1J1L | pdb_00001j1l

Crystal structure of human Pirin: a Bcl-3 and Nuclear factor I interacting protein and a cupin superfamily member


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.249 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.223 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1J1L

This is version 1.4 of the entry. See complete history

Literature

Crystal structure of human pirin: an iron-binding nuclear protein and transcription cofactor

Pang, H.Bartlam, M.Zeng, Q.Miyatake, H.Hisano, T.Miki, K.Wong, L.L.Gao, G.F.Rao, Z.

(2004) J Biological Chem 279: 1491-1498

  • DOI: https://doi.org/10.1074/jbc.M310022200
  • Primary Citation Related Structures: 
    1J1L

  • PubMed Abstract: 

    Pirin is a newly identified nuclear protein that interacts with the oncoprotein B-cell lymphoma 3-encoded (Bcl-3) and nuclear factor I (NFI). The crystal structure of human Pirin at 2.1-A resolution shows it to be a member of the functionally diverse cupin superfamily. The structure comprises two beta-barrel domains, with an Fe(II) cofactor bound within the cavity of the N-terminal domain. These findings suggest an enzymatic role for Pirin, most likely in biological redox reactions involving oxygen, and provide compelling evidence that Pirin requires the participation of the metal ion for its interaction with Bcl-3 to co-regulate the NF-kappaB transcription pathway and the interaction with NFI in DNA replication. Substitution of iron by heavy metals thus provides a novel pathway for these metals to directly influence gene transcription. The structure suggests an interesting new role of iron in biology and that Pirin may be involved in novel mechanisms of gene regulation.


  • Organizational Affiliation
    • Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China.

Macromolecule Content 

  • Total Structure Weight: 32.5 kDa 
  • Atom Count: 2,430 
  • Modeled Residue Count: 288 
  • Deposited Residue Count: 290 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pirin290Homo sapiensMutation(s): 6 
EC: 1.13.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for O00625 (Homo sapiens)
Explore O00625 
Go to UniProtKB:  O00625
PHAROS:  O00625
GTEx:  ENSG00000087842 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00625
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE2

Query on FE2



Download:Ideal Coordinates CCD File
B [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.249 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.223 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.278α = 90
b = 67.116β = 90
c = 106.389γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-11-13
    Changes: Structure summary