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- EMDB-39743: The structure of TGEV RBD and dog APN complex -

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Basic information

Entry
Database: EMDB / ID: EMD-39743
TitleThe structure of TGEV RBD and dog APN complex
Map data
Sample
  • Complex: The PDCoV RBD-dAPN complex
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Aminopeptidase N
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsTGEV / PROTEIN BINDING / ISOMERASE
Function / homology
Function and homology information


alanyl aminopeptidase activity / membrane alanyl aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / peptide binding / virus receptor activity / angiogenesis / cell differentiation / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell ...alanyl aminopeptidase activity / membrane alanyl aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / peptide binding / virus receptor activity / angiogenesis / cell differentiation / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / virion membrane / proteolysis / extracellular space / zinc ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain ...Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / 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 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Aminopeptidase N / Spike glycoprotein
Similarity search - Component
Biological speciesCanis lupus familiaris (dog) / TGEV virulent Purdue (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsSun JQ / Niu S
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270157 China
CitationJournal: PLoS Pathog / Year: 2025
Title: Cross-species recognition of two porcine coronaviruses to their cellular receptor aminopeptidase N of dogs and seven other species.
Authors: Yuyang Tian / Junqing Sun / Xiaohan Hou / Zhimin Liu / Zeao Chen / Xiaoqian Pan / Ying Wang / Jianle Ren / Ding Zhang / Bo Yang / Longlong Si / Yuhai Bi / Kefang Liu / Guijun Shang / Wen-Xia ...Authors: Yuyang Tian / Junqing Sun / Xiaohan Hou / Zhimin Liu / Zeao Chen / Xiaoqian Pan / Ying Wang / Jianle Ren / Ding Zhang / Bo Yang / Longlong Si / Yuhai Bi / Kefang Liu / Guijun Shang / Wen-Xia Tian / Qihui Wang / George Fu Gao / Sheng Niu /
Abstract: Porcine deltacoronavirus (PDCoV) and transmissible gastroenteritis coronavirus (TGEV), the two causative agents of porcine diarrhea, have been reported to be at risk of cross-species transmission, ...Porcine deltacoronavirus (PDCoV) and transmissible gastroenteritis coronavirus (TGEV), the two causative agents of porcine diarrhea, have been reported to be at risk of cross-species transmission, including to humans. However, the potential host range in which these two CoVs interact remains unclear. We screened 16 animal counterparts for porcine aminopeptidase N (APN), the receptor of PDCoV and TGEV, and found that APNs from eight of 17 animals could bind to the receptor-binding domains (RBDs) of PDCoV and TGEV. Furthermore, the animal APNs that could bind to the RBDs could mediate cellular infection by both viruses. Dog APN (dAPN) has been identified as the animal receptor with the highest capability to mediate the virus infection. We further resolved the complex structures of dAPN bound to the PDCoV RBD/TGEV RBD, respectively, establishing its divergent receptor-binding modes. We identified R325 of dAPN as an important residue in the PDCoV RBD-dAPN interaction, and found the central role of Q746 and T749 in dAPN in the interaction with the TGEV RBD. These findings provide the molecular basis of the potential cross-species transmission of these two porcine CoVs and shed light on future surveillance of these CoVs.
History
DepositionApr 12, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39743.png

Downloads & links

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Map

FileDownload / File: emd_39743.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 400 pix.
= 276. Å		0.69 Å/pix.
x 400 pix.
= 276. Å		0.69 Å/pix.
x 400 pix.
= 276. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.126
Minimum - Maximum-0.36984435 - 1.150758
Average (Standard dev.)0.00076091324 (±0.025732657)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 276.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39743_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_39743_half_map_2.map
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Sample components

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Entire : The PDCoV RBD-dAPN complex

EntireName: The PDCoV RBD-dAPN complex
Components
  • Complex: The PDCoV RBD-dAPN complex
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Aminopeptidase N
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: The PDCoV RBD-dAPN complex

SupramoleculeName: The PDCoV RBD-dAPN complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Canis lupus familiaris (dog)

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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: TGEV virulent Purdue (virus)
Molecular weightTheoretical: 19.363834 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
TANLNNGFYP VSSSEVGLVN KSVVLLPSFY THTIVNITID LGMKRSGYGQ PIASTLSNIT LPMQDNNTDV YCIRSDQFSV YVHSTCKSS LWDNIFKRNC TDVLDATAVI KTGTCPFSFD KLNNYLTFNK FCLSLSPVGA NCKFDVAART RTNEQVVRSL Y VIYEEGDN IVGVPSD

UniProtKB: Spike glycoprotein

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Macromolecule #2: Aminopeptidase N

MacromoleculeName: Aminopeptidase N / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: membrane alanyl aminopeptidase
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 107.002961 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EKNKNAESSP VSSPVSSPVS SPVSPTNPST TAATTLAQSK PWNHYRLPKT LIPSSYNVTL RPYLTPNSNG LYTFKGSSTV RFTCKESTS MIIIHSKKLN YTNIQGQRVA LRGVGGSQAP AIDRTELVEV TEYLVVHLRE PLQVNSQYEM DSKFEGELAD D LAGFYRSE ...String:
EKNKNAESSP VSSPVSSPVS SPVSPTNPST TAATTLAQSK PWNHYRLPKT LIPSSYNVTL RPYLTPNSNG LYTFKGSSTV RFTCKESTS MIIIHSKKLN YTNIQGQRVA LRGVGGSQAP AIDRTELVEV TEYLVVHLRE PLQVNSQYEM DSKFEGELAD D LAGFYRSE YTENGVKKVL ATTQMQAADA RKSFPCFDEP AMKATFNITL IHPSNLVALS NMLPRGPSVP FTEEPNWNVT EF ETTPIMS TYLLAYIVSE FKNVQENTPS NVLIRIWARP SAMDQGHGNY ALRVTGPILD FFSRHYDTPY PLNKSDQIAL PDF NAGAME NWGLVTYRES ALLYDPQSSS IGNKERVVTV IAHELAHQWF GNLVTLEWWN DLWLNEGFAS YVEYLGADYA EPTW NLKDL IVLNEVYRVM AVDALASSHP LSSPASEVNT PAQISEVFDS ISYSKGASVL RMLSSFLTED LFKKGVASYL HTFAY QNTI YLDLWNHLQW ALGNQTAINL PYTVNAIMDR WILQMGFPVV TVDTTTGTLS QKHFLLDPQS NVTRPSKFNY LWIIPI SSV KSGTQQAHYW MPDNAKVQND LFKTTGDEWV LLNLNVTGYY LVNYDQNNWK KIHTQLQTDL SVIPVINRAQ VIHDTFD LA SAQIVPVTLA LNSTLFLNQE TEYMPWEAAL SSLSYFKLMF DRSEVYGPMK NYLRKQVTPL FNHFEKITQN WTDHPQTL T EQYNEINAVS TACTYGVPKC KDLVSTLFAE WRKNPQNNPI YPNLRSTVYC NAIAQGGEEE WNFVWEQFRN TSLVNEADK LRSALACSTQ VWILNRYLSY TLNPEFIRKQ DVISTLSSIA SNVIGQSLAW DFIQSNWKKL FEDYGTGSFS FSNLIQAVTR RFSTEFELQ QLEQFKANNM DTGFGSGTRA LEQALEKTKA NIKWVKENKE AVLQWFRENS QGGS

UniProtKB: Aminopeptidase N

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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: 1 / 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

MicroscopeFEI TITAN 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 / Cs: 0.001 mm / 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: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 295620
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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