5JW5 | pdb_00005jw5

Structure of MEDI8852 Fab Fragment

• PDB DOI: https://doi.org/10.2210/pdb5JW5/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2016-05-11 Released: 2016-08-03 
• Deposition Author(s): Neu, U., Collins, P.J., Walker, P.A., Vorlaender, M.K., Ogrodowicz, R.W., Martin, S.R., Gamblin, S.J., Skehel, J.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.217 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Models: experimental

Literature

Structure and Function Analysis of an Antibody Recognizing All Influenza A Subtypes.

Kallewaard, N.L., Corti, D., Collins, P.J., Neu, U., McAuliffe, J.M., Benjamin, E., Wachter-Rosati, L., Palmer-Hill, F.J., Yuan, A.Q., Walker, P.A., Vorlaender, M.K., Bianchi, S., Guarino, B., De Marco, A., Vanzetta, F., Agatic, G., Foglierini, M., Pinna, D., Fernandez-Rodriguez, B., Fruehwirth, A., Silacci, C., Ogrodowicz, R.W., Martin, S.R., Sallusto, F., Suzich, J.A., Lanzavecchia, A., Zhu, Q., Gamblin, S.J., Skehel, J.J.

(2016) Cell 166: 596-608

• PubMed: 27453466 
• DOI: https://doi.org/10.1016/j.cell.2016.05.073
• Primary Citation Related Structures: 
  5JW3, 5JW4, 5JW5


• PubMed Abstract: 
  

  Influenza virus remains a threat because of its ability to evade vaccine-induced immune responses due to antigenic drift. Here, we describe the isolation, evolution, and structure of a broad-spectrum human monoclonal antibody (mAb), MEDI8852, effectively reacting with all influenza A hemagglutinin (HA) subtypes. MEDI8852 uses the heavy-chain VH6-1 gene and has higher potency and breadth when compared to other anti-stem antibodies. MEDI8852 is effective in mice and ferrets with a therapeutic window superior to that of oseltamivir. Crystallographic analysis of Fab alone or in complex with H5 or H7 HA proteins reveals that MEDI8852 binds through a coordinated movement of CDRs to a highly conserved epitope encompassing a hydrophobic groove in the fusion domain and a large portion of the fusion peptide, distinguishing it from other structurally characterized cross-reactive antibodies. The unprecedented breadth and potency of neutralization by MEDI8852 support its development as immunotherapy for influenza virus-infected humans.

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Organizational Affiliation: 
• Department of Infectious Disease and Vaccines, MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA.
Humabs BioMed SA, Via Mirasole 1, 6500 Bellinzona, Switzerland.
Mill Hill Laboratory, The Francis Crick Institute, London NW7 1AA, UK.
Department of Antibody Discovery and Protein Engineering, MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA.
Structural Biology Science Technology Platform, Mill Hill Laboratory, Francis Crick Institute, London NW7 1AA, UK.
Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland.
Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland; Institute for Microbiology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland.
Department of Infectious Disease and Vaccines, MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA. Electronic address: [e-mail].
Mill Hill Laboratory, The Francis Crick Institute, London NW7 1AA, UK. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 95.02 kDa 
• Atom Count: 7,333 
• Modeled Residue Count: 862 
• Deposited Residue Count: 874 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MEDI8852 Heavy chain	A [auth H], C [auth A]	227	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MEDI8852 Light chain	B [auth L], D [auth B]	210	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth H], F [auth L], G [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.217 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.22	α = 90
b = 109.92	β = 90
c = 139.89	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-03 
Deposition Author(s): Neu, U., Collins, P.J., Walker, P.A., Vorlaender, M.K., Ogrodowicz, R.W., Martin, S.R., Gamblin, S.J., Skehel, J.J.

Revision History  

• Version 1.0: 2016-08-03
  Type: Initial release
  
• Version 1.1: 2016-08-10
  Changes: Database references
• Version 1.2: 2019-04-03
  Changes: Data collection, Source and taxonomy
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary