7AD7

Crystal structure of human complement C5 in complex with the K8 bovine knob domain peptide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The allosteric modulation of Complement C5 by knob domain peptides.

Macpherson, A.Laabei, M.Ahdash, Z.Graewert, M.A.Birtley, J.R.Schulze, M.E.Crennell, S.Robinson, S.A.Holmes, B.Oleinikovas, V.Nilsson, P.H.Snowden, J.Ellis, V.Mollnes, T.E.Deane, C.M.Svergun, D.Lawson, A.D.van den Elsen, J.M.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.63586
  • Primary Citation of Related Structures:  
    7AD6, 7AD7

  • PubMed Abstract: 

    Bovines have evolved a subset of antibodies with ultra-long heavy chain complementarity determining regions that harbour cysteine-rich knob domains. To produce high-affinity peptides, we previously isolated autonomous 3-6 kDa knob domains from bovine antibodies. Here, we show that binding of four knob domain peptides elicits a range of effects on the clinically validated drug target complement C5. Allosteric mechanisms predominated, with one peptide selectively inhibiting C5 cleavage by the alternative pathway C5 convertase, revealing a targetable mechanistic difference between the classical and alternative pathway C5 convertases. Taking a hybrid biophysical approach, we present C5-knob domain co-crystal structures and, by solution methods, observed allosteric effects propagating >50 Å from the binding sites. This study expands the therapeutic scope of C5, presents new inhibitors, and introduces knob domains as new, low molecular weight antibody fragments, with therapeutic potential.


  • Organizational Affiliation

    UCB, Slough, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C5A [auth B],
B [auth A]
1,676Homo sapiensMutation(s): 0 
Gene Names: C5CPAMD4
UniProt & NIH Common Fund Data Resources
Find proteins for P01031 (Homo sapiens)
Explore P01031 
Go to UniProtKB:  P01031
PHAROS:  P01031
GTEx:  ENSG00000106804 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01031
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
K8 peptide52Bos taurusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MHA (Subject of Investigation/LOI)
Query on MHA

Download Ideal Coordinates CCD File 
G [auth B](CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID
C6 H10 N2 O5
QZTKDVCDBIDYMD-UHFFFAOYSA-N
TAM (Subject of Investigation/LOI)
Query on TAM

Download Ideal Coordinates CCD File 
M [auth C]TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
CYS (Subject of Investigation/LOI)
Query on CYS

Download Ideal Coordinates CCD File 
K [auth A]CYSTEINE
C3 H7 N O2 S
XUJNEKJLAYXESH-REOHCLBHSA-N
MPD (Subject of Investigation/LOI)
Query on MPD

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
EOH (Subject of Investigation/LOI)
Query on EOH

Download Ideal Coordinates CCD File 
E [auth B],
F [auth B],
H [auth A],
L [auth C]
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.559α = 90
b = 161.695β = 90
c = 187.38γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
BALBESphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-10
    Type: Initial release
  • Version 1.1: 2021-07-07
    Changes: Structure summary
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description