8ZVX | pdb_00008zvx

Crystal structure of snFPITE-n2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.186 (Depositor), 0.189 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.164 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

A facultative plasminogen-independent thrombolytic enzyme from Sipunculus nudus.

Tang, M.Ma, G.Xu, C.Yang, H.Lin, H.Bian, C.Hu, C.Lu, M.Chen, L.Jie, W.Yue, Z.Jian, J.Sun, Y.Yan, H.Zhou, J.Zhang, X.Liao, S.Li, Z.Cai, S.Wu, Y.Yang, K.Xiong, Y.Zhao, Y.Lv, Z.Xu, X.Liu, C.Xin, P.Ye, L.Cui, X.Shi, Q.Chen, X.Xu, R.

(2025) Nat Commun 16: 3852-3852

  • DOI: https://doi.org/10.1038/s41467-025-58915-y
  • Primary Citation Related Structures: 
    8ZVS, 8ZVX

  • PubMed Abstract: 

    Current thrombolytic therapies primarily function by converting plasminogen into plasmin, a process dependent on the fibrin-activator complex. This dependence, coupled with the substantial molecular size of plasmin, constrains its effectiveness in degrading D-dimer and restricts its diffusion within thrombi. Here, we introduce a small facultative plasminogen-independent thrombolytic enzyme, snFPITE, isolated from Sipunculus nudus. Compared to traditional thrombolytic agents, snFPITE does not require plasminogen for thrombolysis, although its presence enhances lytic activity. This enzyme fully degrades cross-linked fibrin without leaving residual nondegradable D-dimer and generates a smaller fibrinolytic-active agent from plasminogen. A series of male rats and mice models further confirm that snFPITE is a safety injectable thrombolytic agent. Mechanistically, snFPITE activates plasminogen and degrades fibrin(ogen) in a multisite cleavage manner. snFPITE is inhibited by plasminogen activator inhibitor 1 and α2-antiplasmin via a competitive inhibition. We further identify 28 snFPITE candidate sequences, of which 10 are confirmed as functional genes.


  • Organizational Affiliation
    • Engineering Research Centre of Molecular Medicine of Ministry of Education, Fujian Key Laboratory of Molecular Medicine, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Xiamen Key Laboratory of Marine and Gene Drugs, School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China.

Macromolecule Content 

  • Total Structure Weight: 51.37 kDa 
  • Atom Count: 4,045 
  • Modeled Residue Count: 478 
  • Deposited Residue Count: 478 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
snFPITE-n2 A chain239Sipunculus nudusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
snFPITE-n2 B chain239Sipunculus nudusMutation(s): 0 

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
M [auth B]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PMS

Query on PMS



Download:Ideal Coordinates CCD File
C [auth A],
I [auth B]
phenylmethanesulfonic acid
C7 H8 O3 S
NIXKBAZVOQAHGC-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
J [auth B],
K [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.186 (Depositor), 0.189 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.262α = 90
b = 59.738β = 90
c = 193.702γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21807088

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-02
    Type: Initial release
  • Version 1.1: 2025-05-07
    Changes: Database references