3LZF

Crystal Structure of Fab 2D1 in Complex with the 1918 Influenza Virus Hemagglutinin

• PDB DOI: https://doi.org/10.2210/pdb3LZF/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Influenza A virus (A/South Carolina/1/1918(H1N1)), Homo sapiens
• Expression System: Trichoplusia ni, Homo sapiens
• Mutation(s): No 


• Deposited: 2010-03-01 Released: 2010-04-07 
• Deposition Author(s): Ekiert, D.C., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.259 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 106.18 kDa 
• Atom Count: 7,207 
• Modelled Residue Count: 924 
• Deposited Residue Count: 957 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin, HA1 Subunit	A	331	Influenza A virus (A/South Carolina/1/1918(H1N1))	Mutation(s): 0  Gene Names: HA, Hemagglutinin
UniProt
Find proteins for Q9WFX3 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)) Explore Q9WFX3  Go to UniProtKB:  Q9WFX3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin, HA2 Subunit	B	179	Influenza A virus (A/South Carolina/1/1918(H1N1))	Mutation(s): 0  Gene Names: HA, Hemagglutinin
UniProt
Find proteins for Q9WFX3 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)) Explore Q9WFX3  Go to UniProtKB:  Q9WFX3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
2D1 Fab, Heavy Chain	C [auth H]	230	Homo sapiens	Mutation(s): 0  Gene Names: Immunoglobulin, Gamma Chain

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
2D1 Fab, Light Chain	D [auth L]	217	Homo sapiens	Mutation(s): 0  Gene Names: Immunoglobulin, Lambda Chain

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], G [auth E]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	F [auth D]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	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: 2.80 Å
• R-Value Free: 0.259 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.745	α = 90
b = 161.745	β = 90
c = 143.473	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
XPREP	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-07 
Deposition Author(s): Ekiert, D.C., Wilson, I.A.

Revision History  

• Version 1.0: 2010-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary