Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 12-mer - A3BCD 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 105.72 kDa 
• Atom Count: 6639 
• Residue Count: 845 
• Unique protein chains: 4

4HF5

Crystal structure of Fab 8F8 in complex a H2N2 influenza virus hemagglutinin

• DOI: 10.2210/pdb4HF5/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Influenza A virus (A/Japan/305+/1957(H2N2)), Homo sapiens
• Expression System: Trichoplusia ni, Homo sapiens
• Mutation(s): No 


• Deposited: 2012-10-04 Released: 2013-02-13 
• Deposition Author(s): Xu, R., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.282 
• R-Value Work: 0.229 
• R-Value Observed: 0.232 

Literature

A recurring motif for antibody recognition of the receptor-binding site of influenza hemagglutinin.

Xu, R., Krause, J.C., McBride, R., Paulson, J.C., Crowe, J.E., Wilson, I.A.

(2013) Nat Struct Mol Biol 20: 363-370

• PubMed: 23396351 
• DOI: 10.1038/nsmb.2500
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Influenza virus hemagglutinin (HA) mediates receptor binding and viral entry during influenza infection. The development of receptor analogs as viral-entry blockers has not been successful, which suggests that sialic acid may not be an ideal scaffold to obtain broad, potent HA inhibitors. Here, we report crystal structures of Fab fragments from three human antibodies that neutralize the 1957 pandemic H2N2 influenza virus in complex with H2 HA. All three antibodies use an aromatic residue to plug a conserved cavity in the HA receptor-binding site. Each antibody interacts with the absolutely conserved HA1 Trp153 at the cavity base through π-π stacking with the signature Phe54 of two VH1-69-encoded antibodies or a tyrosine from HCDR3 in the other antibody. This highly conserved interaction can be used as a starting point to design inhibitors targeting this conserved hydrophobic pocket in influenza viruses.

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Organizational Affiliation: 

Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Hemagglutinin HA1	A	327	Influenza A virus (A/Japan/305+/1957(H2N2))	Mutation(s): 0  Gene Names: HA
Find proteins for C7S226 (Influenza A virus (strain A/Japan/305/1957 H2N2)) Go to UniProtKB:  C7S226

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Hemagglutinin HA2	B	174	Influenza A virus (A/Japan/305+/1957(H2N2))	Mutation(s): 0  Gene Names: HA
Find proteins for C7S226 (Influenza A virus (strain A/Japan/305/1957 H2N2)) Go to UniProtKB:  C7S226

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Fab 8F8 heavy chain	H	233	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Fab 8F8 light chain	L	218	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
BMA	A	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.282 
• R-Value Work: 0.229 
• R-Value Observed: 0.232 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.615	α = 90
b = 136.615	β = 90
c = 142.134	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-10-04 
• Released Date: 2013-02-13 
Deposition Author(s): Xu, R., Wilson, I.A.

Revision History 

• Version 1.0: 2013-02-13
  Type: Initial release
  
• Version 1.1: 2013-05-22
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description