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- EMDB-62523: Overall structure of HKU5 S protein with S468A/Y463A mutation -

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Basic information

Entry
Database: EMDB / ID: EMD-62523
TitleOverall structure of HKU5 S protein with S468A/Y463A mutation
Map data
Sample
  • Complex: Overall structure of HKU5 S protein with S468A/Y463A mutation
    • Protein or peptide: Spike glycoprotein
  • Ligand: PALMITIC ACID
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHKU5 / 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, 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 (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, 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. / 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 S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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
Biological speciesBat coronavirus HKU5
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsZhang YY / Xia LY / Zhou Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82241081 China
CitationJournal: To Be Published
Title: Molecular Insights into Species-Specific ACE2 Recognition of Coronavirus HKU5
Authors: Zhang YY / Xia LY / Zhou Q
History
DepositionNov 27, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62523.png

Downloads & links

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Map

FileDownload / File: emd_62523.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 320 pix.
= 347.84 Å		1.09 Å/pix.
x 320 pix.
= 347.84 Å		1.09 Å/pix.
x 320 pix.
= 347.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.4910882 - 4.299586
Average (Standard dev.)0.003796696 (±0.13487221)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 347.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62523_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62523_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 : Overall structure of HKU5 S protein with S468A/Y463A mutation

EntireName: Overall structure of HKU5 S protein with S468A/Y463A mutation
Components
  • Complex: Overall structure of HKU5 S protein with S468A/Y463A mutation
    • Protein or peptide: Spike glycoprotein
  • Ligand: PALMITIC ACID
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Overall structure of HKU5 S protein with S468A/Y463A mutation

SupramoleculeName: Overall structure of HKU5 S protein with S468A/Y463A mutation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bat coronavirus HKU5

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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: Bat coronavirus HKU5
Molecular weightTheoretical: 149.705922 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MIRSVLVLMC SLTFIGNLTR GQSVDMGHNG TGSCLDSQVQ PDYFESVHTT WPMPIDTSKA EGVIYPNGKS YSNITLTYTG LYPKANDLG KQYLFSDGHS APGRLNNLFV SNYSSQVESF DDGFVVRIGA AANKTGTTVI SQSTFKPIKK IYPAFLLGHS V GNYTPSNR ...String:
MIRSVLVLMC SLTFIGNLTR GQSVDMGHNG TGSCLDSQVQ PDYFESVHTT WPMPIDTSKA EGVIYPNGKS YSNITLTYTG LYPKANDLG KQYLFSDGHS APGRLNNLFV SNYSSQVESF DDGFVVRIGA AANKTGTTVI SQSTFKPIKK IYPAFLLGHS V GNYTPSNR TGRYLNHTLV ILPDGCGTIL HAFYCVLHPR TQQNCAGETN FKSLSLWDTP ASDCVSGSYN QEATLGAFKV YF DLINCTF RYNYTITEDE NAEWFGITQD TQGVHLYSSR KENVFRNNMF HFATLPVYQK ILYYTVIPRS IRSPFNDRKA WAA FYIYKL HPLTYLLNFD VEGYITKAVD CGYDDLAQLQ CSYESFEVET GVYSVSSFEA SPRGEFIEQA TTQECDFTPM LTGT PPPIY NFKRLVFTNC NYNLTKLLSL FQVSEFSCHQ VSPSSLATGC YSSLTVDYFA YSTDMSSALQ PGAAGAIVQF NYKQD FSNP TCRVLATVPQ NLTTITKPSN YAYLTECYKT SAYGKNYLYN APGAYTPCLS LASRGFSTKY QSHSDGELTT TGYIYP VTG NLQMAFIISV QYGTDTNSVC PMQALRNDTS IEDKLDVCVE YSLHGITGRG VFHNCTSVGL RNQRFVYDTF DNLVGYH SD NGNYYCVRPC VSVPVSVIYD KASNSHATLF GSVACSHVTT MMSQFSRMTK TNLLARTTPG PLQTTVGCAM GFINSSMV V DECQLPLGQS LCAIPPTTSS RVRRATSGAS DVFQIATLNF TSPLTLAPIN STGFVVAVPT NFTFGVTQEF IETTIQKIT VDCKQYVCNG FKKCEDLLKE YGQFCSKINQ ALHGANLRQD ESIANLFSSI KTQNTQPLQA GLNGDFNLTM LQIPQVTTGE RKYRSTIED LLFNKVTIAD PGYMQGYDEC MQQGPQSARD LICAQYVAGY KVLPPLYDPY MEAAYTSSLL GSIAGASWTA G LSSFAAIP FAQSIFYRLN GVGITQQVLS ENQKIIANKF NQALGAMQTG FTTTNLAFNK VQDAVNANAM ALSKLAAELS NT FGAISSS ISDILARLDT VEQEAQIDRL INGRLTSLNA FVAQQLVRTE AAARSAQLAQ DKVNECVKSQ SKRNGFCGTG THI VSFAIN APNGLYFFHV GYQPTSHVNA TAAYGLCNTE NPQKCIAPID GYFVLNQTTS TVADSDQQWY YTGSSFFHPE PITE ANSKY VSMDVKFENL TNRLPPPLLS NSTDLDFKEE LEEFFKNVSS QGPNFQEISK INTTLLNLNT ELMVLSEVVK QLNES YIDL KELGNYTFYQ KWPWYIWLGF IAGLVALALC VFFILCCTGC GTSCLGKLKC NRCCDSYDEY EVEKIHVH

UniProtKB: Spike glycoprotein

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Macromolecule #4: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 4 / Number of copies: 3 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 30 / 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: GATAN K3 BIOQUANTUM (6k 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: 2.2 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.6.0) / Number images used: 40837
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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