5O35

Structure of complement proteins complex

• PDB DOI:  https://doi.org/10.2210/pdb5O35/pdb

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


• Deposited: 2017-05-23 Released: 2017-06-28 
• Deposition Author(s): Xue, X., Wu, J., Forneris, F., Gros, P.
• Funding Organization(s): National Institutes of Health, NWO, European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free: 0.246 
• R-Value Work: 0.216 
• R-Value Observed: 0.217 

Literature

Regulator-dependent mechanisms of C3b processing by factor I allow differentiation of immune responses.

Xue, X., Wu, J., Ricklin, D., Forneris, F., Di Crescenzio, P., Schmidt, C.Q., Granneman, J., Sharp, T.H., Lambris, J.D., Gros, P.

(2017) Nat Struct Mol Biol 24: 643-651

• PubMed: 28671664 
• DOI: https://doi.org/10.1038/nsmb.3427
• Primary Citation of Related Structures:  
  5O32, 5O35


• PubMed Abstract: 
  

The complement system labels microbes and host debris for clearance. Degradation of surface-bound C3b is pivotal to direct immune responses and protect host cells. How the serine protease factor I (FI), assisted by regulators, cleaves either two or three distant peptide bonds in the CUB domain of C3b remains unclear. We present a crystal structure of C3b in complex with FI and regulator factor H (FH; domains 1-4 with 19-20). FI binds C3b-FH between FH domains 2 and 3 and a reoriented C3b C-terminal domain and docks onto the first scissile bond, while stabilizing its catalytic domain for proteolytic activity. One cleavage in C3b does not affect its overall structure, whereas two cleavages unfold CUB and dislodge the thioester-containing domain (TED), affecting binding of regulators and thereby determining the number of cleavages. These data explain how FI generates late-stage opsonins iC3b or C3dg in a context-dependent manner, to react to foreign, danger or healthy self signals.

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Organizational Affiliation: 

Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 218.69 kDa 
• Atom Count: 15,181 
• Modelled Residue Count: 1,921 
• Deposited Residue Count: 1,943 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C3	A	645	Homo sapiens	Mutation(s): 0  Gene Names: C3, CPAMD1
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens) Explore P01024  Go to UniProtKB:  P01024
PHAROS:  P01024

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C3	B	915	Homo sapiens	Mutation(s): 0  Gene Names: C3, CPAMD1
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens) Explore P01024  Go to UniProtKB:  P01024
PHAROS:  P01024

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement factor H,Complement factor H	C	383	Homo sapiens	Mutation(s): 0  Gene Names: CFH, HF, HF1, HF2
UniProt & NIH Common Fund Data Resources
Find proteins for P08603 (Homo sapiens) Explore P08603  Go to UniProtKB:  P08603
PHAROS:  P08603

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free: 0.246 
• R-Value Work: 0.216 
• R-Value Observed: 0.217 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.9	α = 90
b = 142.9	β = 90
c = 312.721	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-28 
Deposition Author(s): Xue, X., Wu, J., Forneris, F., Gros, P.

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Funding Organization	Location	Grant Number
National Institutes of Health	United States	R01AI030040-16
NWO	Netherlands	Spinoza 01.80.104.00
European Research Council	Netherlands	AdG 233229

Revision History  

• Version 1.0: 2017-06-28
  Type: Initial release
  
• Version 1.1: 2017-07-12
  Changes: Database references
• Version 1.2: 2017-08-16
  Changes: Database references
• Version 1.3: 2018-01-31
  Changes: Author supporting evidence
• Version 1.4: 2019-10-16
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary