7NOZ

Structure of the nanobody stablized properdin bound alternative pathway proconvertase C3b:FB:FP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 

Starting Model: experimental
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Literature

Structure determination of an unstable macromolecular complex enabled by nanobody-peptide bridging.

Lorentzen, J.Pedersen, D.V.Gadeberg, T.A.F.Andersen, G.R.

(2022) Protein Sci 31: e4432-e4432

  • DOI: https://doi.org/10.1002/pro.4432
  • Primary Citation of Related Structures:  
    7NOZ

  • PubMed Abstract: 

    Structure determination of macromolecular complexes is challenging if subunits can dissociate during crystallization or preparation of electron microscopy grids. We present an approach where a labile complex is stabilized by linking subunits though introduction of a peptide tag in one subunit that is recognized by a nanobody tethered to a second subunit. This allowed crystal structure determination at 3.9 Å resolution of the highly non-globular 320 kDa proconvertase formed by complement components C3b, factor B, and properdin. Whereas the binding mode of properdin to C3b is preserved, an internal rearrangement occurs in the zymogen factor B von Willebrand domain type A domain compared to the proconvertase not bound to properdin. The structure emphasizes the role of two noncanonical loops in thrombospondin repeats 5 and 6 of properdin in augmenting the activity of the C3 convertase. We suggest that linking of subunits through peptide specific tethered nanobodies represents a simple alternative to approaches like affinity maturation and chemical cross-linking for the stabilization of large macromolecular complexes. Besides applications for structural biology, nanobody bridging may become a new tool for biochemical analysis of unstable macromolecular complexes and in vitro selection of highly specific binders for such complexes.


  • Organizational Affiliation

    Department of Molecular Biology and Genetics, Section for Protein Science, Aarhus Universitet, Aarhus, Denmark.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C3 beta chain645Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens)
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Go to UniProtKB:  P01024
PHAROS:  P01024
GTEx:  ENSG00000125730 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01024
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01024-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C3 alpha chain912Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens)
Explore P01024 
Go to UniProtKB:  P01024
PHAROS:  P01024
GTEx:  ENSG00000125730 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01024
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01024-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Properdin163Homo sapiensMutation(s): 0 
Gene Names: CFPPFC
UniProt & NIH Common Fund Data Resources
Find proteins for P27918 (Homo sapiens)
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Go to UniProtKB:  P27918
PHAROS:  P27918
GTEx:  ENSG00000126759 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27918
Glycosylation
Glycosylation Sites: 5Go to GlyGen: P27918-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Properdin207Homo sapiensMutation(s): 0 
Gene Names: CFPPFC
UniProt & NIH Common Fund Data Resources
Find proteins for P27918 (Homo sapiens)
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Go to UniProtKB:  P27918
PHAROS:  P27918
GTEx:  ENSG00000126759 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27918
Glycosylation
Glycosylation Sites: 5Go to GlyGen: P27918-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Complement factor BE [auth F]731Homo sapiensMutation(s): 1 
Gene Names: CFBBFBFD
EC: 3.4.21.47
UniProt & NIH Common Fund Data Resources
Find proteins for P00751 (Homo sapiens)
Explore P00751 
Go to UniProtKB:  P00751
PHAROS:  P00751
GTEx:  ENSG00000243649 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00751
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P00751-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
hFPNb1 nanobodyF [auth R]124Lama glamaMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth E],
H [auth G],
M [auth L]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-3)-alpha-L-fucopyranoseI [auth H],
J [auth I],
K [auth J]
2O-Glycosylation
Glycosylation Resources
GlyTouCan:  G36855WW
GlyCosmos:  G36855WW
GlyGen:  G36855WW
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseL [auth K],
N [auth M]
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
U [auth F]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN
Query on MAN

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O [auth C]
P [auth C]
Q [auth C]
R [auth D]
S [auth D]
O [auth C],
P [auth C],
Q [auth C],
R [auth D],
S [auth D],
T [auth D]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
V [auth F]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.69α = 90
b = 179.46β = 90
c = 192.6γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LundbeckfondenDenmarkR155-2015-2666

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-27
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description