Movatterモバイル変換


[0]ホーム

URL:


RCSB PDB
233,605 Structures from the PDB
1,068,577 Computed Structure Models (CSM)
  • PDB-101
  • wwPDB
  • EMDataResource
  • NAKB: Nucleic Acid Knowledgebase
  • wwPDB Foundation
  • PDB-IHM Logo

 3FW4|pdb_00003fw4

Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric Catechol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.284 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.256 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.258 (Depositor) 

Starting Model:experimental
View more details

wwPDB Validation  3D Report Full Report


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

  • PubMed20581821 Search on PubMedSearch on PubMed Central
  • DOI: https://doi.org/10.1038/nchembio.402
  • Primary Citation of 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.

Biological Assembly 1  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (CAQ)


Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 


Find Similar Assemblies

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (CAQ)


Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 


Find Similar Assemblies

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (CAQ)


Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 


Find Similar Assemblies

Biological assembly 3 assigned by authors and generated by PISA (software)

PreviousNext

Macromolecule Content

  • Total Structure Weight: 63.49 kDa 
  • Atom Count: 4,056 
  • Modelled Residue Count: 489 
  • Deposited Residue Count: 534 
  • Unique protein chains: 1

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neutrophil gelatinase-associated lipocalin
A,B,C
178Homo sapiensMutation(s): 1 
Gene Names: HNLLCN2NGAL
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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CAQ
Query on CAQ

Download Ideal Coordinates CCD File 
E [auth A],
T [auth C]
CATECHOL
C6 H6 O2
YCIMNLLNPGFGHC-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
I [auth A],
J [auth A],
K [auth A],
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],
P [auth B],
S [auth C]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
GA [auth C]
H [auth A]
L [auth A]
M [auth A]
N [auth A]
GA [auth C],
H [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
Q [auth B],
R [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
U [auth C]
V [auth C]
W [auth C]
F [auth A],
G [auth A],
U [auth C],
V [auth C],
W [auth C],
X [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.284 (Depositor), 0.290 (DCC) 
  • R-Value Work: 0.256 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.258 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.421α = 90
b = 115.421β = 90
c = 118.801γ = 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: 2024-10-16
    Changes: Structure summary

RCSB PDB is hosted by


The Rutgers Artificial Intelligence and Data Science Collaboratory logo
Uiversity of California San Diego logoSan Diego Supercomputer Center logo
University of California San Francisco Logo

RCSB PDB is a member of the


wwPDB
EMDataResource

RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729.


[8]ページ先頭

©2009-2025 Movatter.jp