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- EMDB-46569: Structure of HKU5-20s spike glycoprotein -

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Basic information

Entry
Database: EMDB / ID: EMD-46569
TitleStructure of HKU5-20s spike glycoprotein
Map data
Sample
  • Complex: HKU5-20s Spike glycoprotein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsMerbecovirus / HKU5 / HKU5-20s / Spike / VIRAL PROTEIN
Function / homology
Function and homology information


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 / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV-like / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. ...Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV-like / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-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
Biological speciesPipistrellus bat coronavirus HKU5
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsWu Z / Fan C / Bjorkman PJ
Funding support United States, 2 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-034638 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI165075 United States
CitationJournal: Nat Commun / Year: 2025
Title: ACE2 from Pipistrellus abramus bats is a receptor for HKU5 coronaviruses.
Authors: Nicholas J Catanzaro / Ziyan Wu / Chengcheng Fan / Victoria Jefferson / Anfal Abdelgadir / Alexandra Schäfer / Boyd L Yount / Pamela J Bjorkman / Ralph Baric / Michael Letko /
Abstract: The merbecovirus subgenus of coronaviruses includes Middle East Respiratory Syndrome Coronavirus (MERS-CoV), a zoonotic pathogen transmitted from dromedary camels to humans that causes severe ...The merbecovirus subgenus of coronaviruses includes Middle East Respiratory Syndrome Coronavirus (MERS-CoV), a zoonotic pathogen transmitted from dromedary camels to humans that causes severe respiratory disease. Viral discovery efforts uncover hundreds of merbecoviruses in different species across multiple continents, but few are studied under laboratory conditions, leaving basic questions regarding their human threat potential unresolved. Viral entry into host cells is a critical step for transmission between hosts. Here, we develop and apply a scalable approach to assesses novel merbecovirus cell entry across the entire merbecovirus subgenus. Merbecoviruses are sorted into clades based on the receptor-binding domain of the spike glycoprotein. Receptor tropism is clade-specific, with the clade including MERS-CoV using DPP4 and multiple clades using ACE2, including HKU5 bat coronaviruses. Mutational analysis identifies possible structural limitations to HKU5 adaptability and a cryo-EM structure of the HKU5-20s spike trimer reveals only 'down' RBDs.
History
DepositionAug 12, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46569.png

Downloads & links

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Map

FileDownload / File: emd_46569.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.)
0.87 Å/pix.
x 360 pix.
= 312.84 Å		0.87 Å/pix.
x 360 pix.
= 312.84 Å		0.87 Å/pix.
x 360 pix.
= 312.84 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.869 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0649
Minimum - Maximum-0.1788785 - 0.4850626
Average (Standard dev.)-0.000008524979 (±0.017625201)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 312.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_46569_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_46569_half_map_1.map
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_46569_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : HKU5-20s Spike glycoprotein

EntireName: HKU5-20s Spike glycoprotein
Components
  • Complex: HKU5-20s Spike glycoprotein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HKU5-20s Spike glycoprotein

SupramoleculeName: HKU5-20s Spike glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pipistrellus bat coronavirus HKU5
Molecular weightTheoretical: 450 KDa

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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: Pipistrellus bat coronavirus HKU5
Molecular weightTheoretical: 148.600734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VDMGTTGSGN CIESQVAPDF FETARNIWPL PIDTSKAEGV IYPNGKSYSN ISLTYTGLYP KANDLGKQYI FSDGHSSPGT LSRLFVSNY SRQVETFDDG FIVRIGAASN KTGTTVISQS TNRPIKKIYP AFMLGHSVGN YTPTNITGRY LNHTLVILPD G CGTLVHAF ...String:
VDMGTTGSGN CIESQVAPDF FETARNIWPL PIDTSKAEGV IYPNGKSYSN ISLTYTGLYP KANDLGKQYI FSDGHSSPGT LSRLFVSNY SRQVETFDDG FIVRIGAASN KTGTTVISQS TNRPIKKIYP AFMLGHSVGN YTPTNITGRY LNHTLVILPD G CGTLVHAF YCILQPRTQA YCAGASTFTS VTVWDTPASD CANSQSYNQL ANLNAFKLYF DLINCTFRYN YTITEDENAE WF GITQDTQ GVHLYSSRKE NVFRNNMFHF ATLPVYQKIL YYTVIPRSIR SPFNDRKAWA AFYIYKLHPL TYLLNFDVEG YIT KAVDCG YDDFAQLQCS YENFDVETGV YSVSSFEASP RGEFIEQSVT KECDFSPMLT GTPPPIYDFK RLVFTNCNYN LTKL LSLFQ VSEFSCHQVS PSSLATGCYS SLTVDYFAYS TDMSSYLQPG SAGEIVQFNY KQDFSNPTCR VLATVPTNLT TITKP SNYV HLTECYISTA YGKNYLFNAP GGYTPCLSLA SSGFSRDRQS HSQELPDGSF LTTTGSVYSV GSNLQMAFII SVQYGT DTN SVCPMQALRN DTSIEDKLDV CVEYSLHGIT GRGVFHNCTS VGLRNQRFVY DTFDNLVGYH SHNGNYYCVR PCVSVPV SV IYDKVSNSHA TLFGSVACSH VTTMMSQFSR MTKTNLLART TPGPLQTTVG CAMGFINSSM VVDECQLPLG QSLCAIPP T ISTASVGATS GVSDVFQIAT LNFTSPLTLA PINSTGFVVA VPTNFTFGVT QEFIETTIQK ITVDCKQYVC NGFKKCEDL LKEYGQFCSK INQALHGANL RQDESIANLF SSIKTQNTQP LQAGLNGDFN LTMLQIPQVT TGERKYRSAI EDLLFNKVTI ADPGYMQGY DECMQQGPQS ARDLICAQYV AGYKVLPPLY DPYMEAAYTS SLLGSIAGAS WTAGLSSFAA IPFAQSIFYR L NGVGITQQ VLSENQKIIA NKFNQALGAM QTGFTTTNLA FNKVQDAVNA NAMALSKLAA ELSNTFGAIS SSISDILARL DP PEQEAQI DRLINGRLTS LNAFVAQQLV RTEAAARSAQ LAQDKVNECV KSQSKRNGFC GTGTHIVSFA INAPNGLYFF HVG YQPTSH VNATAAYGLC NTENPPKCIA PIDGYFVLNQ TISTVANSDQ QWYYTGSSFF HPEPITEANS KYVSMDVKFE NLTN KLPPP LLSNSTDLDF KEELEEFFKN VSSQGPNFQE ISKINTTLLN LNTELMVLSE VVKQLNESYI DLKELGNYTF YQKGS GREN LYFQGGGGSG YIPEAPRDGQ AYVRKDGEWV LLSTFLGHHH HHHHHGLNDI FEAQKIEWHE

UniProtKB: Spike glycoprotein

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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: 36 / 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

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
0.05 mol/LTris
0.15 mol/Lsodium chlorideNaCl
0.02 %NaN3NaN3
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Details: 20 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 310 K / Instrument: FEI VITROBOT MARK IV
DetailsHKU5-20s Spike mix with paACE2-Fc (1:3 molar ratio)

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 2478 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 45000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 532998
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6nb3

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 270453
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.5.3)

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Atomic model buiding 1

Initial modelPDB ID:

6nb3


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: UCSF ChimeraX (ver. 1.8)
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9d4t:
Structure of HKU5-20s spike glycoprotein

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