Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33359.20 
• Atom Count: 2347 
• 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): 1 


• 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: 1.8 Å
• R-Value Free: 0.230 
• R-Value Work: 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 


• 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
C3D	A	294	Homo sapiens	Mutation(s): 1  Gene Names: C3 (CPAMD1)
Find proteins for P01024 (Homo sapiens) Go to Gene View: C3 Go to UniProtKB:  P01024

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.230 
• R-Value Work: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 60.820	α = 90.00
b = 64.378	β = 90.00
c = 87.160	γ = 90.00

Software Package:

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

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance
• Version 1.3: 2018-03-14
  Type: Database references