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- PDB-9k3t: Cryo-EM structure of TMPRSS2 in complex with Fab fragments of 752... -

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Basic information

Entry
Database: PDB / ID: 9k3t
TitleCryo-EM structure of TMPRSS2 in complex with Fab fragments of 752 mAb and 2228 mAb
Components
  • Fab 2228 heavy chain
  • Fab 2228 light chain
  • Fab 752 heavy chain
  • Fab 752 light chain
  • Transmembrane protease serine 2
KeywordsMEMBRANE PROTEIN / HYDROLASE / IMMUNE SYSTEM
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 / positive regulation of viral entry into host cell / serine-type endopeptidase activity ...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 / positive regulation of viral entry into host cell / serine-type endopeptidase activity / proteolysis / extracellular exosome / extracellular region / nucleoplasm / plasma membrane
Similarity search - Function
Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / 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 ...Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Transmembrane protease serine 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsKatsura, K. / Hisano, T. / Matsumoto, T. / Shirouzu, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Iscience / Year: 2025
Title: Monoclonal antibodies against human TMPRSS2 prevent infection by any SARS-CoV-2 variant
Authors: Harada, M. / Matsumoto, T. / Yamamoto, M. / Goda, J. / Idei, A. / Ohtaki, K. / Kojima, N. / Yoneda, N. / Miyauchi, K. / Katsura, K. / Ikeda, M. / Hanada, K. / Ishizuka-Katsura, Y. / Hosaka, ...Authors: Harada, M. / Matsumoto, T. / Yamamoto, M. / Goda, J. / Idei, A. / Ohtaki, K. / Kojima, N. / Yoneda, N. / Miyauchi, K. / Katsura, K. / Ikeda, M. / Hanada, K. / Ishizuka-Katsura, Y. / Hosaka, T. / Hisano, T. / Kaizuka, T. / Yamamoto, T. / Matsuda, M. / Nakayama, M. / Sugimoto-Ishige, A. / Sakuma, M. / Hashimoto, R. / Takayama, K. / Nakayama, M. / Nguyen, C.T. / Ishigaki, H. / Itoh, Y. / Hashizume, Y. / Yoshida, M. / Kawaguchi, Y. / Takeda, M. / Koseki, H. / Shirouzu, M. / Inoue, J.I. / Saito, T.
History
DepositionOct 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transmembrane protease serine 2
L: Fab 752 light chain
H: Fab 752 heavy chain
l: Fab 2228 light chain
h: Fab 2228 heavy chain


Theoretical massNumber of molelcules
Total (without water)140,1585
Polymers140,1585
Non-polymers00
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 Transmembrane protease serine 2 / Serine protease 10


Mass: 43250.609 Da / Num. of mol.: 1 / Mutation: 250SSRQSR255 replaced with DDDDDK
Source method: isolated from a genetically manipulated source
Details: The sequence responsible for TMPRSS2 autoactivation (250SSRQSR255) was substituted with the 6 residues containing an enterokinase cleavage site.
Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS2, PRSS10 / Production host: Baculovirus transfer vector pFASTBAC1
References: UniProt: O15393, transmembrane protease serine 2
#2: Antibody Fab 752 light chain


Mass: 23749.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody Fab 752 heavy chain


Mass: 24654.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Antibody Fab 2228 light chain


Mass: 23919.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#5: Antibody Fab 2228 heavy chain


Mass: 24584.455 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
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

Component
IDNameTypeEntity IDParent-IDSource
1TMPRSS2 ECD and Fab fragments complexCOMPLEXall0RECOMBINANT
2TMPRSS2COMPLEX#11RECOMBINANT
3Fab 752COMPLEX#2-#31RECOMBINANT
4Fab 2228COMPLEX#4-#51RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Mus musculus (house mouse)10090
34Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Baculovirus transfer vector pFASTBAC1136645
23Homo sapiens (human)9606
34Homo sapiens (human)9606
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: 20000 nm / Nominal defocus min: 8000 nm
Image recordingElectron dose: 50.1 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419: / Category: model refinement
CTF correctionDetails: CTFFind4 and CTFRefine were used within the RELION3.1.3
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80052 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037627
ELECTRON MICROSCOPYf_angle_d0.51910375
ELECTRON MICROSCOPYf_dihedral_angle_d5.0131047
ELECTRON MICROSCOPYf_chiral_restr0.0441126
ELECTRON MICROSCOPYf_plane_restr0.0041326

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