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- EMDB-39502: Structure of HKU1B RBD with TMPRSS2 -

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Basic information

Entry
Database: EMDB / ID: EMD-39502
TitleStructure of HKU1B RBD with TMPRSS2
Map data
Sample
  • Complex: HKU1B-RBD with TMPRSS2 receptor
    • Protein or peptide: Spike protein S1
    • Protein or peptide: Transmembrane protease serine 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHKU1B / RBD / TMPRSS2 / VIRAL PROTEIN/HYDROLASE / VIRAL PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


transmembrane protease serine 2 / symbiont-mediated induction of syncytium formation / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / viral translation / Induction of Cell-Cell Fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell ...transmembrane protease serine 2 / symbiont-mediated induction of syncytium formation / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / viral translation / Induction of Cell-Cell Fusion / 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 / identical protein binding / 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, 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 / 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 speciesHomo sapiens (human) / Candidatus Accumulibacter adiacens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsGao X / Cui S / Ding W / Zhu K / Shang K / Zhu H
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Discov / Year: 2024
Title: Structural basis for the interaction between human coronavirus HKU1 spike receptor binding domain and its receptor TMPRSS2.
Authors: Xiaopan Gao / Kaixiang Zhu / Lin Wang / Kun Shang / Lei Hua / Bo Qin / Hongtao Zhu / Wei Ding / Sheng Cui /
History
DepositionMar 19, 2024-
Header (metadata) releaseAug 28, 2024-
Map releaseAug 28, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39502.png

Downloads & links

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Map

FileDownload / File: emd_39502.map.gz / Format: CCP4 / Size: 115.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 312 pix.
= 252.72 Å		0.81 Å/pix.
x 312 pix.
= 252.72 Å		0.81 Å/pix.
x 312 pix.
= 252.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.008306593 - 2.8566873
Average (Standard dev.)0.0015486672 (±0.031027261)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions312312312
Spacing312312312
CellA=B=C: 252.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : HKU1B-RBD with TMPRSS2 receptor

EntireName: HKU1B-RBD with TMPRSS2 receptor
Components
  • Complex: HKU1B-RBD with TMPRSS2 receptor
    • Protein or peptide: Spike protein S1
    • Protein or peptide: Transmembrane protease serine 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HKU1B-RBD with TMPRSS2 receptor

SupramoleculeName: HKU1B-RBD with TMPRSS2 receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 1
Details: Sequence reference for Candidatus Accumulibacter adiacens (2954378) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID Q0ZME7.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Accumulibacter adiacens (bacteria)
Molecular weightTheoretical: 31.703457 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: NLPDCDIDNW LNNVSVPSPL NWERRIFSNC NFNLSTLLRL VHVDSFSCNN LDKSKIFGSC FNSITVDKFA IPNRRRDDLQ LGSSGFLQS SNYKIDISSS SCQLYYSLPL VNVTINNFNP SSWNRRYGFG SFNLSSYDVV YSDHCFSVNS DFCPCADPSV V NSCAKSKP ...String:
NLPDCDIDNW LNNVSVPSPL NWERRIFSNC NFNLSTLLRL VHVDSFSCNN LDKSKIFGSC FNSITVDKFA IPNRRRDDLQ LGSSGFLQS SNYKIDISSS SCQLYYSLPL VNVTINNFNP SSWNRRYGFG SFNLSSYDVV YSDHCFSVNS DFCPCADPSV V NSCAKSKP PSAICPAGTK YRHCDLDTTL YVKNWCRCSC LPDPISTYSP NTCPQKKVVV GIGEHCPGLG INEEKCGTQL NH SSCFCSP DAFLGWSFDS CISNNRCNIF SNFIFNGINS GTTCSNDL

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: 1 / Enantiomer: LEVO / EC number: transmembrane protease serine 2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.381848 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: MGSKCSNSGI ECDSSGTCIN PSNWCDGVSH CPGGEDENRC VRLYGPNFIL QVYSSQRKSW HPVCQDDWNE NYGRAACRDM GYKNNFYSS QGIVDDSGST SFMKLNTSAG NVDIYKKLYH SDACSSKAVV SLRCIACGVN LNSSRQSRIV GGESALPGAW P WQVSLHVQ ...String:
MGSKCSNSGI ECDSSGTCIN PSNWCDGVSH CPGGEDENRC VRLYGPNFIL QVYSSQRKSW HPVCQDDWNE NYGRAACRDM GYKNNFYSS QGIVDDSGST SFMKLNTSAG NVDIYKKLYH SDACSSKAVV SLRCIACGVN LNSSRQSRIV GGESALPGAW P WQVSLHVQ NVHVCGGSII TPEWIVTAAH CVEKPLNNPW HWTAFAGILR QSFMFYGAGY QVEKVISHPN YDSKTKNNDI AL MKLQKPL TFNDLVKPVC LPNPGMMLQP EQLCWISGWG ATEEKGKTSE VLNAAKVLLI ETQRCNSRYV YDNLITPAMI CAG FLQGNV DSCQGDAGGP LVTSKNNIWW LIGDTSWGSG CAKAYRPGVY GNVMVFTDWI YRQMRADG

UniProtKB: Transmembrane protease serine 2

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 6 / 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 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.8 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 709482
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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