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 5CJQ | pdb_00005cjq

Crystal structure of a trimeric influenza hemagglutinin stem in complex with an broadly neutralizing antibody CR9114


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 
    0.369 (Depositor), 0.376 (DCC) 
  • R-Value Work: 
    0.346 (Depositor), 0.351 (DCC) 
  • R-Value Observed: 
    0.347 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history. 

Literature

A stable trimeric influenza hemagglutinin stem as a broadly protective immunogen.

Impagliazzo, A., Milder, F., Kuipers, H., Wagner, M.V., Zhu, X., Hoffman, R.M., van Meersbergen, R., Huizingh, J., Wanningen, P., Verspuij, J., de Man, M., Ding, Z., Apetri, A., Kukrer, B., Sneekes-Vriese, E., Tomkiewicz, D., Laursen, N.S., Lee, P.S., Zakrzewska, A., Dekking, L., Tolboom, J., Tettero, L., van Meerten, S., Yu, W., Koudstaal, W., Goudsmit, J., Ward, A.B., Meijberg, W., Wilson, I.A., Radosevic, K.

(2015) Science 349: 1301-1306

  • DOI: https://doi.org/10.1126/science.aac7263
  • Primary Citation Related Structures: 
    5CJQ, 5CJS

  • PubMed Abstract: 

    The identification of human broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin (HA) stem revitalized hopes of developing a universal influenza vaccine. Using a rational design and library approach, we engineered stable HA stem antigens ("mini-HAs") based on an H1 subtype sequence. Our most advanced candidate exhibits structural and bnAb binding properties comparable to those of full-length HA, completely protects mice in lethal heterologous and heterosubtypic challenge models, and reduces fever after sublethal challenge in cynomolgus monkeys. Antibodies elicited by this mini-HA in mice and nonhuman primates bound a wide range of HAs, competed with human bnAbs for HA stem binding, neutralized H5N1 viruses, and mediated antibody-dependent effector activity. These results represent a proof of concept for the design of HA stem mimics that elicit bnAbs against influenza A group 1 viruses.


  • Organizational Affiliation: 
    • Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands. aimpagli@its.jnj.com wilson@scripps.edu.

Macromolecule Content 

  • Total Structure Weight: 76.19 kDa 
  • Atom Count: 4,812 
  • Modeled Residue Count: 634 
  • Deposited Residue Count: 704 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CR9114 light chainA [auth L]215Homo sapiensMutation(s): 0 
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CR9114 heavy chainB [auth H]230Homo sapiensMutation(s): 0 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Designed influenza hemagglutinin stem #4900, HA1C [auth A]66synthetic constructMutation(s): 0 
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Designed influenza hemagglutinin stem #4900, HA2D [auth B]193synthetic constructMutation(s): 0 
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free:  0.369 (Depositor), 0.376 (DCC) 
  • R-Value Work:  0.346 (Depositor), 0.351 (DCC) 
  • R-Value Observed: 0.347 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.696α = 90
b = 157.696β = 90
c = 202.645γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-09-30
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Structure summary