2XWA | pdb_00002xwa

Crystal Structure of Complement Factor D Mutant R202A

• PDB DOI: https://doi.org/10.2210/pdb2XWA/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2010-11-01 Released: 2011-01-12 
• Deposition Author(s): Forneris, F., Ricklin, D., Wu, J., Tzekou, A., Wallace, R.S., Lambris, J.D., Gros, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.283 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

Structures of C3B in Complex with Factors B and D Give Insight Into Complement Convertase Formation.

Forneris, F., Ricklin, D., Wu, J., Tzekou, A., Wallace, R.S., Lambris, J.D., Gros, P.

(2010) Science 330: 1816

• PubMed: 21205667 
• DOI: https://doi.org/10.1126/science.1195821
• Primary Citation Related Structures: 
  2XW9, 2XWA, 2XWB, 2XWJ


• PubMed Abstract: 
  

  Activation of the complement cascade induces inflammatory responses and marks cells for immune clearance. In the central complement-amplification step, a complex consisting of surface-bound C3b and factor B is cleaved by factor D to generate active convertases on targeted surfaces. We present crystal structures of the pro-convertase C3bB at 4 angstrom resolution and its complex with factor D at 3.5 angstrom resolution. Our data show how factor B binding to C3b forms an open "activation" state of C3bB. Factor D specifically binds the open conformation of factor B through a site distant from the catalytic center and is activated by the substrate, which displaces factor D's self-inhibitory loop. This concerted proteolytic mechanism, which is cofactor-dependent and substrate-induced, restricts complement amplification to C3b-tagged target cells.

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Organizational Affiliation: 
• Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.89 kDa 
• Atom Count: 3,496 
• Modeled Residue Count: 456 
• Deposited Residue Count: 456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEMENT FACTOR D	A, B	228	Homo sapiens	Mutation(s): 1  EC: 3.4.21.46
UniProt & NIH Common Fund Data Resources
Find proteins for P00746 (Homo sapiens) Explore P00746  Go to UniProtKB:  P00746
PHAROS:  P00746 GTEx:  ENSG00000197766

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.283 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.222	α = 90
b = 67.491	β = 90
c = 133.588	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-12 
Deposition Author(s): Forneris, F., Ricklin, D., Wu, J., Tzekou, A., Wallace, R.S., Lambris, J.D., Gros, P.

Revision History  

• Version 1.0: 2011-01-12
  Type: Initial release
  
• Version 1.1: 2012-04-11
  Changes: Database references, Non-polymer description, Version format compliance
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary