Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 4 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 566.82 kDa 
• Atom Count: 39285 
• Residue Count: 4963 
• Unique protein chains: 4

2XWB

Crystal Structure of Complement C3b in complex with Factors B and D

• DOI: 10.2210/pdb2XWB/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: 3.49 Å
• R-Value Free: 0.244 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 

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: 10.1126/science.1195821
• Primary Citation of Related Structures:  
  2XW9, 2XWJ, 2XWA, 2XWB


• 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.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEMENT C3B BETA CHAIN	A, C	642	Homo sapiens	Mutation(s): 0  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
COMPLEMENT C3B ALPHA' CHAIN	B, D	912	Homo sapiens	Mutation(s): 0  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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEMENT FACTOR B	F, H	732	Homo sapiens	Mutation(s): 2  Gene Names: CFB, BF, BFD EC: 3.4.21.47
Find proteins for P00751 (Homo sapiens) Explore P00751  Go to UniProtKB:  P00751
NIH Common Fund Data Resources
PHAROS:  P00751 GTEx:  ENSG00000243649

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEMENT FACTOR D	I, J	228	Homo sapiens	Mutation(s): 1  Gene Names: CFD, DF, PFD EC: 3.4.21.46
Find proteins for P00746 (Homo sapiens) Explore P00746  Go to UniProtKB:  P00746
NIH Common Fund Data Resources
PHAROS:  P00746 GTEx:  ENSG00000197766

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G, K	2		N-Glycosylation

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L, M	3		N-Glycosylation

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D, F, H	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	I, J	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	A, C, F, H	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.49 Å
• R-Value Free: 0.244 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.275	α = 95.47
b = 135.775	β = 110.69
c = 149.975	γ = 113.39

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-11-01 
• 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, Other, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary