4HWJ | pdb_00004hwj

Crystal Structure of the Human C3a desArg anaphylatoxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.270 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4HWJ

This is version 1.3 of the entry. See complete history

Literature

Human C3a and C3a desArg anaphylatoxins have conserved structures, in contrast to C5a and C5a desArg.

Bajic, G.Yatime, L.Klos, A.Andersen, G.R.

(2013) Protein Sci 22: 204-212

  • DOI: https://doi.org/10.1002/pro.2200
  • Primary Citation Related Structures: 
    4HW5, 4HWJ

  • PubMed Abstract: 

    Complement is a part of innate immunity that has a critical role in the protection against microbial infections, bridges the innate with the adaptive immunity and initiates inflammation. Activation of the complement, by specific recognition of molecular patterns presented by an activator, for example, a pathogen cell, in the classical and lectin pathways or spontaneously in the alternative pathway, leads to the opsonization of the activator and the production of pro-inflammatory molecules such as the C3a anaphylatoxin. The biological function of this anaphylatoxin is regulated by carboxypeptidase B, a plasma protease that cleaves off the C-terminal arginine yielding C3a desArg, an inactive form. While functional assays demonstrate strikingly different physiological effects between C3a and C3a desArg, no structural information is available on the possible conformational differences between the two proteins. Here, we report a novel and simple expression and purification protocol for recombinant human C3a and C3a desArg anaphylatoxins, as well as their crystal structures at 2.3 and 2.6 Å, respectively. Structural analysis revealed no significant conformational differences between the two anaphylatoxins in contrast to what has been reported for C5a and C5a desArg. We compare the structures of different anaphylatoxins and discuss the relevance of their observed conformations to complement activation and binding of the anaphylatoxins to their cognate receptors.


  • Organizational Affiliation
    • Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus, Denmark.

Macromolecule Content 

  • Total Structure Weight: 9.44 kDa 
  • Atom Count: 641 
  • Modeled Residue Count: 75 
  • Deposited Residue Count: 82 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Complement C382Homo sapiensMutation(s): 0 
Gene Names: C3CPAMD1
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens)
Explore P01024 
Go to UniProtKB:  P01024
PHAROS:  P01024
GTEx:  ENSG00000125730 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01024
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.270 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.75α = 90
b = 63.75β = 90
c = 106.43γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-12
    Type: Initial release
  • Version 1.1: 2013-02-13
    Changes: Database references
  • Version 1.2: 2018-03-07
    Changes: Data collection
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary