6CNW | pdb_00006cnw

STRUCTURE OF HUMANIZED SINGLE DOMAIN ANTIBODY SD84

• PDB DOI: https://doi.org/10.2210/pdb6CNW/pdb

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


• Deposited: 2018-03-09 Released: 2018-11-14 
• Deposition Author(s): Luo, J., Obmolova, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.92 Å
• R-Value Free: 
  0.139 (Depositor), 0.148 (DCC) 
• R-Value Work: 
  0.126 (Depositor) 
• R-Value Observed: 
  0.126 (Depositor) 

Literature

Universal protection against influenza infection by a multidomain antibody to influenza hemagglutinin.

Laursen, N.S., Friesen, R.H.E., Zhu, X., Jongeneelen, M., Blokland, S., Vermond, J., van Eijgen, A., Tang, C., van Diepen, H., Obmolova, G., van der Neut Kolfschoten, M., Zuijdgeest, D., Straetemans, R., Hoffman, R.M.B., Nieusma, T., Pallesen, J., Turner, H.L., Bernard, S.M., Ward, A.B., Luo, J., Poon, L.L.M., Tretiakova, A.P., Wilson, J.M., Limberis, M.P., Vogels, R., Brandenburg, B., Kolkman, J.A., Wilson, I.A.

(2018) Science 362: 598-602

• PubMed: 30385580 
• DOI: https://doi.org/10.1126/science.aaq0620
• Primary Citation Related Structures: 
  6CK8, 6CNV, 6CNW, 6FYS, 6FYT, 6FYU, 6FYW


• PubMed Abstract: 
  

  Broadly neutralizing antibodies against highly variable pathogens have stimulated the design of vaccines and therapeutics. We report the use of diverse camelid single-domain antibodies to influenza virus hemagglutinin to generate multidomain antibodies with impressive breadth and potency. Multidomain antibody MD3606 protects mice against influenza A and B infection when administered intravenously or expressed locally from a recombinant adeno-associated virus vector. Crystal and single-particle electron microscopy structures of these antibodies with hemagglutinins from influenza A and B viruses reveal binding to highly conserved epitopes. Collectively, our findings demonstrate that multidomain antibodies targeting multiple epitopes exhibit enhanced virus cross-reactivity and potency. In combination with adeno-associated virus-mediated gene delivery, they may provide an effective strategy to prevent infection with influenza virus and other highly variable pathogens.

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Organizational Affiliation: 
• Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
Janssen Research and Development, Spring House, PA 19002, USA.
Janssen Vaccines and Prevention, Archimedesweg 4-6, 2333 CN, Leiden, Netherlands.
Janssen Prevention Center, Archimedesweg 6, 2333 CN, Leiden, Netherlands.
Quantitative Sciences, Janssen Pharmaceutical Companies of Johnson and Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium.
Center of Influenza Research and School of Public Health, The University of Hong Kong, Hong Kong SAR, China.
Gene Therapy Program, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Janssen Infectious Diseases, Turnhoutseweg 30, 2340, Beerse, Belgium. [e-mail] [e-mail].
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. [e-mail] [e-mail].
Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 13.17 kDa 
• Atom Count: 1,068 
• Modeled Residue Count: 116 
• Deposited Residue Count: 116 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
humanized antibody SD84h	A	116	hybrid	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	E [auth A], F [auth A], G [auth A], H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACT	B [auth A], C [auth A], D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.92 Å
• R-Value Free:  0.139 (Depositor), 0.148 (DCC) 
• R-Value Work:  0.126 (Depositor) 
• R-Value Observed: 0.126 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.57	α = 90
b = 54.57	β = 90
c = 35.85	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-11-14 
Deposition Author(s): Luo, J., Obmolova, O.

Revision History  

• Version 1.0: 2018-11-14
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Database references, Structure summary