5UJZ

CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface - Class 1

• PDB DOI: https://doi.org/10.2210/pdb5UJZ/pdb
• EM Map EMD-8561: EMDB EMDataResource

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


• Deposited: 2017-01-19 Released: 2017-05-31 
• Deposition Author(s): Liu, Y., Pan, J., Caradonna, T., Jenni, S., Raymond, D.D., Schmidt, A.G., Harrison, S.C., Grigorieff, N.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 257.5 kDa 
• Atom Count: 17,547 
• Modelled Residue Count: 2,196 
• Deposited Residue Count: 2,286 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	A, C, E	323	Influenza A virus (A/Solomon Islands/3/2006(H1N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A7UPX0 (Influenza A virus) Explore A7UPX0  Go to UniProtKB:  A7UPX0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	B, D, F	173	Influenza A virus (A/Solomon Islands/3/2006(H1N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A7UPX0 (Influenza A virus) Explore A7UPX0  Go to UniProtKB:  A7UPX0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv	G, H, I	266	Homo sapiens	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, L, N	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K, M, O	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth D], BA [auth E], CA [auth E], DA [auth E], EA [auth E], FA [auth E], GA [auth F], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth B], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	FREALIGN	9.11
MODEL REFINEMENT	PHENIX	1.10_2155

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-05-31 
Deposition Author(s): Liu, Y., Pan, J., Caradonna, T., Jenni, S., Raymond, D.D., Schmidt, A.G., Harrison, S.C., Grigorieff, N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01 AI-089618

Revision History  

• Version 1.0: 2017-05-31
  Type: Initial release
  
• Version 1.1: 2017-06-21
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence, Experimental preparation
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary