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- EMDB-64732: Complex structure of 2014-422 spike RBD bound to human DPP4 -

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Basic information

Entry
Database: EMDB / ID: EMD-64732
TitleComplex structure of 2014-422 spike RBD bound to human DPP4
Map data
Sample
  • Complex: Complex structure of 2014-422 spike RBD bound to human DPP4
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Dipeptidyl peptidase 4 soluble form
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywords2014-422 RBD / human DPP4 / viral protein / hydrolase / VIRAL PROTEIN/HYDROLASE / VIRAL PROTEIN-HYDROLASE 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 / psychomotor behavior / dipeptidyl-peptidase activity ...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 / psychomotor behavior / dipeptidyl-peptidase activity / peptide hormone processing / lamellipodium membrane / locomotory exploration behavior / aminopeptidase activity / endocytic vesicle / 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 / endocytosis involved in viral entry into host cell / membrane raft / signaling receptor binding / serine-type endopeptidase activity / fusion of virus membrane with host plasma membrane / lysosomal membrane / focal adhesion / fusion of virus membrane with host endosome membrane / viral envelope / positive regulation of cell population proliferation / 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, HKU4-like / 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, HKU4-like / 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 speciesHomo sapiens (human) / Middle East respiratory syndrome-related coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsWang X / Lin Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Complex structure of 2014-422 spike RBD bound to human DPP4
Authors: Wang X / Lin Z
History
DepositionMay 20, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64732.png

Downloads & links

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Map

FileDownload / File: emd_64732.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.062 Å		1.1 Å/pix.
x 256 pix.
= 281.062 Å		1.1 Å/pix.
x 256 pix.
= 281.062 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0979 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-3.7627563 - 5.051737
Average (Standard dev.)0.0009359686 (±0.11382873)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.0624 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_64732_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_64732_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 : Complex structure of 2014-422 spike RBD bound to human DPP4

EntireName: Complex structure of 2014-422 spike RBD bound to human DPP4
Components
  • Complex: Complex structure of 2014-422 spike RBD bound to human DPP4
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Dipeptidyl peptidase 4 soluble form
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex structure of 2014-422 spike RBD bound to human DPP4

SupramoleculeName: Complex structure of 2014-422 spike RBD bound to human DPP4
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Middle East respiratory syndrome-related coronavirus
Molecular weightTheoretical: 24.5146 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: EVHSRGQFIE QPNSVECDFT KLLSGTPPQV YNFNRLVFTN CNYNLTKLLS LFMVNEFSCD GISPDAIARG CYSSLTVDYF AYPLSMKSY MQPGSAGVIS QYNYKQSFAN PTCRIFATAP ANLTITKPSS YSFISKCSRL TGDNSHIETP IVINPGEYSI C KNFAPNGF ...String:
EVHSRGQFIE QPNSVECDFT KLLSGTPPQV YNFNRLVFTN CNYNLTKLLS LFMVNEFSCD GISPDAIARG CYSSLTVDYF AYPLSMKSY MQPGSAGVIS QYNYKQSFAN PTCRIFATAP ANLTITKPSS YSFISKCSRL TGDNSHIETP IVINPGEYSI C KNFAPNGF SQDGDYFTRQ LSQLEGGGIL VGVGSVTPMT DTLQMGFIIS VQYGTDTNSV CPMMD

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: 84.375547 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RKTYTLTDYL KNTYRLKLYS LRWISDHEYL YKQENNILVF NAEYGNSSVF LENSTFDEFG HSINDYSISP DGQFILLEYN YVKQWRHSY TASYDIYDLN KRQLITEERI PNNTQWVTWS PVGHKLAYVW NNDIYVKIEP NLPSYRITWT GKEDIIYNGI T DWVYEEEV ...String:
RKTYTLTDYL KNTYRLKLYS LRWISDHEYL YKQENNILVF NAEYGNSSVF LENSTFDEFG HSINDYSISP DGQFILLEYN YVKQWRHSY TASYDIYDLN KRQLITEERI PNNTQWVTWS PVGHKLAYVW NNDIYVKIEP NLPSYRITWT GKEDIIYNGI T DWVYEEEV FSAYSALWWS PNGTFLAYAQ FNDTEVPLIE YSFYSDESLQ YPKTVRVPYP KAGAVNPTVK FFVVNTDSLS SV TNATSIQ ITAPASMLIG DHYLCDVTWA TQERISLQWL RRIQNYSVMD ICDYDESSGR WNCLVARQHI EMSTTGWVGR FRP SEPHFT LDGNSFYKII SNEEGYRHIC YFQIDKKDCT FITKGTWEVI GIEALTSDYL YYISNEYKGM PGGRNLYKIQ LSDY TKVTC LSCELNPERC QYYSVSFSKE AKYYQLRCSG PGLPLYTLHS SVNDKGLRVL EDNSALDKML QNVQMPSKKL DFIIL NETK FWYQMILPPH FDKSKKYPLL LDVYAGPCSQ KADTVFRLNW ATYLASTENI IVASFDGRGS GYQGDKIMHA INRRLG TFE VEDQIEAARQ FSKMGFVDNK RIAIWGWSYG GYVTSMVLGS GSGVFKCGIA VAPVSRWEYY DSVYTERYMG LPTPEDN LD HYRNSTVMSR AENFKQVEYL LIHGTADDNV HFQQSAQISK ALVDVGVDFQ AMWYTDEDHG IASSTAHQHI YTHMSHFI K QCFSLP

UniProtKB: Dipeptidyl peptidase 4

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 7 / 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: 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: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 591107
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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