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- PDB-9opq: TMPRSS2 (S441A) bound to the HCoV-NL63 S2'region genetically fuse... -

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Basic information

Entry
Database: PDB / ID: 9opq
TitleTMPRSS2 (S441A) bound to the HCoV-NL63 S2'region genetically fused to the HCoV-HKU1 RBD
Components
  • NL63-S2prime/HKU1-RBD
  • Transmembrane protease serine 2
KeywordsVIRAL PROTEIN/HYDROLASE / TMPRSS2 / NL63 / HKU1 / RBD / S2prime / coronavirus / cleavage / SARS-CoV-2 / spike / fusion / protease / entry / antiviral / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


transmembrane protease serine 2 / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / Induction of Cell-Cell Fusion / positive regulation of viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell ...transmembrane protease serine 2 / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / Induction of Cell-Cell Fusion / positive regulation of viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / 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 glycoprotein, Alphacoronavirus / Scavenger receptor cysteine-rich domain / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / 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 / Spike glycoprotein S2, coronavirus, C-terminal ...Spike glycoprotein, Alphacoronavirus / Scavenger receptor cysteine-rich domain / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / 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 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / 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. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 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 / Spike glycoprotein
Similarity search - Component
Biological speciesHuman coronavirus HKU1
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsMcCallum, M. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Veesler, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2026
Title: TMPRSS2-mediated coronavirus spike activation and inhibition.
Authors: McCallum, M. / Case, J.B. / Brown, J.T. / Park, Y.J. / Lee, J. / Sutherland, E. / Aggarwal, A. / Gibson, C. / Lempp, F.A. / Stewart, C. / Tortorici, M.A. / Sanapala, S. / Low, J.S. / ...Authors: McCallum, M. / Case, J.B. / Brown, J.T. / Park, Y.J. / Lee, J. / Sutherland, E. / Aggarwal, A. / Gibson, C. / Lempp, F.A. / Stewart, C. / Tortorici, M.A. / Sanapala, S. / Low, J.S. / Asarnow, D. / Bohan, D. / Dellota Jr., E. / Merz, B. / Chawla, B. / Kar, S. / Lanzavecchia, A. / Sallusto, F. / Riley, N.M. / Turville, S. / Purcell, L. / Diamond, M.S. / Veesler, D.
History
DepositionMay 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NL63-S2prime/HKU1-RBD
B: Transmembrane protease serine 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6038
Polymers97,2762
Non-polymers1,3276
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein NL63-S2prime/HKU1-RBD / S glycoprotein / E2 / Peplomer protein


Mass: 41123.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The NL63-S2'/HKU1-RBD construct comprises a signal peptide (MGILPSPGMPALLSLVSLLSVLLMGCVAETGT), HKU1 (Uniprot: Q5MQD0, isolate N1) residues 320-509, HCoV-NL63 residues I867-L877 (IAGRSALEDLL, ...Details: The NL63-S2'/HKU1-RBD construct comprises a signal peptide (MGILPSPGMPALLSLVSLLSVLLMGCVAETGT), HKU1 (Uniprot: Q5MQD0, isolate N1) residues 320-509, HCoV-NL63 residues I867-L877 (IAGRSALEDLL, Uniprot: Q6Q1S2), a GSGSGSP linker and HKU1 (Uniprot: Q5MQD0, isolate N1) residues 511-614, a GSSGGS linker, an avi-tag (GLNDIFEAQKIEWHE), a GGS linker and an octa-histidine tag
Source: (gene. exp.) Human coronavirus HKU1 / Gene: S, 3, S, 2 / Production host: Homo sapiens (human) / References: UniProt: Q5MQD0, UniProt: Q6Q1S2
#2: Protein Transmembrane protease serine 2 / Serine protease 10


Mass: 56152.125 Da / Num. of mol.: 1 / Mutation: S441A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS2, PRSS10 / Production host: Homo sapiens (human)
References: UniProt: O15393, transmembrane protease serine 2
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: TMPRSS2 (S441A) bound to the HCoV-NL63 S2'region genetically fused to the HCoV-HKU1 RBD
Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 163873 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034693
ELECTRON MICROSCOPYf_angle_d0.5016419
ELECTRON MICROSCOPYf_dihedral_angle_d3.922676
ELECTRON MICROSCOPYf_chiral_restr0.046711
ELECTRON MICROSCOPYf_plane_restr0.004834

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