5DI0 | pdb_00005di0

Crystal structure of Dln1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.209 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5DI0

This is version 1.2 of the entry. See complete history

Literature

Structural basis for receptor recognition and pore formation of a zebrafish aerolysin-like protein.

Jia, N.Liu, N.Cheng, W.Jiang, Y.L.Sun, H.Chen, L.L.Peng, J.Zhang, Y.Ding, Y.H.Zhang, Z.H.Wang, X.Cai, G.Wang, J.Dong, M.Q.Zhang, Z.Wu, H.Wang, H.W.Chen, Y.Zhou, C.Z.

(2016) EMBO Rep 17: 235-248

  • DOI: https://doi.org/10.15252/embr.201540851
  • Primary Citation Related Structures: 
    4ZNO, 4ZNQ, 4ZNR, 5DI0

  • PubMed Abstract: 

    Various aerolysin-like pore-forming proteins have been identified from bacteria to vertebrates. However, the mechanism of receptor recognition and/or pore formation of the eukaryotic members remains unknown. Here, we present the first crystal and electron microscopy structures of a vertebrate aerolysin-like protein from Danio rerio, termed Dln1, before and after pore formation. Each subunit of Dln1 dimer comprises a β-prism lectin module followed by an aerolysin module. Specific binding of the lectin module toward high-mannose glycans triggers drastic conformational changes of the aerolysin module in a pH-dependent manner, ultimately resulting in the formation of a membrane-bound octameric pore. Structural analyses combined with computational simulations and biochemical assays suggest a pore-forming process with an activation mechanism distinct from the previously characterized bacterial members. Moreover, Dln1 and its homologs are ubiquitously distributed in bony fishes and lamprey, suggesting a novel fish-specific defense molecule.


  • Organizational Affiliation
    • Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China.

Macromolecule Content 

  • Total Structure Weight: 76.84 kDa 
  • Atom Count: 6,071 
  • Modeled Residue Count: 636 
  • Deposited Residue Count: 670 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Natterin-like protein
A, B
335Danio rerioMutation(s): 0 
Gene Names: zgc113413
UniProt
Find proteins for Q5CZR5 (Danio rerio)
Explore Q5CZR5 
Go to UniProtKB:  Q5CZR5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5CZR5
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4

Query on PG4



Download:Ideal Coordinates CCD File
GA [auth B]
HA [auth B]
IA [auth B]
JA [auth B]
R [auth A]
GA [auth B],
HA [auth B],
IA [auth B],
JA [auth B],
R [auth A],
S [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
DA [auth B]
EA [auth B]
FA [auth B]
N [auth A]
O [auth A]
DA [auth B],
EA [auth B],
FA [auth B],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
BA [auth B]
CA [auth B]
H [auth A]
I [auth A]
J [auth A]
BA [auth B],
CA [auth B],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
AA [auth B]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
AA [auth B],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
KA [auth B],
T [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.209 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.111α = 90
b = 95.1β = 90
c = 147.406γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-03-30
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description