Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 64.49 kDa 
• Atom Count: 5132 
• Modelled Residue Count: 570 
• Deposited Residue Count: 576 
• Unique protein chains: 2

1GHQ

CR2-C3D COMPLEX STRUCTURE

• DOI: 10.2210/pdb1GHQ/pdb

• Classification: Immune system/viral protein receptor
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 2001-01-11 Released: 2001-06-13 
• Deposition Author(s): Szakonyi, G., Guthridge, J.M., Li, D., Holers, V.M., Chen, X.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.239 
• R-Value Work: 0.195 

Literature

Structure of complement receptor 2 in complex with its C3d ligand.

Szakonyi, G., Guthridge, J.M., Li, D., Young, K., Holers, V.M., Chen, X.S.

(2001) Science 292: 1725-1728

• PubMed: 11387479 
• DOI: 10.1126/science.1059118
• Primary Citation of Related Structures:  
  1GHQ


• PubMed Abstract: 
  

Complement receptor 2 (CR2/CD21) is an important receptor that amplifies B lymphocyte activation by bridging the innate and adaptive immune systems. CR2 ligands include complement C3d and Epstein-Barr virus glycoprotein 350/220. We describe the x-ray structure of this CR2 domain in complex with C3d at 2.0 angstroms. The structure reveals extensive main chain interactions between C3d and only one short consensus repeat (SCR) of CR2 and substantial SCR side-side packing. These results provide a detailed understanding of receptor-ligand interactions in this protein family and reveal potential target sites for molecular drug design.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Genetics, University of Colorado Health Science Center, School of Medicine, Denver, CO 80262, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEMENT C3	A	308	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CR2/CD121/C3D/EPSTEIN-BARR VIRUS RECEPTOR	B, C	134	Homo sapiens	Mutation(s): 0  Gene Names: CR2, C3DR
Find proteins for P20023 (Homo sapiens) Explore P20023  Go to UniProtKB:  P20023
NIH Common Fund Data Resources
PHAROS:  P20023 GTEx:  ENSG00000117322

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDG	E [auth B], G [auth C]	2-acetamido-2-deoxy-alpha-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
ZN	D [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.239 
• R-Value Work: 0.195 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170	α = 90
b = 170	β = 90
c = 174	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-01-11 
• Released Date: 2001-06-13 
Deposition Author(s): Szakonyi, G., Guthridge, J.M., Li, D., Holers, V.M., Chen, X.S.

Revision History  

• Version 1.0: 2001-06-13
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary