Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.36 kDa 
• Atom Count: 2449 
• Residue Count: 294 
• Unique protein chains: 1

1C3D

X-RAY CRYSTAL STRUCTURE OF C3D: A C3 FRAGMENT AND LIGAND FOR COMPLEMENT RECEPTOR 2

• DOI: 10.2210/pdb1C3D/pdb

• Classification: COMPLEMENT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 1998-05-19 Released: 1998-10-07 
• Deposition Author(s): Nagar, B., Jones, R.G., Diefenbach, R.J., Isenman, D.E., Rini, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.230 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 

Literature

X-ray crystal structure of C3d: a C3 fragment and ligand for complement receptor 2.

Nagar, B., Jones, R.G., Diefenbach, R.J., Isenman, D.E., Rini, J.M.

(1998) Science 280: 1277-1281

• PubMed: 9596584 
• DOI: 10.1126/science.280.5367.1277
• Primary Citation of Related Structures:  
  1C3D


• PubMed Abstract: 
  

Activation and covalent attachment of complement component C3 to pathogens is the key step in complement-mediated host defense. Additionally, the antigen-bound C3d fragment interacts with complement receptor 2 (CR2; also known as CD21) on B cells and thereby contributes to the initiation of an acquired humoral response. The x-ray crystal structure of human C3d solved at 2.0 angstroms resolution reveals an alpha-alpha barrel with the residues responsible for thioester formation and covalent attachment at one end and an acidic pocket at the other. The structure supports a model whereby the transition of native C3 to its functionally active state involves the disruption of a complementary domain interface and provides insight into the basis for the interaction between C3d and CR2.

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Organizational Affiliation: 

Department of Biochemistry and Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C3D	A	294	Homo sapiens	Mutation(s): 1  Gene Names: C3, CPAMD1
Find proteins for P01024 (Homo sapiens) Explore P01024  Go to UniProtKB:  P01024
NIH Common Fund Data Resources
PHAROS:  P01024 GTEx:  ENSG00000125730

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.230 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.82	α = 90
b = 64.378	β = 90
c = 87.16	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASES	phasing
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-05-19 
• Released Date: 1998-10-07 
Deposition Author(s): Nagar, B., Jones, R.G., Diefenbach, R.J., Isenman, D.E., Rini, J.M.

Revision History 

• Version 1.0: 1998-10-07
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2018-03-14
  Changes: Database references