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- EMDB-48048: Structure of the prefusion HKU5-19s Spike trimer (conformation 2) -

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Basic information

Entry
Database: EMDB / ID: EMD-48048
TitleStructure of the prefusion HKU5-19s Spike trimer (conformation 2)
Map data
Sample
  • Complex: Prefusion HKU5-19s S trimer
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: FOLIC ACID
  • Ligand: LINOLEIC ACID
  • Ligand: water
KeywordsMERS-related HKU5 coronaviruses / MERSr-CoV / Spike glycoprotein / fusion protein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 speciesHomo sapiens (human) / Pipistrellus bat coronavirus HKU5
Methodsingle particle reconstruction / cryo EM / Resolution: 2.0 Å
AuthorsPark YJ / Gen R / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Veesler D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI158186 United States
CitationJournal: Cell / Year: 2025
Title: Molecular basis of convergent evolution of ACE2 receptor utilization among HKU5 coronaviruses.
Authors: Young-Jun Park / Chen Liu / Jimin Lee / Jack T Brown / Cheng-Bao Ma / Peng Liu / Risako Gen / Qing Xiong / Samantha K Zepeda / Cameron Stewart / Amin Addetia / Caroline J Craig / M Alejandra ...Authors: Young-Jun Park / Chen Liu / Jimin Lee / Jack T Brown / Cheng-Bao Ma / Peng Liu / Risako Gen / Qing Xiong / Samantha K Zepeda / Cameron Stewart / Amin Addetia / Caroline J Craig / M Alejandra Tortorici / Abeer N Alshukairi / Tyler N Starr / Huan Yan / David Veesler /
Abstract: DPP4 was considered a canonical receptor for merbecoviruses until the recent discovery of African bat-borne MERS-related coronaviruses using ACE2. The extent and diversity of ACE2 utilization among ...DPP4 was considered a canonical receptor for merbecoviruses until the recent discovery of African bat-borne MERS-related coronaviruses using ACE2. The extent and diversity of ACE2 utilization among merbecoviruses and their receptor species tropism remain unknown. Here, we reveal that HKU5 enters host cells utilizing Pipistrellus abramus (P.abr) and several non-bat mammalian ACE2s through a binding mode distinct from that of any other known ACE2-using coronaviruses. We defined the molecular determinants of receptor species tropism and identified a single amino acid mutation enabling HKU5 to utilize human ACE2, providing proof of principle for machine-learning-assisted outbreak preparedness. We show that MERS-CoV and HKU5 have markedly distinct antigenicity and identified several HKU5 inhibitors, including two clinical compounds. Our findings profoundly alter our understanding of coronavirus evolution, as several merbecovirus clades independently evolved ACE2 utilization, and pave the way for developing countermeasures against viruses poised for human emergence.
History
DepositionNov 22, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48048.png

Downloads & links

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Map

FileDownload / File: emd_48048.map.gz / Format: CCP4 / Size: 857.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 608 pix.
= 512.544 Å		0.84 Å/pix.
x 608 pix.
= 512.544 Å		0.84 Å/pix.
x 608 pix.
= 512.544 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.843 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.3915946 - 4.265596
Average (Standard dev.)-0.000091661466 (±0.059822362)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions608608608
Spacing608608608
CellA=B=C: 512.544 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_48048_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48048_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48048_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Prefusion HKU5-19s S trimer

EntireName: Prefusion HKU5-19s S trimer
Components
  • Complex: Prefusion HKU5-19s S trimer
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: FOLIC ACID
  • Ligand: LINOLEIC ACID
  • Ligand: water

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Supramolecule #1: Prefusion HKU5-19s S trimer

SupramoleculeName: Prefusion HKU5-19s S trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: 150.750672 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTQSVDMGTT GSGNCIESQV QPDFFETARN TWPLSIDTSK AEGVIYPNGK SYSNITLTY TGLYPKANDL GKQYVFSDGH SSPGTLSRLF VSNYSRQVEP FDSGFVVRIG AAANKTGTTI ISQSTNRPIK K IYPAFMLG ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTQSVDMGTT GSGNCIESQV QPDFFETARN TWPLSIDTSK AEGVIYPNGK SYSNITLTY TGLYPKANDL GKQYVFSDGH SSPGTLSRLF VSNYSRQVEP FDSGFVVRIG AAANKTGTTI ISQSTNRPIK K IYPAFMLG HSVGNYTPTN ITGRYLNHTL VILPDGCGTL VHAFYCILQP RTQAYCAGAS TFTSVTVWDT PASDCANSQS YN RLANLNA FKLYFDLINC TFRYNYTITE DENAEWFGIT QDTQGVHLYS SRKENVFRNN MFHFATLPVY QKILYYTVIP RSI RSPFND RKAWAAFYIY KLHPLTYLLN FDVEGYITKA VDCGYDDLAQ LQCSYQSFDV ETGVYSVSSF EASPRGEFIE QATT QECDF TPMLTGTPPP IYNFKRLVFT NCNYNLTKLL SLFQVSEFSC HQVSPSSLAT GCYSSLTVDY FAYSTDMSSY LQPGS AGEI VQFNYKQDFS NPTCRVLATV PQNLTTITKP SNYAYLTECY KTSAYGKNYL YNAPGGYTPC LSLASRGFST KYQSHS DGE LTTTGYIYPV TGNLQMAFII SVQYGTDTNS VCPMQALRND TSIEDKLDVC VEYSLHGITG RGVFHNCTSV GLRNQRF VY DTFDNLVGYH SYNGNYYCVR PCVSVPVSVI YDKVSNSHAT LFGSVACSHV TTMMSQFSRM TKTNLLARTT PGPLQTVV G CAMGFINTSM VVDECQLPLG QSLCAIPPNP SARLARASSG VTDVFQIATL NFTSPLTLAP INSTGFVVAV PTNFTFGVT QEYIETTIQK ITVDCKQYVC NGFKKCEELL TEYGQFCSKI NQALHGANLR QDESIANLFS SIKTQNTQPL QAGLNGDFNL TMLQIPQVT TGERKYRSAI EDLLFNKVTI ADPGYMQGYD ECMQQGPQSA RDLICAQYVA GYKVLPPLYD PYMEAAYTSS L LGSIAGAS WTAGLSSFAA IPFAQSIFYR LNGVGITQQV LSENQKIIAN KFNQALGAMQ TGFTTTNLAF NKVQDAVNAN AM ALSKLAA ELSNTFGAIS SSISDILARL DPPEQEAQID RLINGRLTSL NAFVAQQLVR TEAAARSAQL AQDKVNECVK SQS KRNGFC GTGTHIVSFA INAPNGLYFF HVGYQPTSHV NATAAYGLCN TENPPKCIAP IGGYFVLNQT TSTVANSEQQ WYYT GSSFF HPEPITEVNS KYVSMDVKFE NLTNKLPPPL LSNTTDLDFK EELEEFFKNV SSQGPNFQEI SKINTTLLNL NTELM VLSE VVKQLNESYI DLKELGNYTF YQKGSGYIPE APRDGQAYVR KDGEWVLLST FLGGSGLNDI FEAQKIEWHE GGSHHH HHH HH

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: 15 / 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: FOLIC ACID

MacromoleculeName: FOLIC ACID / type: ligand / ID: 8 / Number of copies: 3 / Formula: FOL
Molecular weightTheoretical: 441.397 Da
Chemical component information

ChemComp-FA:
FOLIC ACID

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Macromolecule #9: LINOLEIC ACID

MacromoleculeName: LINOLEIC ACID / type: ligand / ID: 9 / Number of copies: 3 / Formula: EIC
Molecular weightTheoretical: 280.445 Da
Chemical component information

ChemComp-EIC:
LINOLEIC ACID

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Macromolecule #10: water

MacromoleculeName: water / type: ligand / ID: 10 / Number of copies: 813 / 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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 / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1022249
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Image processing #2

Image processing ID2
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1022249
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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