[English] 日本語
Yorodumi
- EMDB-48809: Cryo-EM structure of HCoV-HKU1 spike glycoprotein in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-48809
TitleCryo-EM structure of HCoV-HKU1 spike glycoprotein in complex with 9OAc-GD3 tetrasacchride (Deletion 33Pro34Arg)
Map data
Sample
  • Complex: Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9OAc-GD3 tetrasacchride (Deletion 33Pro34Arg)
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid
KeywordsHCoV-HKU1 spike glycoprotein ectodomain / proline stablized / 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, N-terminal domain, murine hepatitis virus-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 (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-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 speciesHuman coronavirus HKU1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsJin M / Rini JM
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nat Commun / Year: 2025
Title: Human coronavirus HKU1 spike structures reveal the basis for sialoglycan specificity and carbohydrate-promoted conformational changes.
Authors: Min Jin / Zaky Hassan / Zhijie Li / Ying Liu / Aleksandra Marakhovskaia / Alan H M Wong / Adam Forman / Mark Nitz / Michel Gilbert / Hai Yu / Xi Chen / James M Rini /
Abstract: The human coronavirus HKU1 uses both sialoglycoconjugates and the protein transmembrane serine protease 2 (TMPRSS2) as receptors. Carbohydrate binding leads to the spike protein up conformation ...The human coronavirus HKU1 uses both sialoglycoconjugates and the protein transmembrane serine protease 2 (TMPRSS2) as receptors. Carbohydrate binding leads to the spike protein up conformation required for TMPRSS2 binding, an outcome suggesting a distinct mechanism for driving fusion of the viral and host cell membranes. Nevertheless, the conformational changes promoted by carbohydrate binding have not been fully elucidated and the basis for HKU1's carbohydrate binding specificity remains unknown. Reported here are high resolution cryo-EM structures of the HKU1 spike protein trimer in its apo form and in complex with the carbohydrate moiety of a candidate carbohydrate receptor, the 9-O-acetylated GD3 ganglioside. The structures show that the spike monomer can exist in four discrete conformational states and that progression through them would promote the up conformation upon carbohydrate binding. We also show that a six-amino-acid insert is a determinant of HKU1's specificity for gangliosides containing a 9-O-acetylated α2-8-linked disialic acid moiety and that HKU1 shows weak affinity for the 9-O-acetylated sialic acids found on decoy receptors such as mucins.
History
DepositionJan 24, 2025-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_48809.png

Downloads & links

-
Map

FileDownload / File: emd_48809.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 256 pix.
= 288. Å		1.13 Å/pix.
x 256 pix.
= 288. Å		1.13 Å/pix.
x 256 pix.
= 288. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.125 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.40263706 - 1.0288614
Average (Standard dev.)0.0014233515 (±0.048894297)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 288.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_48809_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_48809_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_48809_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9OAc-...

EntireName: Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9OAc-GD3 tetrasacchride (Deletion 33Pro34Arg)
Components
  • Complex: Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9OAc-GD3 tetrasacchride (Deletion 33Pro34Arg)
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid

-
Supramolecule #1: Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9OAc-...

SupramoleculeName: Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9OAc-GD3 tetrasacchride (Deletion 33Pro34Arg)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Ectodomain generated by recombinant expression in HEK293 Freestyle cells
Source (natural)Organism: Human coronavirus HKU1
Molecular weightTheoretical: 457.593 KDa

-
Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human coronavirus HKU1
Molecular weightTheoretical: 150.378422 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VIGDFNCTNF AINDLNTTVI SEYVVDVSYG LGTYYILDRV YLNTTILFTG YFPKSGANFR DLSLKGTTYL STLWYQKPFL SDFNNGIFS RVKNTKLYVN KTLYSEFSTI VIGSVFINNS YTIVVQPHNG VLEITACQYT MCEYPHTICK SKGSSRNESW H FDKSEPLC ...String:
VIGDFNCTNF AINDLNTTVI SEYVVDVSYG LGTYYILDRV YLNTTILFTG YFPKSGANFR DLSLKGTTYL STLWYQKPFL SDFNNGIFS RVKNTKLYVN KTLYSEFSTI VIGSVFINNS YTIVVQPHNG VLEITACQYT MCEYPHTICK SKGSSRNESW H FDKSEPLC LFKKNFTYNV STDWLYFHFY QERGTFYAYY ADSGMPTTFL FSLYLGTLLS HYYVLPLTCN AISSNTDNET LQ YWVTPLS KRQYLLKFDN RGVITNAVDC SSSFFSEIQC KTKSLLPNTG VYDLSGFTVK PVATVHRRIP DLPDCDIDKW LNN FNVPSP LNWERKIFSN CNFNLSTLLR LVHTDSFSCN NFDESKIYGS CFKSIVLDKF AIPNSRRSDL QLGSSGFLQS SNYK IDTTS SSCQLYYSLP AINVTINNYN PSSWNRRYGF NNFNLSSHSV VYSRYCFSVN NTFCPCAKPS FASSCKSHKP PSASC PIGT NYRSCESTTV LDHTDWCRCS CLPDPITAYD PRSCSQKKSL VGVGEHCAGF GVDEEKCGVL DGSYNVSCLC STDAFL GWS YDTCVSNNRC NIFSNFILNG INSGTTCSND LLQPNTEVFT DVCVDYDLYG ITGQGIFKEV SAVYYNSWQN LLYDSNG NI IGFKDFVTNK TYNIFPCYAG RVSAAFHQNA SSLALLYRNL KCSYVLNNIS LTTQPYFDSY LGCVFNADNL TDYSVSSC A LRMGSGFCVD YNSPSSSSSR RKRRSISASY RFVTFEPFNV SFVNDSIESV GGLYEIKIPT NFTIVGQEEF IQTNSPKVT IDCSLFVCSN YAACHDLLSE YGTFCDNINS ILDEVNGLLD TTQLHVADTL MQGVTLSSNL NTNLHFDVDN INFKSLVGCL GPHCGSSSR SFFEDLLFDK VKLSDVGFVE AYNNCTGGSE IRDLLCVQSF NGIKVLPPIL SESQISGYTT AATVAAMFPP W SAAAGIPF SLNVQYRING LGVTMDVLNK NQKLIATAFN NALLSIQNGF SAPNSALAKI QSVVNSNAQA LNSLLQQLFN KF GAISSSL QEILSRLDPP EAQVQIDRLI NGRLTALNAY VSQQLSDISL VKFGAALAME KVNECVKSQS PRINFCGNGN HIL SLVQNA PYGLLFMHFS YKPISFKTVL VSPGLCISGD VGIAPKQGYF IKHNDHWMFT GSSYYYPEPI SDKNVVFMNT CSVN FTKAP LVYLNHSVPK LSDFESELSH WFKNQTSIAP NLTLNLHTIN ATFLDLYYEM NLIQESIKSL NNSYINLKDI GTYEM YVKS GGYIPEAPRD GQAYVRKDGE WVLLSTFLNS GRAHHHHHHG AGGLNDIFEA QKIEWHEDTA AA

UniProtKB: Spike glycoprotein

-
Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 39 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Macromolecule #6: 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alp...

MacromoleculeName: 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid
type: ligand / ID: 6 / Number of copies: 3 / Formula: A1AR1
Molecular weightTheoretical: 642.561 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.15 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Tris
50.0 mMNaClNaCl
GridModel: C-flat-2/2 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 20
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 36.0 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: 1.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 92000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Details: A initial 3D map was generated by ab-initio reconstruction in cryoSPARC v4
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 264396
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9n18:
Cryo-EM structure of HCoV-HKU1 spike glycoprotein in complex with 9OAc-GD3 tetrasacchride (Deletion 33Pro34Arg)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more