Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 9-mer - A3B3C3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 73.68 kDa 
• Atom Count: 5,096 
• Modelled Residue Count: 619 
• Deposited Residue Count: 628 
• Unique protein chains: 3

 6FYT

Structure of H1 (A/solomon Islands/3/06) Influenza Hemagglutinin in complex with SD38

• PDB DOI:  https://doi.org/10.2210/pdb6FYT/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/Solomon Islands/3/2006(H1N1)), Lama glama
• Expression System: Trichoplusia ni, Homo sapiens
• Mutation(s): No 


• Deposited: 2018-03-12 Released: 2018-11-07 
• Deposition Author(s): Laursen, N.S., Wilson, I.A.
• Funding Organization(s): National Institutes of Health

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.235 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

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 of 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: 

Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A	330	Influenza A virus (A/Solomon Islands/3/2006(H1N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A7Y8I1 (Influenza A virus) Explore A7Y8I1  Go to UniProtKB:  A7Y8I1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B	174	Influenza A virus (A/Solomon Islands/3/2006(H1N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A7Y8I1 (Influenza A virus) Explore A7Y8I1  Go to UniProtKB:  A7Y8I1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Single domain antibody SD38	C [auth I]	124	Lama glama	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C], H [auth G]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G63564LA GlyCosmos:  G63564LA

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth D], G [auth F]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 6
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	F [auth E]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I [auth A], J [auth A], K [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.235 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.54	α = 90
b = 107.54	β = 90
c = 198.33	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-11-07 
Deposition Author(s): Laursen, N.S., Wilson, I.A.

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Funding Organization	Location	Grant Number
National Institutes of Health	United States	R56 AI117675
National Institutes of Health	United States	R56 AI127371

Revision History  

• Version 1.0: 2018-11-07
  Type: Initial release
  
• Version 1.1: 2018-11-14
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary