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- EMDB-39769: MERS-CoV S ectodomain trimer in complex with receptor DPP4-750E -

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Basic information

Entry
Database: EMDB / ID: EMD-39769
TitleMERS-CoV S ectodomain trimer in complex with receptor DPP4-750E
Map data
Sample
  • Complex: MERS-CoV spike glycoprotein
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Dipeptidyl peptidase 4 soluble form
KeywordsMERS-CoV / spike / DPP4 / 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 / 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 / positive regulation of viral entry into host cell / 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, receptor-binding domain, MERS-CoV / 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, MERS-CoV / 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 speciesMiddle East respiratory syndrome-related coronavirus / Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.93 Å
AuthorsWang X / Wang Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: MERS-CoV S ectodomain trimer in complex with receptor DPP4-750E
Authors: Wang X / Wang Z
History
DepositionApr 17, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39769.png

Downloads & links

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Map

FileDownload / File: emd_39769.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 340 pix.
= 329.8 Å		0.97 Å/pix.
x 340 pix.
= 329.8 Å		0.97 Å/pix.
x 340 pix.
= 329.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.001
Minimum - Maximum-0.85745484 - 1.5193359
Average (Standard dev.)-0.0009785589 (±0.03591786)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 329.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39769_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39769_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : MERS-CoV spike glycoprotein

EntireName: MERS-CoV spike glycoprotein
Components
  • Complex: MERS-CoV spike glycoprotein
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Dipeptidyl peptidase 4 soluble form

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Supramolecule #1: MERS-CoV spike glycoprotein

SupramoleculeName: MERS-CoV spike glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Middle East respiratory syndrome-related coronavirus

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)
Molecular weightTheoretical: 132.30125 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: VDVGPDSVKS ACIEVDIQQT FFDKTWPRPI DVSKADGIIY PQGRTYSNIT ITYQGLFPYQ GDHGDMYVYS AGHATGTTPQ KLFVANYSQ DVKQFANGFV VRIGAAANST GTVIISPSTS ATIRKIYPAF MLGSSVGNFS DGKMGRFFNH TLVLLPDGCG T LLRAFYCI ...String:
VDVGPDSVKS ACIEVDIQQT FFDKTWPRPI DVSKADGIIY PQGRTYSNIT ITYQGLFPYQ GDHGDMYVYS AGHATGTTPQ KLFVANYSQ DVKQFANGFV VRIGAAANST GTVIISPSTS ATIRKIYPAF MLGSSVGNFS DGKMGRFFNH TLVLLPDGCG T LLRAFYCI LEPRSGNHCP AGNSYTSFAT YHTPATDCSD GNYNRNASLN SFKEYFNLRN CTFMYTYNIT EDEILEWFGI TQ TAQGVHL FSSRYVDLYG GNMFQFATLP VYDTIKYYSI IPHSIRSIQS DRKAWAAFYV YKLQPLTFLL DFSVDGYIRR AID CGFNDL SQLHCSYESF DVESGVYSVS SFEAKPSGSV VEQAEGVECD FSPLLSGTPP QVYNFKRLVF TNCNYNLTKL LSLF SVNDF TCSQISPAAI ASNCYSSLIL DYFSYPLSMK SDLSVSSAGP ISQFNYKQSF SNPTCLILAT VPHNLTTITK PLKYS YINK CSRLLSDDRT EVPQLVNANQ YSPCVSIVPS TVWEDGDYYR KQLSPLEGGG WLVASGSTVA MTEQLQMGFG ITVQYG TDT NSVCPKLEFA NDTKIASQLG NCVEYSLYGV SGRGVFQNCT AVGVRQQRFV YDAYQNLVGY YSDDGNYYCL RACVSVP VS VIYDKETKTH ATLFGSVACE HISSTMSQYS RSTRSMLKRR DSTYGPLQTP VGCVLGLVNS SLFVEDCKLP LGQSLCAL P DTPSTLTPSS VGSVPGEMRL ASIAFNHPIQ VDQLNSSYFK LSIPTNFSFG VTQEYIQTTI QKVTVDCKQY VCNGFQKCE QLLREYGQFC SKINQALHGA NLRQDDSVRN LFASVKSSQS SPIIPGFGGD FNLTLLEPVS ISTGSRSARS AIEDLLFDKV TIADPGYMQ GYDDCMQQGP ASARDLICAQ YVAGYKVLPP LMDVNMEAAY TSSLLGSIAG VGWTAGLSSF AAIPFAQSIF Y RLNGVGIT QQVLSENQKL IANKFNQALG AMQTGFTTTN EAFQKVQDAV NNNAQALSKL ASELSNTFGA ISASIGDIIQ RL DPPEQDA QIDRLINGRL TTLNAFVAQQ LVRSESAALS AQLAKDKVNE CVKAQSKRSG FCGQGTHIVS FVVNAPNGLY FMH VGYYPS NHIEVVSAYG LCDAANPTNC IAPVNGYFIK TNNTRIVDEW SYTGSSFYAP EPITSLNTKY VAPQVTYQNI STNL PPPLL G

UniProtKB: Spike glycoprotein

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Macromolecule #2: Dipeptidyl peptidase 4 soluble form

MacromoleculeName: Dipeptidyl peptidase 4 soluble form / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.453586 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SRKTYTLTDY LKNTYRLKLY SLRWISDHEY LYKQENNILV FNAEYGNSSV FLENSTFDEF GHSINDYSIS PDGQFILLEY NYVKQWRHS YTASYDIYDL NKRQLITEER IPNNTQWVTW SPVGHKLAYV WNNDIYVKIE PNLPSYRITW TGKEDIIYNG I TDWVYEEE ...String:
SRKTYTLTDY LKNTYRLKLY SLRWISDHEY LYKQENNILV FNAEYGNSSV FLENSTFDEF GHSINDYSIS PDGQFILLEY NYVKQWRHS YTASYDIYDL NKRQLITEER IPNNTQWVTW SPVGHKLAYV WNNDIYVKIE PNLPSYRITW TGKEDIIYNG I TDWVYEEE VFSAYSALWW SPNGTFLAYA QFNDTEVPLI EYSFYSDESL QYPKTVRVPY PKAGAVNPTV KFFVVNTDSL SS VTNATSI QITAPASMLI GDHYLCDVTW ATQERISLQW LRRIQNYSVM DICDYDESSG RWNCLVARQH IEMSTTGWVG RFR PSEPHF TLDGNSFYKI ISNEEGYRHI CYFQIDKKDC TFITKGTWEV IGIEALTSDY LYYISNEYKG MPGGRNLYKI QLSD YTKVT CLSCELNPER CQYYSVSFSK EAKYYQLRCS GPGLPLYTLH SSVNDKGLRV LEDNSALDKM LQNVQMPSKK LDFII LNET KFWYQMILPP HFDKSKKYPL LLDVYAGPCS QKADTVFRLN WATYLASTEN IIVASFDGRG SGYQGDKIMH AINRRL GTF EVEDQIEAAR QFSKMGFVDN KRIAIWGWSY GGYVTSMVLG SGSGVFKCGI AVAPVSRWEY YDSVYTERYM GLPTPED NL DHYRNSTVMS RAENFKQVEY LLIHGTADDN VHFQQSAQIS KALVDVGVDF QAMWYTDEDH GIASSTAHQE IYTHMSHF I KQCFSLP

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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 1.8 µm / Nominal defocus min: 1.3 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: PDB ENTRY
PDB model - PDB ID:

6q06

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 397140
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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