSFYAPEP ITSL NTKYV APQVTYQNIS TNLPPPLLGN STGIDFQDEL DEFFKNVSTS IPNFGSLTQI NTTLLDLTYE MLSLQQVVKA LNESY IDLK ELGNYTYGSG YIPEAPRDGQ AYVRKDGEWV LLSTFLGRSL EVLFQGPGHH HHHHHH

UniProtKB: Spike glycoprotein

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Macromolecule #2: Dipeptidyl peptidase 4 membrane form

MacromoleculeName: Dipeptidyl peptidase 4 membrane form / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.249156 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAAD MGSNKGTDDA TADSRKTYTL TDYLKNTYRL KLYSLRWISD HEYLYKQEN NILVFNAEYG NSSVFLENST FDEFGHSIND YSISPDGQFI LLEYNYVKQW RHSYTASYDI YDLNKRQLIT E ERIPNNTQ ...String:
MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAAD MGSNKGTDDA TADSRKTYTL TDYLKNTYRL KLYSLRWISD HEYLYKQEN NILVFNAEYG NSSVFLENST FDEFGHSIND YSISPDGQFI LLEYNYVKQW RHSYTASYDI YDLNKRQLIT E ERIPNNTQ WVTWSPVGHK LAYVWNNDIY VKIEPNLPSY RITWTGKEDI IYNGITDWVY EEEVFSAYSA LWWSPNGTFL AY AQFNDTE VPLIEYSFYS DESLQYPKTV RVPYPKAGAV NPTVKFFVVN TDSLSSVTNA TSIQITAPAS MLIGDHYLCD VTW ATQERI SLQWLRRIQN YSVMDICDYD ESSGRWNCLV ARQHIEMSTT GWVGRFRPSE PHFTLDGNSF YKIISNEEGY RHIC YFQID KKDCTFITKG TWEVIGIEAL TSDYLYYISN EYKGMPGGRN LYKIQLSDYT KVTCLSCELN PERCQYYSVS FSKEA KYYQ LRCSGPGLPL YTLHSSVNDK GLRVLEDNSA LDKMLQNVQM PSKKLDFIIL NETKFWYQMI LPPHFDKSKK YPLLLD VYA GPCSQKADTV FRLNWATYLA STENIIVASF DGRGSGYQGD KIMHAINRRL GTFEVEDQIE AARQFSKMGF VDNKRIA IW GWSYGGYVTS MVLGSGSGVF KCGIAVAPVS RWEYYDSVYT ERYMGLPTPE DNLDHYRNST VMSRAENFKQ VEYLLIHG T ADDNVHFQQS AQISKALVDV GVDFQAMWYT DEDHGIASST AHQHIYTHMS HFIKQCFSLP GSHHHHHHHH

UniProtKB: Dipeptidyl peptidase 4

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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: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 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: OTHER / Details: Predict the initial structure with SWISS
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 133001
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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