5UG0

Human antibody H2897 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

CryoEM Structure of an Influenza Virus Receptor-Binding Site Antibody-Antigen Interface.

Liu, Y.Pan, J.Jenni, S.Raymond, D.D.Caradonna, T.Do, K.T.Schmidt, A.G.Harrison, S.C.Grigorieff, N.

(2017) J. Mol. Biol. 429: 1829-1839

  • DOI: 10.1016/j.jmb.2017.05.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Structure-based vaccine design depends on extensive structural analyses of antigen-antibody complexes.Single-particle electron cryomicroscopy (cryoEM) can circumvent some of the problems of x-ray crystallography as a pipeline for obtaining the requir ...

    Structure-based vaccine design depends on extensive structural analyses of antigen-antibody complexes.Single-particle electron cryomicroscopy (cryoEM) can circumvent some of the problems of x-ray crystallography as a pipeline for obtaining the required structures. We have examined the potential of single-particle cryoEM for determining the structure of influenza-virus hemagglutinin (HA):single-chain variable-domain fragment complexes, by studying a complex we failed to crystallize in pursuing an extended project on the human immune response to influenza vaccines.The result shows that a combination of cryoEM and molecular modeling can yield details of the antigen-antibody interface, although small variation in the twist of the rod-likeHA trimer limited the overall resolution to about 4.5Å.Comparison of principal 3D classes suggests ways to modify the HA trimer to overcome this limitation. A closely related antibody from the same donor did yield crystals when bound with the same HA, giving us an independent validation of the cryoEM results.The two structures also augment our understanding of receptor-binding site recognition by antibodies that neutralize a wide range of influenza-virus variants.


    Organizational Affiliation

    Laboratory of Molecular Medicine, Boston Children's Hospital, 3 Blackfan Circle, Boston,MA 02115, USA; Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA1
A
327Influenza A virusMutation(s): 0 
Gene Names: HA
Find proteins for A7UPX0 (Influenza A virus)
Go to UniProtKB:  A7UPX0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA2
B
182Influenza A virusMutation(s): 0 
Gene Names: HA
Find proteins for A7UPX0 (Influenza A virus)
Go to UniProtKB:  A7UPX0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
2897 light chain
C
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
2897 heavy chain
D
232N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.240 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 142.200α = 90.00
b = 142.200β = 90.00
c = 200.410γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-06-21
    Type: Database references