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- EMDB-38828: Closed conformation of HKU1-B S protein after incubation of the r... -

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Basic information

Entry
Database: EMDB / ID: EMD-38828
TitleClosed conformation of HKU1-B S protein after incubation of the receptor
Map data
Sample
  • Complex: Closed conformation of HKU1-B S protein after incubation of the receptor
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHCoV-HKU1 / 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, HKU1-like / 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, 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, HKU1-like / 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, 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 speciesHuman coronavirus HKU1 (isolate N2)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsXia LY / Zhang YY / Zhou Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971123 China
CitationJournal: Cell Res / Year: 2024
Title: Structural basis for the recognition of HCoV-HKU1 by human TMPRSS2.
Authors: Lingyun Xia / Yuanyuan Zhang / Qiang Zhou /
History
DepositionJan 24, 2024-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38828.png

Downloads & links

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Map

FileDownload / File: emd_38828.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 434.8 Å		1.09 Å/pix.
x 400 pix.
= 434.8 Å		1.09 Å/pix.
x 400 pix.
= 434.8 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: 0.65
Minimum - Maximum-3.8094013 - 7.1290846
Average (Standard dev.)-0.0023663354 (±0.14578953)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 434.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38828_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_38828_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 : Closed conformation of HKU1-B S protein after incubation of the r...

EntireName: Closed conformation of HKU1-B S protein after incubation of the receptor
Components
  • Complex: Closed conformation of HKU1-B S protein after incubation of the receptor
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Closed conformation of HKU1-B S protein after incubation of the r...

SupramoleculeName: Closed conformation of HKU1-B S protein after incubation of the receptor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Human coronavirus HKU1 (isolate N2)

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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: Human coronavirus HKU1 (isolate N2)
Molecular weightTheoretical: 143.475344 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFLIIFILPT TLAVIGDFNC TNSFINDYNK TIPRISEDVV DVSLGLGTYY VLNRVYLNTT LLFTGYFPKS GANFRDLALK GSKYLSTLW YKPPFLSDFN NGIFSKVKNT KLYVNNTLYS EFSTIVIGSV FVNTSYTIVV QPHNGILEIT ACQYTMCEYP H TVCKSKGS ...String:
MFLIIFILPT TLAVIGDFNC TNSFINDYNK TIPRISEDVV DVSLGLGTYY VLNRVYLNTT LLFTGYFPKS GANFRDLALK GSKYLSTLW YKPPFLSDFN NGIFSKVKNT KLYVNNTLYS EFSTIVIGSV FVNTSYTIVV QPHNGILEIT ACQYTMCEYP H TVCKSKGS IRNESWHIDS SEPLCLFKKN FTYNVSADWL YFHFYQERGV FYAYYADVGM PTTFLFSLYL GTILSHYYVM PL TCKAISS NTDNETLEYW VTPLSRRQYL LNFDEHGVIT NAVDCSSSFL SEIQCKTQSF APNTGVYDLS GFTVKPVATV YRR IPNLPD CDIDNWLNNV SVPSPLNWER RIFSNCNFNL STLLRLVHVD SFSCNNLDKS KIFGSCFNSI TVDKFAIPNR RRDD LQLGS SGFLQSSNYK IDISSSSCQL YYSLPLVNVT INNFNPSSWN RRYGFGSFNV SSYDVVYSDH CFSVNSDFCP CADPS VVNS CVKSKPLSAI CPAGTKYRHC DLDTTLYVNN WCRCSCLPDP ISTYSPNTCP QKKVVVGIGE HCPGLGINEE KCGTQL NHS SCSCSPDAFL GWSFDSCISN NRCNIFSNFI FNGINSGTTC SNDLLYSNTE VSTGVCVNYD LYGITGQGIF KEVSAAY YN NWQNLLYDSN GNIIGFKDFL TNKTYTILPC YSGRVSAAFY QNSSSPALLY RNLKCSYVLN NISFISQPFY FDSYLGCV L NAVNLTSYSV SSCDLRMGSG FCIDYALPSS GSASRGISSP YRFVTFEPFN VSFVNDSVET VGGLFEIQIP TNFTIAGHE EFIQTSSPKV TIDCSAFVCS NYAACHDLLS EYGTFCDNIN SILNEVNDLL DITQLQVANA LMQGVTLSSN LNTNLHSDVD NIDFKSLLG CLGSQCGSSS RSLLEDLLFN KVKLSDVGFV EAYNNCTGGS EIRDLLCVQS FNGIKVLPPI LSETQISGYT T AATVAAMF PPWSAAAGVP FSLNVQYRIN GLGVTMDVLN KNQKLIANAF NKALLSIQNG FTATNSALAK IQSVVNANAQ AL NSLLQQL FNKFGAISSS LQEILSRLDP PEAQVQIDRL INGRLTALNA YVSQQLSDIT LIKAGASRAI EKVNECVKSQ SPR INFCGN GNHILSLVQN APYGLLFIHF SYKPTSFKTV LVSPGLCLSG DRGIAPKQGY FIKQNDSWMF TGSSYYYPEP ISDK NVVFM NSCSVNFTKA PFIYLNNSIP NLSDFEAEFS LWFKNHTSIA PNLTFNSHIN ATFLDLYYEM NVIQESIKSL NSSFI NLKE IGTYEM

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: 51 / 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 TITAN KRIOS
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: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 622548
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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