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- EMDB-72852: Structure of mink-derived HKU5 RBD in complex with ACE2 of N. vison -

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Basic information

Entry
Database: EMDB / ID: EMD-72852
TitleStructure of mink-derived HKU5 RBD in complex with ACE2 of N. vison
Map data
Sample
  • Complex: Mink HKU5 RBD in complex with mink ACE2
    • Protein or peptide: Angiotensin-converting enzyme
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsImmune system / ACE2 / mink HKU5 / bat coronavirus / VIRAL PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / carboxypeptidase activity / peptidyl-dipeptidase activity / metallopeptidase activity / cilium / apical plasma membrane / proteolysis / extracellular region / cytoplasm
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile.
Similarity search - Domain/homology
Angiotensin-converting enzyme
Similarity search - Component
Biological speciesNeogale vison (American mink) / Pipistrellus bat coronavirus HKU5
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLi N / Keeler E / Tsybovsky Y / Zhou T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Adaptation to intermediate 1 host expands zoonotic risk of bat-origin merbecoviruses
Authors: Keeler EL / Li N / Arinola R / Teng I / Grunst MW / Kaur R / Zepeda S / Okten A / Menasche B / Catanzaro NJ / Young S / Bourgikos E / Grubaugh N / Mothes W / Baric RS / Spaulding AB / ...Authors: Keeler EL / Li N / Arinola R / Teng I / Grunst MW / Kaur R / Zepeda S / Okten A / Menasche B / Catanzaro NJ / Young S / Bourgikos E / Grubaugh N / Mothes W / Baric RS / Spaulding AB / Serebryannyy L / Jangra RK / Tsybovsky Y / Alfajaro MM / Zhou T / Douek DC / Wilen CB
History
DepositionSep 24, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72852.png

Downloads & links

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Map

FileDownload / File: emd_72852.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.)
1 Å/pix.
x 360 pix.
= 360. Å		1 Å/pix.
x 360 pix.
= 360. Å		1 Å/pix.
x 360 pix.
= 360. Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.0017437346 - 1.938441
Average (Standard dev.)0.00086379953 (±0.022741769)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 360.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72852_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_72852_additional_1.map
Projections & Slices
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Additional map: #2

Fileemd_72852_additional_2.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_72852_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72852_half_map_2.map
Projections & Slices
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Sample components

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Entire : Mink HKU5 RBD in complex with mink ACE2

EntireName: Mink HKU5 RBD in complex with mink ACE2
Components
  • Complex: Mink HKU5 RBD in complex with mink ACE2
    • Protein or peptide: Angiotensin-converting enzyme
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Mink HKU5 RBD in complex with mink ACE2

SupramoleculeName: Mink HKU5 RBD in complex with mink ACE2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Neogale vison (American mink)
Molecular weightTheoretical: 160 KDa

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Macromolecule #1: Angiotensin-converting enzyme

MacromoleculeName: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Neogale vison (American mink)
Molecular weightTheoretical: 93.30125 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLGSSWLLLS LAALTAAQST TEDLAKTFLE KFNYEAEELS YQNSLASWNY NTNITDENIQ KMNIAGAKWS AFYEEESQHA KTYPLEEIQ DPIIKRQLRA LQQSGSSVLS ADKRERLNTI LNAMSTIYST GKACNPNNPQ ECLLLEPGLD DIMENSKDYN E RLWAWEGW ...String:
MLGSSWLLLS LAALTAAQST TEDLAKTFLE KFNYEAEELS YQNSLASWNY NTNITDENIQ KMNIAGAKWS AFYEEESQHA KTYPLEEIQ DPIIKRQLRA LQQSGSSVLS ADKRERLNTI LNAMSTIYST GKACNPNNPQ ECLLLEPGLD DIMENSKDYN E RLWAWEGW RSEVGKQLRP LYEEYVALKN EMARANNYED YGDYWRGDYE EEWADGYNYS RNQLIEDVEH TFTQIKPLYE HL HAYVRAK LMDAYPSRIS PTGCLPAHLL GDMWGRFWTN LYPLMVPFGQ KPNIDVTDAM VNQSWDARRI FKEAEKFFVS VGL PNMTEG FWQNSMLTEP GDNRKVVCHP TAWDLGKHDF RIKMCTKVTM DDFLTAHHEM GHIQYDMAYA AQPFLLRNGA NEGF HEAVG EIMSLSAATP NHLKNIGLLP PDFSEDSETD INFLLKQALT IVGTLPFTYM LEKWRWMVFK GEIPKEQWMQ KWWEM KRDI VGVVEPLPHD ETYCDPAALF HVANDYSFIR YYTRTIYQFQ FQEALCQIAK HEGPLYKCDI SNSREAGQKL HEMLSL GRS KPWTFALERV VGAKTMDVRP LLNYFEPLFT WLKEQNRNSF VGWNTDWSPY ADQSIKVRIS LKSALGEKAY EWNDNEM YF FQSSIAYAMR EYFSKVKKQT IPFVDKDVRV SDLKPRISFN FIVTSPENMS DIIPRADVEE AIRKSRGRIN DAFRLDDN S LEFLGIQPTL EPPYQPPVTI WLIVFGVVMG VVVVGIFLLI FSGIRNRRKN NQARSEENPY ASVDLSKGEN NPGFQNVDD VQTSF

UniProtKB: Angiotensin-converting enzyme

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Macromolecule #2: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pipistrellus bat coronavirus HKU5
Molecular weightTheoretical: 150.201516 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MIRSVSVLMC LLTSLGSLIN SQSVDMGPSG SSSCLKSQVR PDFFETPRNV WPLPIDTSKA EGVIYPNGRS YSNITLTYTG LYPKANDLG TQYIFSDAHS GVGSSMDLFV SNYSRQVETF ANGFVVRIGA AADKTGSTII SQSTNRPIKK IYPAFMLGHA V GNYTPANI ...String:
MIRSVSVLMC LLTSLGSLIN SQSVDMGPSG SSSCLKSQVR PDFFETPRNV WPLPIDTSKA EGVIYPNGRS YSNITLTYTG LYPKANDLG TQYIFSDAHS GVGSSMDLFV SNYSRQVETF ANGFVVRIGA AADKTGSTII SQSTNRPIKK IYPAFMLGHA V GNYTPANI TGRYLNHTLV ILPDECGTTL HAFYCVLQPR NQTNCAGAPT FTSVTVWDTP TTNCAKTRSY NNLTNLNAFK LY FDLVNCT FRYNYTITED ENAEWFGITQ DTQGVHLYSS RKENVFRNNM FHFATLPVYQ QILYYTIIPR SIRSPSNGTA WAA FYVYKL HPLTYLLNFD VDGYITKAVD CGYDDLAQLQ CSYESFDVET GVYSVSSFEA SPRGEFIEQS TAKECDFSPM LQGT PPPIY DFKRLVFTNC NYNLTKLLNL FQVSEFSCHQ VSPSSLATGC YSSLTVDYFA YPTSMSSYLQ PGFAGEIVKF NYKQD FSSP TCRVLATVPS NLTTITKPSN YVHLTECYKG TAYGKNYLYN APGGYTPCLS LASSGFSSDR QSHRQQLSDG YLVTTG SVY AVNGNLQMAF IISVQYGTDT NSVCPMQALR NDTSIEDKLD TCVQYSLHGI TGRGVFHNCT PVGLRNQRFV YDSFDNL VG YHSDNGNYYC VRPCVSVPVS VIYDKVSNSY ATLLGSVSCS HVTTMMSQFS RMTKTNLHMR ITPGPLQTTV GCAMGFIN T SMVVDECQLP LGQSLCAIPP IPSARLARAA SSGGTDVFQI ATLNFTSPLT LAPINSTGFV VAVPTNFTFG VTQEYIETT IQKITVDCKQ YVCNGFKKCE ELLSEYGQFC SKINQALHGA NLRQDESISN LFSSIKTQNT QPLQAGLNGD FNLTMLQIPQ VTTGEHKYR SAIEDLLFNK VTIADPGYMQ GYDECMQQGP QSARDLICAQ YVAGYKVLPP LYDPYMEAAY TSSLLGSIAG A SWTAGVSS FAAIPFAQSI FYRLNGVGIT QQVLSENQKI IANKFNQALG TMQTGFSTTN LAFNKVQDAV NANAMALSKL AS ELSNTFG AISSSIGDIL QRLDTVEQEA QIDRLINGRL TSLNAFVAHQ LVRTEAAARS AQLAQDKVNE CVKSQSKRNG FCG TGTHIV SFAINAPNGL YFFHVGYQPT AHVNATAAYG LCNSETPPKC IAPIDGYFVI NQTTSTARSF EDQQWYYTGS SFFH PEPIT TANSKYVSMD VKFENLTNKL PPPLLSNTTD VDFKDELEEF FKNVSSQGPN FQEISKINTT LLNLNQELAV LNEVV KQLN ESYIDLKELG NYTFYQKWPW YIWLGFIAGL VALALCVFFI LCCTGCGTNC LGKLKCYRCC DSYEEYEVEK IHVH

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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: 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

Concentration4.3 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON APOLLO (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 11322 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 47000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3031602
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6) / Number images used: 418147
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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