6GFE | pdb_00006gfe

High-resolution Structure of a therapeutic full-length anti-NPRA Antibody with exceptional Conformational Diversity

• PDB DOI: https://doi.org/10.2210/pdb6GFE/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2018-04-30 Released: 2019-05-15 
• Deposition Author(s): Hoerer, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Structure of a Therapeutic Full-Length Anti-NPRA IgG4 Antibody: Dissecting Conformational Diversity.

Blech, M., Horer, S., Kuhn, A.B., Kube, S., Goddeke, H., Kiefer, H., Zang, Y., Alber, Y., Kast, S.M., Westermann, M., Tully, M.D., Schafer, L.V., Garidel, P.

(2019) Biophys J 116: 1637-1649

• PubMed: 31023536 
• DOI: https://doi.org/10.1016/j.bpj.2019.03.036
• Primary Citation Related Structures: 
  6GFE


• PubMed Abstract: 
  

  We report the x-ray crystal structure of intact, full-length human immunoglobulin (IgG4) at 1.8 Å resolution. The data for IgG4 (S228P), an antibody targeting the natriuretic peptide receptor A, show a previously unrecognized type of Fab-Fc orientation with a distorted λ-shape in which one Fab-arm is oriented toward the Fc portion. Detailed structural analysis by x-ray crystallography and molecular simulations suggest that this is one of several conformations coexisting in a dynamic equilibrium state. These results were confirmed by small angle x-ray scattering in solution. Furthermore, electron microscopy supported these findings by preserving molecule classes of different conformations. This study fosters our understanding of IgG4 in particular and our appreciation of antibody flexibility in general. Moreover, we give insights into potential biological implications, specifically for the interaction of human anti-natriuretic peptide receptor A IgG4 with the neonatal Fc receptor, Fcγ receptors, and complement-activating C1q by considering conformational flexibility.

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Organizational Affiliation: 
• Innovation Unit, Pharmaceutical Development Biologics, Biberach (Riss), Germany. Electronic address: [e-mail].
Department Lead Identification and Optimization Support, Structural Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach (Riss), Germany.
Theoretical Chemistry, Ruhr University Bochum, Bochum, Germany.
Innovation Unit, Pharmaceutical Development Biologics, Biberach (Riss), Germany.
University of Applied Sciences Biberach, Biberach (Riss), Germany.
Physikalische Chemie III, Technische Universität Dortmund, Dortmund, Germany.
Elektronenmikroskopisches Zentrum, Friedrich-Schiller-Universität Jena, Jena, Germany.
European Synchrotron Radiation Facility, Grenoble, France.
Innovation Unit, Pharmaceutical Development Biologics, Biberach (Riss), Germany. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 149.27 kDa 
• Atom Count: 11,641 
• Modeled Residue Count: 1,285 
• Deposited Residue Count: 1,330 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin gamma-4 heavy chain	A [auth H], B [auth K]	450	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin gamma-4 light chain	C [auth L], D [auth M]	215	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth A], F [auth B]	7		N-Glycosylation
Glycosylation Resources
GlyTouCan: G45889JQ GlyCosmos: G45889JQ GlyGen: G45889JQ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	I [auth K], J [auth L], K [auth L]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	G [auth H], H [auth K]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.78	α = 90
b = 160.51	β = 110.72
c = 87.3	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
BUSTER	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-15 
Deposition Author(s): Hoerer, S.

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-10-16
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary