4A5W

Crystal structure of C5b6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.256 

Starting Models: experimental
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This is version 2.0 of the entry. See complete history


Literature

Assembly and Regulation of the Membrane Attack Complex Based on Structures of C5B6 and Sc5B9.

Hadders, M.A.Bubeck, D.Roversi, P.Hakobyan, S.Forneris, F.Morgan, B.P.Pangburn, M.K.Llorca, O.Lea, S.M.Gros, P.

(2012) Cell Rep 1: 200

  • DOI: https://doi.org/10.1016/j.celrep.2012.02.003
  • Primary Citation of Related Structures:  
    4A5W

  • PubMed Abstract: 

    Activation of the complement system results in formation of membrane attack complexes (MACs), pores that disrupt lipid bilayers and lyse bacteria and other pathogens. Here, we present the crystal structure of the first assembly intermediate, C5b6, together with a cryo-electron microscopy reconstruction of a soluble, regulated form of the pore, sC5b9. Cleavage of C5 to C5b results in marked conformational changes, distinct from those observed in the homologous C3-to-C3b transition. C6 captures this conformation, which is preserved in the larger sC5b9 assembly. Together with antibody labeling, these structures reveal that complement components associate through sideways alignment of the central MAC-perforin (MACPF) domains, resulting in a C5b6-C7-C8β-C8α-C9 arc. Soluble regulatory proteins below the arc indicate a potential dual mechanism in protection from pore formation. These results provide a structural framework for understanding MAC pore formation and regulation, processes important for fighting infections and preventing complement-mediated tissue damage.


  • Organizational Affiliation

    Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
COMPLEMENT C51,580Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01031 (Homo sapiens)
Explore P01031 
Go to UniProtKB:  P01031
GTEx:  ENSG00000106804 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01031
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P01031-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
COMPLEMENT COMPONENT C6913Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P13671 (Homo sapiens)
Explore P13671 
Go to UniProtKB:  P13671
GTEx:  ENSG00000039537 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13671
Glycosylation
Glycosylation Sites: 6Go to GlyGen: P13671-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B],
K [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN
Query on MAN

Download Ideal Coordinates CCD File 
H [auth B],
I [auth B],
J [auth B]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
FUC
Query on FUC

Download Ideal Coordinates CCD File 
F [auth B]alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.256 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.217α = 90
b = 230.747β = 90
c = 269.983γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2012-05-09
    Changes: Other
  • Version 1.2: 2012-10-31
    Changes: Database references
  • Version 1.3: 2019-11-13
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.0: 2024-07-24
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary