7DKJ

Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a neutralizing antibody

• PDB DOI: https://doi.org/10.2210/pdb7DKJ/pdb
• EM Map EMD-30707: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/Okuda/1957(H2N2)), Mus musculus
• Expression System: Trichoplusia ni, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-11-24 Released: 2021-11-24 
• Deposition Author(s): Shirouzu, M.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a neutralizing antibody

Makino-Okamura, C., Hata, H., Watanabe, T., Kim, S., Hebrard, M., Sato, R., Yan, M., Onodera, T., Takahashi, Y., Li, Q., Taylor, T., Okuno, Y., Kurosaki, T., Tomabechi, Y., Uchikubo-Kamo, T., Kamada, K., Shirouzu, M., Fukuyama, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 9-mer - A6B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 340.9 kDa 
• Atom Count: 20,112 
• Modelled Residue Count: 2,490 
• Deposited Residue Count: 2,973 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, D [auth E], G [auth I]	599	Influenza A virus (A/Okuda/1957(H2N2))	Mutation(s): 4  Gene Names: HA
UniProt
Find proteins for A0A0A7E4R0 (Influenza A virus) Explore A0A0A7E4R0  Go to UniProtKB:  A0A0A7E4R0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fv-clasp heavy chain	B [auth C], E [auth G], H [auth K]	203	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fv-clasp light chain	C [auth D], F [auth H], I [auth L]	189	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth B], K [auth F], L [auth J], M, N, O	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	P [auth A], Q [auth A], R [auth A], S [auth E], T [auth E], U [auth E], V [auth I], W [auth I], X [auth I]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.18
RECONSTRUCTION	RELION	3.0.8

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-11-24 
Deposition Author(s): Shirouzu, M.

Revision History  

• Version 1.0: 2021-11-24
  Type: Initial release
  
• Version 1.1: 2022-12-14
  Changes: Refinement description, Structure summary
• Version 1.2: 2023-06-14
  Changes: Data collection, Derived calculations, Refinement description, Structure summary