4FXK

Human complement C4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 5JPN


Literature

Structural basis for activation of the complement system by component C4 cleavage.

Kidmose, R.T.Laursen, N.S.Dobo, J.Kjaer, T.R.Sirotkina, S.Yatime, L.Sottrup-Jensen, L.Thiel, S.Gal, P.Andersen, G.R.

(2012) Proc Natl Acad Sci U S A 109: 15425-15430

  • DOI: 10.1073/pnas.1208031109
  • Primary Citation of Related Structures:  
    4FXG, 4FXK

  • PubMed Abstract: 
  • An essential aspect of innate immunity is recognition of molecular patterns on the surface of pathogens or altered self through the lectin and classical pathways, two of the three well-established activation pathways of the complement system. This re ...

    An essential aspect of innate immunity is recognition of molecular patterns on the surface of pathogens or altered self through the lectin and classical pathways, two of the three well-established activation pathways of the complement system. This recognition causes activation of the MASP-2 or the C1s serine proteases followed by cleavage of the protein C4. Here we present the crystal structures of the 203-kDa human C4 and the 245-kDa C4·MASP-2 substrate·enzyme complex. When C4 binds to MASP-2, substantial conformational changes in C4 are induced, and its scissile bond region becomes ordered and inserted into the protease catalytic site in a manner canonical to serine proteases. In MASP-2, an exosite located within the CCP domains recognizes the C4 C345C domain 60 Å from the scissile bond. Mutations in C4 and MASP-2 residues at the C345C-CCP interface inhibit the intermolecular interaction and C4 cleavage. The possible assembly of the huge in vivo enzyme-substrate complex consisting of glycan-bound mannan-binding lectin, MASP-2, and C4 is discussed. Our own and prior functional data suggest that C1s in the classical pathway of complement activated by, e.g., antigen-antibody complexes, also recognizes the C4 C345C domain through a CCP exosite. Our results provide a unified structural framework for understanding the early and essential step of C4 cleavage in the elimination of pathogens and altered self through two major pathways of complement activation.


    Organizational Affiliation

    Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Complement C4 Beta chainA656Homo sapiensMutation(s): 0 
Gene Names: C4ACO4CPAMD2
Find proteins for P0C0L4 (Homo sapiens)
Explore P0C0L4 
Go to UniProtKB:  P0C0L4
NIH Common Fund Data Resources
PHAROS  P0C0L4
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Complement C4-A Alpha chainB767Homo sapiensMutation(s): 0 
Gene Names: C4ACO4CPAMD2
Find proteins for P0C0L4 (Homo sapiens)
Explore P0C0L4 
Go to UniProtKB:  P0C0L4
NIH Common Fund Data Resources
PHAROS  P0C0L4
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Complement C4 gamma chainC291Homo sapiensMutation(s): 0 
Gene Names: C4ACO4CPAMD2
Find proteins for P0C0L4 (Homo sapiens)
Explore P0C0L4 
Go to UniProtKB:  P0C0L4
NIH Common Fund Data Resources
PHAROS  P0C0L4
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, E
2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.45α = 90
b = 103.31β = 90
c = 256.03γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2012-09-19
    Changes: Database references
  • Version 1.2: 2012-10-03
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary