4HKX

Influenza hemagglutinin in complex with CH67 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody.

Schmidt, A.G.Xu, H.Khan, A.R.O'Donnell, T.Khurana, S.King, L.R.Manischewitz, J.Golding, H.Suphaphiphat, P.Carfi, A.Settembre, E.C.Dormitzer, P.R.Kepler, T.B.Zhang, R.Moody, M.A.Haynes, B.F.Liao, H.X.Shaw, D.E.Harrison, S.C.

(2013) Proc Natl Acad Sci U S A 110: 264-269

  • DOI: https://doi.org/10.1073/pnas.1218256109
  • Primary Citation of Related Structures:  
    4HK0, 4HK3, 4HKB, 4HKX

  • PubMed Abstract: 

    Affinity maturation refines a naive B-cell response by selecting mutations in antibody variable domains that enhance antigen binding. We describe a B-cell lineage expressing broadly neutralizing influenza virus antibodies derived from a subject immunized with the 2007 trivalent vaccine. The lineage comprises three mature antibodies, the unmutated common ancestor, and a common intermediate. Their heavy-chain complementarity determining region inserts into the conserved receptor-binding pocket of influenza HA. We show by analysis of structures, binding kinetics and long time-scale molecular dynamics simulations that antibody evolution in this lineage has rigidified the initially flexible heavy-chain complementarity determining region by two nearly independent pathways and that this preconfiguration accounts for most of the affinity gain. The results advance our understanding of strategies for developing more broadly effective influenza vaccines.


  • Organizational Affiliation

    Laboratory of Molecular Medicine, Children's Hospital, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA 02115, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA1A [auth E]220Influenza A virus (A/Solomon Islands/3/2006(H1N1))Mutation(s): 0 
Gene Names: HA1
UniProt
Find proteins for A7UPX0 (Influenza A virus)
Explore A7UPX0 
Go to UniProtKB:  A7UPX0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7UPX0
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CH67 heavy chainB [auth A]231Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CH67 light chainC [auth B]214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
D [auth E],
E
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.099α = 90
b = 69.815β = 107.33
c = 80.343γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-21
    Type: Initial release
  • Version 1.1: 2012-12-05
    Changes: Database references
  • Version 1.2: 2013-01-16
    Changes: Database references
  • Version 1.3: 2013-09-25
    Changes: Structure summary
  • Version 1.4: 2017-11-15
    Changes: Refinement description
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary