1RVX | pdb_00001rvx

1934 H1 Hemagglutinin in complex with LSTA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.260 (Depositor) 
  • R-Value Work: 
    0.227 (Depositor) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 1RVX

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: 336.11 kDa 
  • Atom Count: 25,966 
  • Modeled Residue Count: 2,896 
  • Deposited Residue Count: 2,922 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
hemagglutinin
A, C, E, G, I
A, C, E, G, I, K
327Influenza A virus (A/Puerto Rico/8/1934(H1N1))Mutation(s): 0 
UniProt
Find proteins for P03452 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1))
Explore P03452 
Go to UniProtKB:  P03452
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03452
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin
B, D, F, H, J
B, D, F, H, J, L
160Influenza A virus (A/Puerto Rico/8/1934(H1N1))Mutation(s): 0 
UniProt
Find proteins for P03452 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1))
Explore P03452 
Go to UniProtKB:  P03452
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03452
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M, N, O, P, Q
M, N, O, P, Q, R
3N/A
Glycosylation Resources
GlyTouCan: G00065MO
GlyCosmos: G00065MO
GlyGen: G00065MO

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth K]
BA [auth L]
S [auth A]
T [auth A]
U [auth B]
AA [auth K],
BA [auth L],
S [auth A],
T [auth A],
U [auth B],
V [auth C],
W [auth G],
X [auth G],
Y [auth I],
Z [auth J]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.260 (Depositor) 
  • R-Value Work:  0.227 (Depositor) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 227.878α = 90
b = 131.344β = 110.09
c = 174.708γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

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: Advisory, Atomic model, Data collection, 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