2RFU | pdb_00002rfu

Crystal structure of influenza B virus hemagglutinin in complex with LSTc receptor analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.311 (Depositor) 
  • R-Value Work: 
    0.295 (Depositor) 
  • R-Value Observed: 
    0.296 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2RFU

This is version 2.2 of the entry. See complete history

Literature

Structural basis for receptor specificity of influenza B virus hemagglutinin.

Wang, Q.Tian, X.Chen, X.Ma, J.

(2007) Proc Natl Acad Sci U S A 104: 16874-16879

  • DOI: https://doi.org/10.1073/pnas.0708363104
  • Primary Citation Related Structures: 
    2RFT, 2RFU

  • PubMed Abstract: 

    Receptor-binding specificity of HA, the major surface glycoprotein of influenza virus, primarily determines the host ranges that the virus can infect. Influenza type B virus almost exclusively infects humans and contributes to the annual "flu" sickness. Here we report the structures of influenza B virus HA in complex with human and avian receptor analogs, respectively. These structures provide a structural basis for the different receptor-binding properties of influenza A and B virus HA molecules and for the ability of influenza B virus HA to distinguish human and avian receptors. The structure of influenza B virus HA with avian receptor analog also reveals how mutations in the region of residues 194 to 196, which are frequently observed in egg-adapted and naturally occurring variants, directly affect the receptor binding of the resultant virus strains. Furthermore, these structures of influenza B virus HA are compared with known structures of influenza A virus HAs, which suggests the role of the residue at 222 as a key and likely a universal determinant for the different binding modes of human receptor analogs by different HA molecules.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. qinghuaw@bcm.tmc.edu

Macromolecule Content 

  • Total Structure Weight: 59.15 kDa 
  • Atom Count: 4,065 
  • Modeled Residue Count: 511 
  • Deposited Residue Count: 520 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Influenza B hemagglutinin (HA)344Influenza B virus (B/Hong Kong/8/1973)Mutation(s): 0 
Gene Names: Hemagglutinin
UniProt
Find proteins for P03462 (Influenza B virus (strain B/Hong Kong/8/1973))
Explore P03462 
Go to UniProtKB:  P03462
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03462
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Influenza B hemagglutinin (HA)176Influenza B virus (B/Hong Kong/8/1973)Mutation(s): 0 
Gene Names: Hemagglutinin
UniProt
Find proteins for P03462 (Influenza B virus (strain B/Hong Kong/8/1973))
Explore P03462 
Go to UniProtKB:  P03462
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03462
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, E, F
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G
3N/A
Glycosylation Resources
GlyTouCan: G73578JC
GlyCosmos: G73578JC
GlyGen: G73578JC

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.311 (Depositor) 
  • R-Value Work:  0.295 (Depositor) 
  • R-Value Observed: 0.296 (Depositor) 
Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.369α = 90
b = 98.369β = 90
c = 135.896γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-05
    Type: Initial release
  • Version 1.1: 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: 2024-04-03
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-30
    Changes: Structure summary