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- EMDB-63757: SARS-CoV-2 spike-Crp5 -

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Basic information

Entry
Database: EMDB / ID: EMD-63757
TitleSARS-CoV-2 spike-Crp5
Map data
Sample
  • Complex: SARS-CoV-2 spike-Crp5 Complex
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Alpha-defensin 5
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 / cryo-EM structure / defensin / VIRAL PROTEIN
Function / homology
Function and homology information


Alpha-defensins / Defensins / positive regulation of membrane permeability / disruption of plasma membrane integrity in another organism / pore-forming activity / : / Neutrophil degranulation / secretory granule / positive regulation of interleukin-8 production / midbody ...Alpha-defensins / Defensins / positive regulation of membrane permeability / disruption of plasma membrane integrity in another organism / pore-forming activity / : / Neutrophil degranulation / secretory granule / positive regulation of interleukin-8 production / midbody / symbiont-mediated disruption of host tissue / antimicrobial humoral immune response mediated by antimicrobial peptide / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / Lectin pathway of complement activation / host extracellular region / antibacterial humoral response / symbiont-mediated-mediated suppression of host tetherin activity / killing of cells of another organism / Induction of Cell-Cell Fusion / structural constituent of virion / defense response to Gram-negative bacterium / protein homotetramerization / positive regulation of viral entry into host cell / Initial triggering of complement / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / defense response to bacterium / defense response to Gram-positive bacterium / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / receptor ligand activity / fusion of virus membrane with host plasma membrane / innate immune response / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / protein homodimerization activity / : / membrane / identical protein binding / plasma membrane
Similarity search - Function
Mammalian defensins signature. / Alpha-defensin, C-terminal / Mammalian defensin / Alpha-defensin propeptide / Alpha-defensin / Defensin propeptide / Defensin propeptide / Beta/alpha-defensin, C-terminal / Defensin/corticostatin family / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 ...Mammalian defensins signature. / Alpha-defensin, C-terminal / Mammalian defensin / Alpha-defensin propeptide / Alpha-defensin / Defensin propeptide / Defensin propeptide / Beta/alpha-defensin, C-terminal / Defensin/corticostatin family / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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. / 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 / Alpha-defensin 5
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsYang QX / Yang YL
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970146 China
National Natural Science Foundation of China (NSFC)82030062 China
CitationJournal: Mucosal Immunol / Year: 2026
Title: Enteric α-defensins contribute to intestinal mucosal immunity against SARS-CoV-2 infection.
Authors: Yilin Yang / Qianxi Yang / Xin Huang / Chongbing Liao / Zhenguo Chen / Wuyuan Lu /
Abstract: SARS-CoV-2 primarily targets epithelial cells in the respiratory and intestinal tracts where its cognate receptor ACE2 and obligate processing enzymes furin and TMPRSS2 are richly expressed. However, ...SARS-CoV-2 primarily targets epithelial cells in the respiratory and intestinal tracts where its cognate receptor ACE2 and obligate processing enzymes furin and TMPRSS2 are richly expressed. However, compared with severe inflammation and tissue damage in the lungs of a COVID-19 patient, clinical lesions in the intestine are rare, suggesting an effective intestinal mucosal immunity against SARS-CoV-2 infection. Here, we report that MMP7/hACE2 hybrid mice lacking mature enteric α-defensins or cryptdins were more susceptible to SARS-CoV-2 infection in the intestine than K18-hACE2 transgenic mice. The mouse α-defensin cryptdin-5 (Crp5) displayed potent and broad antiviral activity in vitro and in vivo by two distinct mechanisms, (1) directly targeting the RBD of the spike (S) protein to antagonize its interactions with ACE2, thus blocking viral attachment, membrane fusion and cell-to-cell transmission, and (2) binding to the 630 loop of the S protein to induce its multimerization, thereby impairing proteolytic processing, membrane fusion and, ultimately, viral infectivity. Our findings imply that enteric α-defensins help alleviate, as host protective factors, Covid-19 symptoms in the intestine despite higher ACE2 expression in the gut than in the lungs, and that Crp5 may be developed as a broad-spectrum antiviral for the treatment of coronavirus infection irrespective of virus type and variant.
History
DepositionMar 14, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63757.png

Downloads & links

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Map

FileDownload / File: emd_63757.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 335.52 Å		0.93 Å/pix.
x 360 pix.
= 335.52 Å		0.93 Å/pix.
x 360 pix.
= 335.52 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: 0.1
Minimum - Maximum-0.18400946 - 20.876577000000001
Average (Standard dev.)-0.0045768134 (±0.5301772)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 335.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63757_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_63757_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 spike-Crp5 Complex

EntireName: SARS-CoV-2 spike-Crp5 Complex
Components
  • Complex: SARS-CoV-2 spike-Crp5 Complex
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Alpha-defensin 5
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV-2 spike-Crp5 Complex

SupramoleculeName: SARS-CoV-2 spike-Crp5 Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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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: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 141.291406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF ...String:
MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRDLPQ GFSALEPLVD LPIGINITRF QT LLALHRS YLTPGDSSSG WTAGAAAYYV GYLQPRTFLL KYNENGTITD AVDCALDPLS ETKCTLKSFT VEKGIYQTSN FRV QPTESI VRFPNITNLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNVY ADSF VIRGD EVRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYLYRL FRKSNLKPFE RDISTEIYQA GSTPC NGVE GFNCYFPLQS YGFQPTNGVG YQPYRVVVLS FELLHAPATV CGPKKSTNLV KNKCVNFNFN GLTGTGVLTE SNKKFL PFQ QFGRDIADTT DAVRDPQTLE ILDITPCSFG GVSVITPGTN TSNQVAVLYQ DVNCTEVPVA IHADQLTPTW RVYSTGS NV FQTRAGCLIG AEHVNNSYEC DIPIGAGICA SYQTQTNSPR RARSVASQSI IAYTMSLGAE NSVAYSNNSI AIPTNFTI S VTTEILPVSM TKTSVDCTMY ICGDSTECSN LLLQYGSFCT QLNRALTGIA VEQDKNTQEV FAQVKQIYKT PPIKDFGGF NFSQILPDPS KPSKRSPIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFG AGPALQIPFP MQMAYRFNGI GVTQNVLYEN QKLIANQFNS AIGKIQDSLS STPSALGKLQ DVVNQNAQAL N TLVKQLSS NFGAISSVLN DILSRLDPPE AEVQIDRLIT GRLQSLQTYV TQQLIRAAEI RASANLAATK MSECVLGQSK RV DFCGKGY HLMSFPQSAP HGVVFLHVTY VPAQEKNFTT APAICHDGKA HFPREGVFVS NGTHWFVTQR NFYEPQIITT DNT FVSGNC DVVIGIVNNT VYDPLQPELD SFKEELDKYF KNHTSPDVDL GDISGINASV VNIQKEIDRL NEVAKNLNES LIDL QELGK YEQYIKWPWY IWLGFIAGLI AIVMVTIMLC CMTSCCSCLK GCCSCGSCCK FDEDDSEPVL KGVKLHYT

UniProtKB: Spike glycoprotein

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Macromolecule #2: Alpha-defensin 5

MacromoleculeName: Alpha-defensin 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 4.330334 KDa
SequenceString:
LSKKLICYCR IRGCKRRERV FGTCRNLFLT FVFCCS

UniProtKB: Alpha-defensin 5

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 39 / 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 TALOS ARCTICA
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: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42414
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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