Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 Pseudo Symmetry: Cyclic - C3  (3D View)
Pseudo Stoichiometry: Hetero 12-mer - A6B3C3 

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

Macromolecule Content

• Total Structure Weight: 319.54 kDa 
• Atom Count: 21839 
• Residue Count: 2754 
• Unique protein chains: 4

4HLZ

Crystal Structure of Fab C179 in Complex with a H2N2 influenza virus hemagglutinin

• DOI: 10.2210/pdb4HLZ/pdb

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


• Deposited: 2012-10-17 Released: 2013-04-17 
• Deposition Author(s): Dreyfus, C., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.284 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 

Literature

Structure of a classical broadly neutralizing stem antibody in complex with a pandemic h2 influenza virus hemagglutinin.

Dreyfus, C., Ekiert, D.C., Wilson, I.A.

(2013) J Virol 87: 7149-7154

• PubMed: 23552413 
• DOI: 10.1128/JVI.02975-12
• Primary Citation of Related Structures:  
  4HLZ


• PubMed Abstract: 
  

We report the structural characterization of the first antibody identified to cross-neutralize multiple subtypes of influenza A viruses. The crystal structure of mouse antibody C179 bound to the pandemic 1957 H2N2 hemagglutinin (HA) reveals that it targets an epitope on the HA stem similar to those targeted by the recently identified human broadly neutralizing antibodies. C179 also inhibits the low-pH conformational change of the HA but uses a different angle of approach and both heavy and light chains.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	A, C, E	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)) Explore C7S226  Go to UniProtKB:  C7S226

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	B, D, F	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)) Explore C7S226  Go to UniProtKB:  C7S226

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab C179 heavy chain	G, I, K	229	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab C179 light chain	H, J, L	214	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
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	M, P	3		N-Glycosylation

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N	4		N-Glycosylation

Entity ID: 7
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	O, Q	2		N-Glycosylation

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B, E, F	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	B, D, E, F, H, J, L	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	J	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.284 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.58	α = 90
b = 150.78	β = 90
c = 217.78	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-10-17 
• Released Date: 2013-04-17 
Deposition Author(s): Dreyfus, C., Wilson, I.A.

Revision History 

• Version 1.0: 2013-04-17
  Type: Initial release
  
• Version 1.1: 2013-07-24
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary