Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 190.54 kDa 
• Atom Count: 13184 
• Residue Count: 1665 
• Unique protein chains: 3

6EHG

complement component C3b in complex with a nanobody

• DOI: 10.2210/pdb6EHG/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Lama glama
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-09-13 Released: 2018-02-14 
• Deposition Author(s): Jensen, R.K., Andersen, K.R., Gadeberg, T.A.F., Laursen, N.S., Andersen, G.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å

Literature

A potent complement factor C3-specific nanobody inhibiting multiple functions in the alternative pathway of human and murine complement.

Jensen, R.K., Pihl, R., Gadeberg, T.A.F., Jensen, J.K., Andersen, K.R., Thiel, S., Laursen, N.S., Andersen, G.R.

(2018) J Biol Chem 293: 6269-6281

• PubMed: 29497000 
• DOI: 10.1074/jbc.RA117.001179
• Primary Citation of Related Structures:  
  6EHG


• PubMed Abstract: 
  

The complement system is a complex, carefully regulated proteolytic cascade for which suppression of aberrant activation is of increasing clinical relevance, and inhibition of the complement alternative pathway is a subject of intense research. Here, we describe the nanobody hC3Nb1 that binds to multiple functional states of C3 with subnanomolar affinity. The nanobody causes a complete shutdown of alternative pathway activity in human and murine serum when present in concentrations comparable with that of C3, and hC3Nb1 is shown to prevent proconvertase assembly, as well as binding of the C3 substrate to C3 convertases. Our crystal structure of the C3b-hC3Nb1 complex and functional experiments demonstrate that proconvertase formation is blocked by steric hindrance between the nanobody and an Asn-linked glycan on complement factor B. In addition, hC3Nb1 is shown to prevent factor H binding to C3b, rationalizing its inhibition of factor I activity. Our results identify hC3Nb1 as a versatile, inexpensive, and powerful inhibitor of the alternative pathway in both human and murine in vitro model systems of complement activation.

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Organizational Affiliation: 

From the Departments of Molecular Biology and Genetics and [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C3	A	643	Homo sapiens	Mutation(s): 0  Gene Names: C3, CPAMD1
Find proteins for P01024 (Homo sapiens) Explore P01024  Go to UniProtKB:  P01024
NIH Common Fund Data Resources
PHAROS:  P01024 GTEx:  ENSG00000125730

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C3	B	915	Homo sapiens	Mutation(s): 0  Gene Names: C3, CPAMD1
Find proteins for P01024 (Homo sapiens) Explore P01024  Go to UniProtKB:  P01024
NIH Common Fund Data Resources
PHAROS:  P01024 GTEx:  ENSG00000125730

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
hC3Nb1	C	130	Lama glama	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 255.31	α = 90
b = 64.88	β = 90
c = 144.72	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-09-13 
• Released Date: 2018-02-14 
Deposition Author(s): Jensen, R.K., Andersen, K.R., Gadeberg, T.A.F., Laursen, N.S., Andersen, G.R.

Revision History 

• Version 1.0: 2018-02-14
  Type: Initial release
  
• Version 1.1: 2018-03-14
  Changes: Database references
• Version 1.2: 2018-05-09
  Changes: Data collection, Database references
• Version 1.3: 2019-10-16
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary