1RUZ | pdb_00001ruz

1918 H1 Hemagglutinin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.289 (Depositor) 
  • R-Value Work: 
    0.248 (Depositor) 
  • R-Value Observed: 
    0.248 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1RUZ

This is version 2.2 of the entry. See complete history

Literature

The structure and receptor binding properties of the 1918 influenza hemagglutinin.

Gamblin, S.J.Haire, L.F.Russell, R.J.Stevens, D.J.Xiao, B.Ha, Y.Vasisht, N.Steinhauer, D.A.Daniels, R.S.Elliot, A.Wiley, D.C.Skehel, J.J.

(2004) Science 303: 1838-1842

  • DOI: https://doi.org/10.1126/science.1093155
  • Primary Citation Related Structures: 
    1RU7, 1RUY, 1RUZ, 1RV0, 1RVT, 1RVX, 1RVZ

  • PubMed Abstract: 

    The 1918 influenza pandemic resulted in about 20 million deaths. This enormous impact, coupled with renewed interest in emerging infections, makes characterization of the virus involved a priority. Receptor binding, the initial event in virus infection, is a major determinant of virus transmissibility that, for influenza viruses, is mediated by the hemagglutinin (HA) membrane glycoprotein. We have determined the crystal structures of the HA from the 1918 virus and two closely related HAs in complex with receptor analogs. They explain how the 1918 HA, while retaining receptor binding site amino acids characteristic of an avian precursor HA, is able to bind human receptors and how, as a consequence, the virus was able to spread in the human population.


  • Organizational Affiliation
    • Medical Research Council (MRC) National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.

Macromolecule Content 

  • Total Structure Weight: 165.45 kDa 
  • Atom Count: 12,108 
  • Modeled Residue Count: 1,452 
  • Deposited Residue Count: 1,464 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
hemagglutininA [auth H],
C [auth J],
E [auth L]
328Influenza A virus (A/South Carolina/1/1918(H1N1))Mutation(s): 0 
UniProt
Find proteins for Q9WFX3 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1))
Explore Q9WFX3 
Go to UniProtKB:  Q9WFX3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WFX3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
hemagglutininB [auth I],
D [auth K],
F [auth M]
160Influenza A virus (A/South Carolina/1/1918(H1N1))Mutation(s): 0 
UniProt
Find proteins for Q9WFX3 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1))
Explore Q9WFX3 
Go to UniProtKB:  Q9WFX3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WFX3
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
H,
I [auth H]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NDG

Query on NDG



Download:Ideal Coordinates CCD File
G [auth H]
J [auth H]
K [auth H]
L [auth J]
M [auth J]
G [auth H],
J [auth H],
K [auth H],
L [auth J],
M [auth J],
N [auth K],
O [auth L],
P [auth L],
Q [auth M]
2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.289 (Depositor) 
  • R-Value Work:  0.248 (Depositor) 
  • R-Value Observed: 0.248 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.461α = 90
b = 171.461β = 90
c = 153.445γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-30
    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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-08-23
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-30
    Changes: Structure summary