2OK5 | pdb_00002ok5

Human Complement factor B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.241 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.190 (DCC) 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2OK5

Ligand Structure Quality Assessment 


This is version 2.3 of the entry. See complete history

Literature

Factor B structure provides insights into activation of the central protease of the complement system.

Milder, F.J.Gomes, L.Schouten, A.Janssen, B.J.Huizinga, E.G.Romijn, R.A.Hemrika, W.Roos, A.Daha, M.R.Gros, P.

(2007) Nat Struct Mol Biol 14: 224-228

  • DOI: https://doi.org/10.1038/nsmb1210
  • Primary Citation Related Structures: 
    2OK5

  • PubMed Abstract: 

    Factor B is the central protease of the complement system of immune defense. Here, we present the crystal structure of human factor B at 2.3-A resolution, which reveals how the five-domain proenzyme is kept securely inactive. The canonical activation helix of the Von Willebrand factor A (VWA) domain is displaced by a helix from the preceding domain linker. The two helices conformationally link the scissile-activation peptide and the metal ion-dependent adhesion site required for binding of the ligand C3b. The data suggest that C3b binding displaces the three N-terminal control domains and reshuffles the two central helices. Reshuffling of the helices releases the scissile bond for final proteolytic activation and generates a new interface between the VWA domain and the serine protease domain. This allosteric mechanism is crucial for tight regulation of the complement-amplification step in the immune response.


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

Macromolecule Content 

  • Total Structure Weight: 87.74 kDa 
  • Atom Count: 6,118 
  • Modeled Residue Count: 710 
  • Deposited Residue Count: 752 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Complement factor B752Homo sapiensMutation(s): 0 
Gene Names: CFBBF
EC: 3.4.21.47
UniProt & NIH Common Fund Data Resources
Find proteins for P00751 (Homo sapiens)
Explore P00751 
Go to UniProtKB:  P00751
PHAROS:  P00751
GTEx:  ENSG00000243649 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00751
Glycosylation
Glycosylation Sites: 4Go to GlyGen: P00751-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
7N-Glycosylation
Glycosylation Resources
GlyTouCan: G55220VL
GlyCosmos: G55220VL
GlyGen: G55220VL
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.241 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.190 (DCC) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.031α = 90
b = 104.031β = 90
c = 151.116γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DNAdata collection
MOSFLMdata reduction
CCP4data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2021-03-31
    Changes: Source and taxonomy, Structure summary
  • Version 2.2: 2023-08-30
    Changes: Data collection, Database references, Refinement description
  • Version 2.3: 2024-11-20
    Changes: Structure summary