Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 9-mer - A3B3C3 

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

Macromolecule Content

• Total Structure Weight: 334.06 kDa 
• Atom Count: 20324 
• Modelled Residue Count: 2635 
• Deposited Residue Count: 3030 
• Unique protein chains: 3

5UDC

Crystal Structure of RSV F A2 Bound to MEDI8897

• DOI: 10.2210/pdb5UDC/pdb

• Classification: Viral Protein/Immune System
• Organism(s): Homo sapiens, Human respiratory syncytial virus A2
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2016-12-26 Released: 2017-05-17 
• Deposition Author(s): McLellan, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.232 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Literature

A highly potent extended half-life antibody as a potential RSV vaccine surrogate for all infants.

Zhu, Q., McLellan, J.S., Kallewaard, N.L., Ulbrandt, N.D., Palaszynski, S., Zhang, J., Moldt, B., Khan, A., Svabek, C., McAuliffe, J.M., Wrapp, D., Patel, N.K., Cook, K.E., Richter, B.W.M., Ryan, P.C., Yuan, A.Q., Suzich, J.A.

(2017) Sci Transl Med 9

• PubMed: 28469033 
• DOI: 10.1126/scitranslmed.aaj1928
• Primary Citation of Related Structures:  
  5UDC, 5UDE, 5UDD


• PubMed Abstract: 
  

Prevention of respiratory syncytial virus (RSV) illness in all infants is a major public health priority. However, no vaccine is currently available to protect this vulnerable population. Palivizumab, the only approved agent for RSV prophylaxis, is limited to high-risk infants, and the cost associated with the requirement for dosing throughout the RSV season makes its use impractical for all infants. We describe the development of a monoclonal antibody as potential RSV prophylaxis for all infants with a single intramuscular dose. MEDI8897*, a highly potent human antibody, was optimized from antibody D25, which targets the prefusion conformation of the RSV fusion (F) protein. Crystallographic analysis of Fab in complex with RSV F from subtypes A and B reveals that MEDI8897* binds a highly conserved epitope. MEDI8897* neutralizes a diverse panel of RSV A and B strains with >50-fold higher activity than palivizumab. At similar serum concentrations, prophylactic administration of MEDI8897* was ninefold more potent than palivizumab at reducing pulmonary viral loads by >3 logs in cotton rats infected with either RSV A or B subtypes. MEDI8897 was generated by the introduction of triple amino acid substitutions (YTE) into the Fc domain of MEDI8897*, which led to more than threefold increased half-life in cynomolgus monkeys compared to non-YTE antibody. Considering the pharmacokinetics of palivizumab in infants, which necessitates five monthly doses for protection during an RSV season, the high potency and extended half-life of MEDI8897 support its development as a cost-effective option to protect all infants from RSV disease with once-per-RSV-season dosing in the clinic.

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Organizational Affiliation: 

Department of Infectious Disease, MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA. [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MEDI8897 Fab Heavy Chain	D [auth B], G [auth E], A [auth H]	228	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MEDI8897 Fab Light Chain	E [auth C], H [auth G], B [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	F [auth A], I [auth D], C [auth F]	568	Human respiratory syncytial virus A2	Mutation(s): 4  Gene Names: F
UniProt
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2)) Explore P03420  Go to UniProtKB:  P03420

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth I]	11		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G60230HH GlyCosmos:  G60230HH GlyGen:  G60230HH

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	K [auth F], L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.232 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: P 1 2₁ 1
• Diffraction Data DOI: 10.15785/SBGRID/488 SBGrid

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.78	α = 90
b = 126.31	β = 102.56
c = 162.31	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-12-26 
• Released Date: 2017-05-17 
Deposition Author(s): McLellan, J.S.

Revision History  

• Version 1.0: 2017-05-17
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary