9J3P | pdb_00009j3p

Human Pigment Epithelium-Derived Factor with Zinc Ions Crystallized in P2(1)2(1)2(1) Space Group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.251 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9J3P

This is version 1.2 of the entry. See complete history

Literature

A role of pigment epithelium-derived factor in zinc-mediated mechanism of neurodegeneration in glaucoma.

Chistyakov, D.V.Belousov, A.S.Shevelyova, M.P.Iomdina, E.N.Baksheeva, V.E.Shebardina, N.G.Moysenovich, A.M.Bulgakov, T.K.Petrov, S.Y.Shishkin, M.L.Tulush, S.S.Tiulina, V.V.Pogodina, E.I.Gancharova, O.S.Filippova, O.M.Baldin, A.V.Goriainov, S.V.Nikolskaya, A.I.Zalevsky, A.O.Deviatkin, A.A.Vologzhannikova, A.A.Gorokhovets, N.V.Litus, E.A.Komarov, S.V.Devred, F.Sergeeva, M.G.Mishin, A.V.Bukhdruker, S.S.Wu, L.Araujo, E.A.Zamyatnin Jr., A.A.Senin, I.I.Zinchenko, D.V.Tsvetkov, P.O.Borshchevskiy, V.I.Permyakov, S.E.Zernii, E.Y.

(2025) Commun Biol 8: 965-965

  • DOI: https://doi.org/10.1038/s42003-025-08370-8
  • Primary Citation Related Structures: 
    9J3P, 9J3Q

  • PubMed Abstract: 

    Glaucoma is a neurodegenerative condition involving optic nerve damage and retinal ganglion cells death. Animal studies suggested that the pathway linking these events can be mediated by mobile zinc secreted into the intraretinal space and exerting cytotoxic effects. Whether this mechanism is relevant for human glaucoma and what are the targets of extracellular zinc is unknown. We report that increased zinc content in the aqueous humor and retina is indeed a characteristic of glaucomatous neuropathy, and excess extracellular zinc may be recognized by the key retinal neurotrophic factor PEDF. Biophysical and X-ray crystallographic studies show that PEDF coordinates zinc ions in five types of intermolecular high-affinity sites, leading to a decrease in negative surface charge and reversible oligomerization of the protein, thereby masking the target recognition sites responsible for its neurotrophic and antiangiogenic activities and collagen binding. Notably, PEDF secretion is enhanced in both glaucoma and retinal cell models in response to zinc stress; however, zinc binding negatively affects axogenic, differentiative and prosurvival functions of PEDF by suppressing its ability to activate receptor PEDF-R/PNPLA2. We suggest that glaucomatous neurodegeneration is associated with direct inhibition of PEDF signaling by extracellular zinc, making their complex a promising target for neuroprotective therapy.


  • Organizational Affiliation
    • Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.

Macromolecule Content 

  • Total Structure Weight: 223.72 kDa 
  • Atom Count: 15,370 
  • Modeled Residue Count: 1,856 
  • Deposited Residue Count: 1,990 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pigment epithelium-derived factor
A, B, C, D, E
398Homo sapiensMutation(s): 0 
Gene Names: SERPINF1PEDFPIG35
UniProt & NIH Common Fund Data Resources
Find proteins for P36955 (Homo sapiens)
Explore P36955 
Go to UniProtKB:  P36955
PHAROS:  P36955
GTEx:  ENSG00000132386 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36955
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG0

Query on PG0



Download:Ideal Coordinates CCD File
BA [auth E]
H [auth A]
I [auth A]
L [auth B]
M [auth B]
BA [auth E],
H [auth A],
I [auth A],
L [auth B],
M [auth B],
N [auth B],
W [auth D]
2-(2-METHOXYETHOXY)ETHANOL
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AA [auth E]
G [auth A]
J [auth B]
K [auth B]
Q [auth C]
AA [auth E],
G [auth A],
J [auth B],
K [auth B],
Q [auth C],
R [auth C],
S [auth C],
U [auth D],
V [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
F [auth A]
O [auth C]
P [auth C]
T [auth D]
X [auth E]
F [auth A],
O [auth C],
P [auth C],
T [auth D],
X [auth E],
Y [auth E],
Z [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.251 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.234α = 90
b = 131.567β = 90
c = 227.831γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation21-15-00123

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Derived calculations
  • Version 1.2: 2025-10-15
    Changes: Database references