5HCE

Ternary complex of human Complement C5 with Ornithodoros moubata OmCI and Rhipicephalus appendiculatus RaCI1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.268 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for therapeutic inhibition of complement C5.

Jore, M.M.Johnson, S.Sheppard, D.Barber, N.M.Li, Y.I.Nunn, M.A.Elmlund, H.Lea, S.M.

(2016) Nat Struct Mol Biol 23: 378-386

  • DOI: 10.1038/nsmb.3196
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Activation of complement C5 generates the potent anaphylatoxin C5a and leads to pathogen lysis, inflammation and cell damage. The therapeutic potential of C5 inhibition has been demonstrated by eculizumab, one of the world's most expensive drugs. How ...

    Activation of complement C5 generates the potent anaphylatoxin C5a and leads to pathogen lysis, inflammation and cell damage. The therapeutic potential of C5 inhibition has been demonstrated by eculizumab, one of the world's most expensive drugs. However, the mechanism of C5 activation by C5 convertases remains elusive, thus limiting development of therapeutics. Here we identify and characterize a new protein family of tick-derived C5 inhibitors. Structures of C5 in complex with the new inhibitors, the phase I and phase II inhibitor OmCI, or an eculizumab Fab reveal three distinct binding sites on C5 that all prevent activation of C5. The positions of the inhibitor-binding sites and the ability of all three C5-inhibitor complexes to competitively inhibit the C5 convertase conflict with earlier steric-inhibition models, thus suggesting that a priming event is needed for activation.


    Organizational Affiliation

    Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Complement C5
B
656Homo sapiensMutation(s): 0 
Gene Names: C5CPAMD4
Find proteins for P01031 (Homo sapiens)
Go to UniProtKB:  P01031
NIH Common Fund Data Resources
PHAROS  P01031

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Complement C5
A
998Homo sapiensMutation(s): 0 
Gene Names: C5CPAMD4
Find proteins for P01031 (Homo sapiens)
Go to UniProtKB:  P01031
NIH Common Fund Data Resources
PHAROS  P01031

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Complement inhibitor
C
165Ornithodoros moubataMutation(s): 2 
Gene Names: CI
Find proteins for Q5YD59 (Ornithodoros moubata)
Go to UniProtKB:  Q5YD59

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Rhipicephalus appendiculatus RaCI1
D
81Rhipicephalus appendiculatusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CYS
Query on CYS

Download CCD File 
A
CYSTEINE
C3 H7 N O2 S
XUJNEKJLAYXESH-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.268 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.26α = 90
b = 140.725β = 90
c = 210.367γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom100298
Netherlands Organisation for Scientific ResearchNetherlands825.11.030

Revision History 

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2016-04-06
    Changes: Database references
  • Version 1.2: 2018-01-17
    Changes: Experimental preparation