Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 54.99 kDa 
• Atom Count: 3,782 
• Modelled Residue Count: 454 
• Deposited Residue Count: 455 
• Unique protein chains: 2

 6RUS

Structure of a functional properdin monomer

• PDB DOI: 10.2210/pdb6RUS/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-05-29 Released: 2019-08-21 
• Deposition Author(s): Pedersen, D.V., Andersen, G.R.
• Funding Organization(s): Lundbeckfonden

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.274 
• R-Value Work: 0.238 
• R-Value Observed: 0.241 

Literature

Structural Basis for Properdin Oligomerization and Convertase Stimulation in the Human Complement System.

Pedersen, D.V., Gadeberg, T.A.F., Thomas, C., Wang, Y., Joram, N., Jensen, R.K., Mazarakis, S.M.M., Revel, M., El Sissy, C., Petersen, S.V., Lindorff-Larsen, K., Thiel, S., Laursen, N.S., Fremeaux-Bacchi, V., Andersen, G.R.

(2019) Front Immunol 10: 2007-2007

• PubMed: 31507604 
• DOI: 10.3389/fimmu.2019.02007
• Primary Citation of Related Structures:  
  6RU3, 6RU5, 6RUR, 6RUS, 6RUV, 6RV6, 6SEJ


• PubMed Abstract: 
  

Properdin (FP) is a positive regulator of the immune system stimulating the activity of the proteolytically active C3 convertase C3bBb in the alternative pathway of the complement system. Here we present two crystal structures of FP and two structures of convertase bound FP. A structural core formed by three thrombospondin repeats (TSRs) and a TB domain harbors the convertase binding site in FP that mainly interacts with C3b. Stabilization of the interaction between the C3b C-terminus and the MIDAS bound Mg ²⁺ in the Bb protease by FP TSR5 is proposed to underlie FP convertase stabilization. Intermolecular contacts between FP and the convertase subunits suggested by the structure were confirmed by binding experiments. FP is shown to inhibit C3b degradation by FI due to a direct competition for a common binding site on C3b. FP oligomers are held together by two sets of intermolecular contacts, where the first is formed by the TB domain from one FP molecule and TSR4 from another. The second and largest interface is formed by TSR1 and TSR6 from the same two FP molecules. Flexibility at four hinges between thrombospondin repeats is suggested to enable the oligomeric, polydisperse, and extended architecture of FP. Our structures rationalize the effects of mutations associated with FP deficiencies and provide a structural basis for the analysis of FP function in convertases and its possible role in pattern recognition.

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Related Citations: 

• Crystal structure of peptide-bound neprilysin reveals key binding interactions.
  Moss, S., Subramanian, V., Acharya, K.R.
  (2019) FEBS Lett --: --

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Organizational Affiliation: 

Department of Molecular Biology and Genetics, Center for Structural Biology, Aarhus University, Aarhus, Denmark.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Properdin	A	234	Homo sapiens	Mutation(s): 0  Gene Names: CFP, PFC
UniProt & NIH Common Fund Data Resources
Find proteins for P27918 (Homo sapiens) Explore P27918  Go to UniProtKB:  P27918
PHAROS:  P27918

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Properdin	B	221	Homo sapiens	Mutation(s): 0  Gene Names: CFP, PFC
UniProt & NIH Common Fund Data Resources
Find proteins for P27918 (Homo sapiens) Explore P27918  Go to UniProtKB:  P27918
PHAROS:  P27918

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose	C, D, E, F	2		O-Glycosylation
Glycosylation Resources
GlyTouCan:  G36855WW GlyCosmos:  G36855WW GlyGen:  G36855WW

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
SO4	P [auth A], Q [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.274 
• R-Value Work: 0.238 
• R-Value Observed: 0.241 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.97	α = 90
b = 47.11	β = 119.41
c = 122.93	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-08-21 
Deposition Author(s): Pedersen, D.V., Andersen, G.R.

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Funding Organization	Location	Grant Number
Lundbeckfonden	Denmark	R155-2015-2666

Revision History  

• Version 1.0: 2019-08-21
  Type: Initial release
  
• Version 1.1: 2019-09-25
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary