Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 176.67 kDa 
• Atom Count: 12082 
• Residue Count: 1509 
• Unique protein chains: 2

1RD8

Crystal Structure of the 1918 Human H1 Hemagglutinin Precursor (HA0)

• DOI: 10.2210/pdb1RD8/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2003-11-05 Released: 2004-03-23 
• Deposition Author(s): Stevens, J., Corper, A.L., Basler, C.F., Taubenberger, J.K., Palese, P., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.295 
• R-Value Work: 0.270 
• R-Value Observed: 0.271 

Literature

Structure of the Uncleaved Human H1 Hemagglutinin from the Extinct 1918 Influenza Virus.

Stevens, J., Corper, A.L., Basler, C.F., Taubenberger, J.K., Palese, P., Wilson, I.A.

(2004) Science 303: 1866-1870

• PubMed: 14764887 
• DOI: 10.1126/science.1093373
• Primary Citation of Related Structures:  
  1RD8


• PubMed Abstract: 
  

The 1918 "Spanish" influenza pandemic represents the largest recorded outbreak of any infectious disease. The crystal structure of the uncleaved precursor of the major surface antigen of the extinct 1918 virus was determined at 3.0 angstrom resolution after reassembly of the hemagglutinin gene from viral RNA fragments preserved in 1918 formalin-fixed lung tissues. A narrow avian-like receptor-binding site, two previously unobserved histidine patches, and a less exposed surface loop at the cleavage site that activates viral membrane fusion reveal structural features primarily found in avian viruses, which may have contributed to the extraordinarily high infectivity and mortality rates observed during 1918.

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Organizational Affiliation: 

Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hemagglutinin	A, C, E	335	Influenza A virus	Mutation(s): 0  Gene Names: Hemagglutinin
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	B, D, F	182	Influenza A virus	Mutation(s): 0  Gene Names: Hemagglutinin
Find proteins for Q9WFX3 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)) Explore Q9WFX3  Go to UniProtKB:  Q9WFX3

Oligosaccharides

Help

Entity ID: 3
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	G, I	3		N-Glycosylation

Entity ID: 4
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	H	4		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B, C, E	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4	B	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.295 
• R-Value Work: 0.270 
• R-Value Observed: 0.271 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.529	α = 90
b = 109.953	β = 108.63
c = 136.238	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-11-05 
• Released Date: 2004-03-23 
Deposition Author(s): Stevens, J., Corper, A.L., Basler, C.F., Taubenberger, J.K., Palese, P., Wilson, I.A.

Revision History 

• Version 1.0: 2004-03-23
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2016-12-14
  Changes: Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary