6KD5

Crystal structure of the extracellular domain of MSPL/TMPRSS13 in complex with dec-RVKR-cmk inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.188 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 3.2 of the entry. See complete history


Literature

Crystal structure of inhibitor-bound human MSPL that can activate high pathogenic avian influenza.

Ohno, A.Maita, N.Tabata, T.Nagano, H.Arita, K.Ariyoshi, M.Uchida, T.Nakao, R.Ulla, A.Sugiura, K.Kishimoto, K.Teshima-Kondo, S.Okumura, Y.Nikawa, T.

(2021) Life Sci Alliance 4

  • DOI: https://doi.org/10.26508/lsa.202000849
  • Primary Citation of Related Structures:  
    6KD5

  • PubMed Abstract: 

    Infection of certain influenza viruses is triggered when its HA is cleaved by host cell proteases such as proprotein convertases and type II transmembrane serine proteases (TTSP). HA with a monobasic motif is cleaved by trypsin-like proteases, including TMPRSS2 and HAT, whereas the multibasic motif found in high pathogenicity avian influenza HA is cleaved by furin, PC5/6, or MSPL. MSPL belongs to the TMPRSS family and preferentially cleaves [R/K]-K-K-R↓ sequences. Here, we solved the crystal structure of the extracellular region of human MSPL in complex with an irreversible substrate-analog inhibitor. The structure revealed three domains clustered around the C-terminal α-helix of the SPD. The inhibitor structure and its putative model show that the P1-Arg inserts into the S1 pocket, whereas the P2-Lys and P4-Arg interacts with the Asp/Glu-rich 99-loop that is unique to MSPL. Based on the structure of MSPL, we also constructed a homology model of TMPRSS2, which is essential for the activation of the SARS-CoV-2 spike protein and infection. The model may provide the structural insight for the drug development for COVID-19.


  • Organizational Affiliation

    Department of Nutritional Physiology, Institute of Medical Nutrition, Tokushima University Graduate School, Tokushima, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protease serine 13156Homo sapiensMutation(s): 0 
Gene Names: TMPRSS13MSPTMPRSS11
EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYE2 (Homo sapiens)
Explore Q9BYE2 
Go to UniProtKB:  Q9BYE2
PHAROS:  Q9BYE2
GTEx:  ENSG00000137747 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYE2
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q9BYE2-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protease serine 13261Homo sapiensMutation(s): 1 
Gene Names: TMPRSS13MSPTMPRSS11
EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYE2 (Homo sapiens)
Explore Q9BYE2 
Go to UniProtKB:  Q9BYE2
PHAROS:  Q9BYE2
GTEx:  ENSG00000137747 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYE2
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q9BYE2-1
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR6synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.84α = 90
b = 62.4β = 90
c = 171.63γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan15K13747
Japan Society for the Promotion of Science (JSPS)Japan19K05696
Japan Society for the Promotion of Science (JSPS)Japan15K09585
Japan Society for the Promotion of Science (JSPS)Japan18K08453
Japan Society for the Promotion of Science (JSPS)Japan15J40096
Japan Society for the Promotion of Science (JSPS)Japan18H04981
Japan Society for the Promotion of Science (JSPS)Japan19H04054
Japan Agency for Medical Research and Development (AMED)JapanJP19gm0810009

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2020-07-01
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.0: 2020-11-25
    Type: Coordinate replacement
    Reason: Ligand geometry
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 3.1: 2021-04-14
    Changes: Database references
  • Version 3.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description