4ENZ | pdb_00004enz

Structure of human ceruloplasmin at 2.6 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.234 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Ceruloplasmin: macromolecular assemblies with iron-containing acute phase proteins.

Samygina, V.R.Sokolov, A.V.Bourenkov, G.Petoukhov, M.V.Pulina, M.O.Zakharova, E.T.Vasilyev, V.B.Bartunik, H.Svergun, D.I.

(2013) PLoS One 8: e67145-e67145

  • DOI: https://doi.org/10.1371/journal.pone.0067145
  • Primary Citation Related Structures: 
    4EJX, 4ENZ

  • PubMed Abstract: 

    Copper-containing ferroxidase ceruloplasmin (Cp) forms binary and ternary complexes with cationic proteins lactoferrin (Lf) and myeloperoxidase (Mpo) during inflammation. We present an X-ray crystal structure of a 2Cp-Mpo complex at 4.7 Å resolution. This structure allows one to identify major protein-protein interaction areas and provides an explanation for a competitive inhibition of Mpo by Cp and for the activation of p-phenylenediamine oxidation by Mpo. Small angle X-ray scattering was employed to construct low-resolution models of the Cp-Lf complex and, for the first time, of the ternary 2Cp-2Lf-Mpo complex in solution. The SAXS-based model of Cp-Lf supports the predicted 1:1 stoichiometry of the complex and demonstrates that both lobes of Lf contact domains 1 and 6 of Cp. The 2Cp-2Lf-Mpo SAXS model reveals the absence of interaction between Mpo and Lf in the ternary complex, so Cp can serve as a mediator of protein interactions in complex architecture. Mpo protects antioxidant properties of Cp by isolating its sensitive loop from proteases. The latter is important for incorporation of Fe(3+) into Lf, which activates ferroxidase activity of Cp and precludes oxidation of Cp substrates. Our models provide the structural basis for possible regulatory role of these complexes in preventing iron-induced oxidative damage.


  • Organizational Affiliation
    • Institute of Crystallography RAS, Moscow, Russia. vsamygina@cicbiogune.es

Macromolecule Content 

  • Total Structure Weight: 123.38 kDa 
  • Atom Count: 8,468 
  • Modeled Residue Count: 1,029 
  • Deposited Residue Count: 1,065 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ceruloplasmin1,065Homo sapiensMutation(s): 0 
EC: 1.16.3.1 (PDB Primary Data), 1.16.3.4 (UniProt), 1.11.1.27 (UniProt), 1.11.1.9 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00450 (Homo sapiens)
Explore P00450 
Go to UniProtKB:  P00450
PHAROS:  P00450
GTEx:  ENSG00000047457 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00450
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P00450-1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
B [auth A],
L [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
N [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU

Query on CU



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
K [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
OXY

Query on OXY



Download:Ideal Coordinates CCD File
J [auth A]OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
M [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
O

Query on O



Download:Ideal Coordinates CCD File
I [auth A]OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.234 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.775α = 90
b = 210.775β = 90
c = 84.502γ = 120
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 1.2: 2013-09-11
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-11-27
    Changes: Structure summary