5O32

The structure of complement complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.21 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • DOI: 10.1038/nsmb.3427
  • Structures With Same Primary Citation

  • 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 t ...

    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.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Complement C3
A, E
645Homo sapiensMutation(s): 0 
Gene Names: C3CPAMD1
Find proteins for P01024 (Homo sapiens)
Go to UniProtKB:  P01024
NIH Common Fund Data Resources
PHAROS  P01024

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Complement factor H,Complement factor H
C, G
383Homo sapiensMutation(s): 0 
Gene Names: CFHHFHF1HF2
Find proteins for P08603 (Homo sapiens)
Go to UniProtKB:  P08603
NIH Common Fund Data Resources
PHAROS  P08603

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Complement factor I
D, H
321Homo sapiensMutation(s): 0 
Gene Names: CFIIF
EC: 3.4.21.45
Find proteins for P05156 (Homo sapiens)
Go to UniProtKB:  P05156
NIH Common Fund Data Resources
PHAROS  P05156

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Complement factor I
I, J
244Homo sapiensMutation(s): 0 
Gene Names: CFIIF
EC: 3.4.21.45
Find proteins for P05156 (Homo sapiens)
Go to UniProtKB:  P05156
NIH Common Fund Data Resources
PHAROS  P05156

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Complement C3
B, F
915Homo sapiensMutation(s): 0 
Gene Names: C3CPAMD1
Find proteins for P01024 (Homo sapiens)
Go to UniProtKB:  P01024
NIH Common Fund Data Resources
PHAROS  P01024
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B, D, E, F, H, I, J
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

Download CCD File 
A, E
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MLI
Query on MLI

Download CCD File 
J
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, D, E, H
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.21 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.37α = 69.764
b = 122.79β = 76.101
c = 157.2γ = 70.13
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
ERC Advanced grantNetherlands233229
NWO SpinozaNetherlands01.80.104.00
NIH R01United StatesAI030040-16

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: 2019-10-16
    Changes: Data collection