5JW4 | pdb_00005jw4

Structure of MEDI8852 Fab Fragment in Complex with H5 HA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 
    0.285 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.274 (Depositor), 0.273 (DCC) 
  • R-Value Observed: 
    0.274 (Depositor) 

Starting Models: experimental
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This is version 2.2 of the entry. See complete history

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

  • 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.


  • Organizational Affiliation
    • Department of Infectious Disease and Vaccines, MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA.

Macromolecule Content 

  • Total Structure Weight: 618.41 kDa 
  • Atom Count: 42,466 
  • Modeled Residue Count: 5,368 
  • Deposited Residue Count: 5,504 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin
A, C, E, G, I
A, C, E, G, I, K
321Influenza A virus (A/Vietnam/1194/2004(H5N1))Mutation(s): 1 
Gene Names: HA
UniProt
Find proteins for Q6DQ34 (Influenza A virus)
Explore Q6DQ34 
Go to UniProtKB:  Q6DQ34
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DQ34
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin
B, D, F, H, J
B, D, F, H, J, L
162Influenza A virus (A/Vietnam/1194/2004(H5N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for Q6DQ18 (Influenza A virus (strain A/Chicken/Hong Kong/YU22/2002 H5N1 genotype Z))
Explore Q6DQ18 
Go to UniProtKB:  Q6DQ18
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DQ18
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
MEDI8852 heavy chain
M, O, S, U, W
227Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
MEDI8852 light chain
N, P, T, V, X
206Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
MEDI8852 heavy chain231Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
MEDI8852 light chain210Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseAA [auth a],
BA [auth b],
CA [auth c],
Y,
Z
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
DA [auth A]
EA [auth A]
FA [auth A]
GA [auth C]
HA [auth C]
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth C],
HA [auth C],
IA [auth C],
JA [auth D],
KA [auth E],
LA [auth E],
MA [auth G],
NA [auth G],
OA [auth G],
PA [auth I],
QA [auth I],
RA [auth I],
SA [auth K],
TA [auth K],
UA [auth K],
VA [auth K],
WA [auth L]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free:  0.285 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.274 (Depositor), 0.273 (DCC) 
  • R-Value Observed: 0.274 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.26α = 90
b = 386.36β = 90.44
c = 165.86γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 1.2: 2018-11-21
    Changes: Advisory, Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2019-04-03
    Changes: Data collection, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-06
    Changes: Structure summary