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- EMDB-70927: Hedgehog coronavirus ErinCoV-12-19 spike receptor binding domain ... -

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Basic information

Entry
Database: EMDB / ID: EMD-70927
TitleHedgehog coronavirus ErinCoV-12-19 spike receptor binding domain in complex with hedgehog APN (locally refined)
Map data
Sample
  • Complex: Hedgehog coronavirus spike protein receptor binding domain in complex with hedgehog APN with APN inhibitor amastatin
    • Complex: Hedgehog APN ectodomain
      • Protein or peptide: Aminopeptidase
    • Complex: Hedgehog coronavirus spike protein receptor binding domain
      • Protein or peptide: Spike glycoprotein
    • Complex: Amastatin
      • Protein or peptide: Amastatin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
  • Ligand: water
KeywordsCoronavirus / receptor complex / VIRAL PROTEIN
Function / homology
Function and homology information


alanyl aminopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / peptide catabolic process / metalloaminopeptidase activity / peptide binding / virus receptor activity / angiogenesis / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / cell differentiation / receptor-mediated virion attachment to host cell ...alanyl aminopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / peptide catabolic process / metalloaminopeptidase activity / peptide binding / virus receptor activity / angiogenesis / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / cell differentiation / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / proteolysis / : / zinc ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV-like / Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase ...Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV-like / Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Peptidase M4/M1, CTD superfamily / 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
Aminopeptidase / Spike glycoprotein
Similarity search - Component
Biological speciesErinaceus europaeus arenavirus / Betacoronavirus Erinaceus / Erinaceus europaeus (western European hedgehog) / Streptomyces (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.01 Å
AuthorsJin M / Rini JM
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To Be Published
Title: Hedgehog coronavirus ErinCoV-12-19 spike receptor binding domain in complex with hedgehog APN (locally refined)
Authors: Jin M / Rini JM
History
DepositionJun 2, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70927.png

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 374.784 Å		0.73 Å/pix.
x 512 pix.
= 374.784 Å		0.73 Å/pix.
x 512 pix.
= 374.784 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.732 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-5.4073253 - 4.301146
Average (Standard dev.)0.000012266663 (±0.056711264)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 374.784 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70927_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_70927_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70927_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_70927_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Hedgehog coronavirus spike protein receptor binding domain in com...

EntireName: Hedgehog coronavirus spike protein receptor binding domain in complex with hedgehog APN with APN inhibitor amastatin
Components
  • Complex: Hedgehog coronavirus spike protein receptor binding domain in complex with hedgehog APN with APN inhibitor amastatin
    • Complex: Hedgehog APN ectodomain
      • Protein or peptide: Aminopeptidase
    • Complex: Hedgehog coronavirus spike protein receptor binding domain
      • Protein or peptide: Spike glycoprotein
    • Complex: Amastatin
      • Protein or peptide: Amastatin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: Hedgehog coronavirus spike protein receptor binding domain in com...

SupramoleculeName: Hedgehog coronavirus spike protein receptor binding domain in complex with hedgehog APN with APN inhibitor amastatin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: Hedgehog APN ectodomain

SupramoleculeName: Hedgehog APN ectodomain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Erinaceus europaeus arenavirus

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Supramolecule #3: Hedgehog coronavirus spike protein receptor binding domain

SupramoleculeName: Hedgehog coronavirus spike protein receptor binding domain
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Betacoronavirus Erinaceus

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Supramolecule #4: Amastatin

SupramoleculeName: Amastatin / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2

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Macromolecule #1: Aminopeptidase

MacromoleculeName: Aminopeptidase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases
Source (natural)Organism: Erinaceus europaeus (western European hedgehog)
Molecular weightTheoretical: 102.756328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSKPWNRYRL PESLEPHSYS VVLRPYLDPN AQGLYIFEGN STVRFICKSA TNVIIIHSKK LNYTREPKVV LRGVDAQAPQ IQNIELVEV TEYLVVHLKN NLEVSKTYEM DSTFRGELAD DLAGFYRSEY MEDNVKKVVA TTQMQAADAR KSFPCFDEPA M KAYFNITI ...String:
QSKPWNRYRL PESLEPHSYS VVLRPYLDPN AQGLYIFEGN STVRFICKSA TNVIIIHSKK LNYTREPKVV LRGVDAQAPQ IQNIELVEV TEYLVVHLKN NLEVSKTYEM DSTFRGELAD DLAGFYRSEY MEDNVKKVVA TTQMQAADAR KSFPCFDEPA M KAYFNITI IHPKDRTALS NMPPKGPSKP LPEDNNWLIT EFETTPKMST YLLAYIVSEF KEVNAVTPND IQIRIWARPR AI DAGHGDY ALKVTGPILT FFAQHYNTSY PLSKSDQIGL PDFNAGAMEN WGLVTYRESA LLFDNLTSSI GNQERVVTVI AHE LAHQWF GNLVTIRWWN DLWLNEGFAS YVEYLGADFA EPHWNLKDLI VLNEVYRVMA VDALVSSHPL STPAEEVNTP AQIS EQFDS IAYSKGASVL RMLSNFLTEN VFKEGLASYL HTYQYSNTVY SNLWDHLQLA VNKHPNLGLP RTVSQIMDRW TLQMG FPVI TVDTSTGNIN QKHFLLNSES NVTRPSPFNY LWIVPISSMK NGVEQDHYWL NGSEKEQSSL FQTAADEWVL LNINVT GYF RVNYDQNNWR KIQTQLQSNL KVIPVINRAQ IIHDAFTLAS AGTVPVTLAL SNTLFLSQEL EYMPWQAALD SLSYFKL MF DRSEVYGPMK NYLRKQVTHL FTHFETTTQN WTVRPDTLMD QYNEVNAIST ACSNGLSECQ TLASSLFAKW KDNPDNNP I HPNLRSTIYC NAIARGGVEE WDFAWGQFRN ATIVNEADKL RSALACSNEV WILNRYLDYT LNPNLIRKQD ATSTISSIA SNVIGQDLAW NFVRDNWKKL FQDYGGGSFS FSNLIQAVTR RFNTESDLQQ LEQFKKDNAD IGFGSGTRAL EQALEKTKAN IKWVNANKK AVLDWFIQNS Q

UniProtKB: Aminopeptidase

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Macromolecule #2: Amastatin

MacromoleculeName: Amastatin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces (bacteria)
Molecular weightTheoretical: 474.548 Da
SequenceString:
(L2O)VVD

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Macromolecule #3: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Betacoronavirus Erinaceus
Molecular weightTheoretical: 23.169225 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AAELTECELD VLFKNDAPII ANYSRRVFTN CNYNLTKLLS LVEVDEFICH KTTPEALATG CYSSLTVDWF ALPFSMKSTL AIGSAEAIS MFNYKQDYSN PTCRIHAAVT GNVSTALNFT ASANYAYISR CQGTDGKPIL LQPGQMTNVV CRSGVIARPS D ADYFGYSF ...String:
AAELTECELD VLFKNDAPII ANYSRRVFTN CNYNLTKLLS LVEVDEFICH KTTPEALATG CYSSLTVDWF ALPFSMKSTL AIGSAEAIS MFNYKQDYSN PTCRIHAAVT GNVSTALNFT ASANYAYISR CQGTDGKPIL LQPGQMTNVV CRSGVIARPS D ADYFGYSF QGRTYYLGRK SYNPKVDNDI QMVYVITPNY NKGPDTVCPL K

UniProtKB: Spike glycoprotein

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / 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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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 151 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: A initial 3D map was generated by ab-initio reconstruction in cryoSPARC v4
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1578752
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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