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- EMDB-38833: 3up-TM conformation of HKU1-B S protein after incubation of the r... -

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Basic information

Entry
Database: EMDB / ID: EMD-38833
Title3up-TM conformation of HKU1-B S protein after incubation of the receptor
Map data
Sample
  • Complex: 3up-TM conformation of HKU1-B S protein after incubation of the receptor
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Transmembrane protease serine 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHCoV-HKU1 / VIRAL PROTEIN/HYDROLASE / VIRAL PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


transmembrane protease serine 2 / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / viral translation / Induction of Cell-Cell Fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell ...transmembrane protease serine 2 / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / viral translation / Induction of Cell-Cell Fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / proteolysis / extracellular exosome / extracellular region / nucleoplasm / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, HKU1-like / Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. ...Spike (S) protein S1 subunit, receptor-binding domain, HKU1-like / Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Transmembrane protease serine 2 / Spike glycoprotein
Similarity search - Component
Biological speciesHuman coronavirus HKU1 (isolate N2) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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 20, 2024-
Current statusNov 20, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38833.png

Downloads & links

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Map

FileDownload / File: emd_38833.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: 0.21
Minimum - Maximum-3.5704112 - 5.538716
Average (Standard dev.)-0.0023254696 (±0.10669641)
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: #2

Fileemd_38833_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38833_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 : 3up-TM conformation of HKU1-B S protein after incubation of the r...

EntireName: 3up-TM conformation of HKU1-B S protein after incubation of the receptor
Components
  • Complex: 3up-TM conformation of HKU1-B S protein after incubation of the receptor
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Transmembrane protease serine 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: 3up-TM conformation of HKU1-B S protein after incubation of the r...

SupramoleculeName: 3up-TM conformation of HKU1-B S protein after incubation of the receptor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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 #2: Transmembrane protease serine 2

MacromoleculeName: Transmembrane protease serine 2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: transmembrane protease serine 2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.368785 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSKCSNSGI ECDSSGTCIN PSNWCDGVSH CPGGEDENRC VRLYGPNFIL QVYSSQRKSW HPVCQDDWNE NYGRAACRDM GYKNNFYSS QGIVDDSGST SFMKLNTSAG NVDIYKKLYH SDACSSKAVV SLRCIACGVN LNSSRQSQIV GGESALPGAW P WQVSLHVQ ...String:
MGSKCSNSGI ECDSSGTCIN PSNWCDGVSH CPGGEDENRC VRLYGPNFIL QVYSSQRKSW HPVCQDDWNE NYGRAACRDM GYKNNFYSS QGIVDDSGST SFMKLNTSAG NVDIYKKLYH SDACSSKAVV SLRCIACGVN LNSSRQSQIV GGESALPGAW P WQVSLHVQ NVHVCGGSII TPEWIVTAAH CVEKPLNNPW HWTAFAGILR QSFMFYGAGY QVEKVISHPN YDSKTKNNDI AL MKLQKPL TFNDLVKPVC LPNPGMMLQP EQLCWISGWG ATEEKGKTSE VLNAAKVLLI ETQRCNSRYV YDNLITPAMI CAG FLQGNV DSCQGDSGGP LVTSKNNIWW LIGDTSWGSG CAKAYRPGVY GNVMVFTDWI YRQMRADG

UniProtKB: Transmembrane protease serine 2

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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: 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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 366277
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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