3FW5 | pdb_00003fw5

Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric 4-methyl-catechol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.290 (Depositor), 0.289 (DCC) 
  • R-Value Work: 
    0.244 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 
    0.248 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3FW5

This is version 1.4 of the entry. See complete history

Literature

Iron traffics in circulation bound to a siderocalin (Ngal)-catechol complex.

Bao, G.Clifton, M.Hoette, T.M.Mori, K.Deng, S.X.Qiu, A.Viltard, M.Williams, D.Paragas, N.Leete, T.Kulkarni, R.Li, X.Lee, B.Kalandadze, A.Ratner, A.J.Pizarro, J.C.Schmidt-Ott, K.M.Landry, D.W.Raymond, K.N.Strong, R.K.Barasch, J.

(2010) Nat Chem Biol 6: 602-609

  • DOI: https://doi.org/10.1038/nchembio.402
  • Primary Citation Related Structures: 
    3FW4, 3FW5

  • PubMed Abstract: 

    The lipocalins are secreted proteins that bind small organic molecules. Scn-Ngal (also known as neutrophil gelatinase associated lipocalin, siderocalin, lipocalin 2) sequesters bacterial iron chelators, called siderophores, and consequently blocks bacterial growth. However, Scn-Ngal is also prominently expressed in aseptic diseases, implying that it binds additional ligands and serves additional functions. Using chemical screens, crystallography and fluorescence methods, we report that Scn-Ngal binds iron together with a small metabolic product called catechol. The formation of the complex blocked the reactivity of iron and permitted its transport once introduced into circulation in vivo. Scn-Ngal then recycled its iron in endosomes by a pH-sensitive mechanism. As catechols derive from bacterial and mammalian metabolism of dietary compounds, the Scn-Ngal-catechol-Fe(III) complex represents an unforeseen microbial-host interaction, which mimics Scn-Ngal-siderophore interactions but instead traffics iron in aseptic tissues. These results identify an endogenous siderophore, which may link the disparate roles of Scn-Ngal in different diseases.


  • Organizational Affiliation
    • College of Physicians and Surgeons of Columbia University, New York, New York, USA.

Macromolecule Content 

  • Total Structure Weight: 63.23 kDa 
  • Atom Count: 4,327 
  • Modeled Residue Count: 510 
  • Deposited Residue Count: 534 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Neutrophil gelatinase-associated lipocalin
A, B, C
178Homo sapiensMutation(s): 1 
Gene Names: HNLLCN2NGAL
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P80188 (Homo sapiens)
Explore P80188 
Go to UniProtKB:  P80188
PHAROS:  P80188
GTEx:  ENSG00000148346 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80188
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on MCT



Download:Ideal Coordinates CCD File
E [auth A],
N [auth B],
Q [auth C]
4-METHYLCATECHOL
C7 H8 O2
ZBCATMYQYDCTIZ-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
J [auth A]
K [auth A]
L [auth A]
O [auth B]
V [auth C]
J [auth A],
K [auth A],
L [auth A],
O [auth B],
V [auth C],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
D [auth A],
M [auth B],
P [auth C]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
I [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
R [auth C]
S [auth C]
F [auth A],
G [auth A],
H [auth A],
R [auth C],
S [auth C],
T [auth C],
U [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.290 (Depositor), 0.289 (DCC) 
  • R-Value Work:  0.244 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 0.248 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.904α = 90
b = 114.904β = 90
c = 119.164γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-10-09
    Changes: Structure summary