4I6O | pdb_00004i6o

Crystal structure of chemically synthesized human anaphylatoxin C3a

• PDB DOI: https://doi.org/10.2210/pdb4I6O/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2012-11-29 Released: 2013-02-27 
• Deposition Author(s): Wang, C.I.A., Ghassemian, A., Collins, B., Lewis, R.J., Alewood, P.F., Durek, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.268 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Literature

Efficient chemical synthesis of human complement protein C3a.

Ghassemian, A., Wang, C.I., Yau, M.K., Reid, R.C., Lewis, R.J., Fairlie, D.P., Alewood, P.F., Durek, T.

(2013) Chem Commun (Camb) 49: 2356-2358

• PubMed: 23407800 
• DOI: https://doi.org/10.1039/c3cc40537k
• Primary Citation Related Structures: 
  4I6O


• PubMed Abstract: 
  

  We report the total chemical synthesis of human C3a by one-pot native chemical ligation of three unprotected peptide segments, followed by efficient in vitro folding that yielded the anaphylatoxin C3a in high yield and excellent purity. Synthetic C3a was fully active and its crystal structure at 2.1 Å resolution showed 3 helices and a C-terminal turn motif.

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Organizational Affiliation: 
• Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 9.23 kDa 
• Atom Count: 584 
• Modeled Residue Count: 68 
• Deposited Residue Count: 77 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C3	A	77	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens) Explore P01024  Go to UniProtKB:  P01024
PHAROS:  P01024 GTEx:  ENSG00000125730

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	B [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free:  0.268 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.285	α = 90
b = 68.285	β = 90
c = 39.266	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-27 
Deposition Author(s): Wang, C.I.A., Ghassemian, A., Collins, B., Lewis, R.J., Alewood, P.F., Durek, T.

Revision History  

• Version 1.0: 2013-02-27
  Type: Initial release
  
• Version 1.1: 2013-03-06
  Changes: Database references
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary