5GJS

Crystal structure of H1 hemagglutinin from A/California/04/2009 in complex with a neutralizing antibody 3E1

• PDB DOI: https://doi.org/10.2210/pdb5GJS/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Influenza A virus (A/California/04/2009(H1N1)), Homo sapiens
• Expression System: Baculovirus expression vector pFastBac1-HM, Cloning vector AbVec-hIgKappa, Cloning vector AbVec-hIgG1
• Mutation(s): Yes 


• Deposited: 2016-07-01 Released: 2016-12-07 
• Deposition Author(s): Wang, W., Zhang, T., Ding, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.303 
• R-Value Work: 0.251 
• R-Value Observed: 0.254 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 

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

Macromolecule Content

• Total Structure Weight: 105.16 kDa 
• Atom Count: 7,069 
• Modelled Residue Count: 905 
• Deposited Residue Count: 947 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A	329	Influenza A virus (A/California/04/2009(H1N1))	Mutation(s): 2  Gene Names: HA
UniProt
Find proteins for C3W5S1 (Influenza A virus (strain swl A/California/04/2009 H1N1)) Explore C3W5S1  Go to UniProtKB:  C3W5S1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B	182	Influenza A virus (A/California/04/2009(H1N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for C3W5S1 (Influenza A virus (strain swl A/California/04/2009 H1N1)) Explore C3W5S1  Go to UniProtKB:  C3W5S1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain of human neutralizing antibody 3E1	C [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain of human neutralizing antibody 3E1	D [auth H]	222	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]	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	F [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: 0.303 
• R-Value Work: 0.251 
• R-Value Observed: 0.254 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.162	α = 90
b = 130.162	β = 90
c = 365.853	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-2000	data scaling
PHENIX	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-07 
Deposition Author(s): Wang, W., Zhang, T., Ding, J.

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2016-12-21
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary