5Y2L | pdb_00005y2l

Crystal structure of a group 2 HA binding antibody AF4H1K1 Fab in complex with the 1968 H3N2 pandemic (H3-AC/68) hemagglutinin

• PDB DOI: https://doi.org/10.2210/pdb5Y2L/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Influenza A virus (A/Aichi/2/1968(H3N2)), Homo sapiens
• Expression System: Trichoplusia ni, Homo sapiens
• Mutation(s): No 


• Deposited: 2017-07-26 Released: 2019-01-30 
• Deposition Author(s): Xiao, H., Qi, J., Gao, F.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.244 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

An H3-clade neutralizing antibody screened from an H7N9 patient that binds group 2 influenza A hemagglutinins

Xiao, H., Qi, J., Gao, F.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 107.05 kDa 
• Atom Count: 7,189 
• Modeled Residue Count: 916 
• Deposited Residue Count: 958 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A	329	Influenza A virus (A/Aichi/2/1968(H3N2))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2)) Explore P03437  Go to UniProtKB:  P03437
Glycosylation
Glycosylation Sites: 4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B	176	Influenza A virus (A/Aichi/2/1968(H3N2))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2)) Explore P03437  Go to UniProtKB:  P03437

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
a group 2 HA binding antibody AF4H1K1 Fab heavy chain	C [auth I]	233	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
a group 2 HA binding antibody AF4H1K1 Fab light chain	D [auth J]	220	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

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	E [auth C], F [auth D]	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	G [auth A], H [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: 2.90 Å
• R-Value Free:  0.244 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.482	α = 90
b = 157.482	β = 90
c = 355.344	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-30 
Deposition Author(s): Xiao, H., Qi, J., Gao, F.G.

Revision History  

• Version 1.0: 2019-01-30
  Type: Initial release
  
• Version 1.1: 2020-03-04
  Changes: Data collection, Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-11-13
  Changes: Data collection, Database references, Structure summary