7LUD | pdb_00007lud

Crystal structure of Fab ADI-14442

• PDB DOI: https://doi.org/10.2210/pdb7LUD/pdb

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


• Deposited: 2021-02-22 Released: 2021-06-16 
• Deposition Author(s): Rush, S.A., McLellan, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.195 (DCC) 

Starting Model: experimental

Literature

Vaccination with prefusion-stabilized respiratory syncytial virus fusion protein induces genetically and antigenically diverse antibody responses.

Mukhamedova, M., Wrapp, D., Shen, C.H., Gilman, M.S.A., Ruckwardt, T.J., Schramm, C.A., Ault, L., Chang, L., Derrien-Colemyn, A., Lucas, S.A.M., Ransier, A., Darko, S., Phung, E., Wang, L., Zhang, Y., Rush, S.A., Madan, B., Stewart-Jones, G.B.E., Costner, P.J., Holman, L.A., Hickman, S.P., Berkowitz, N.M., Doria-Rose, N.A., Morabito, K.M., DeKosky, B.J., Gaudinski, M.R., Chen, G.L., Crank, M.C., Misasi, J., Sullivan, N.J., Douek, D.C., Kwong, P.D., Graham, B.S., McLellan, J.S., Mascola, J.R.

(2021) Immunity 54: 769-780.e6

• PubMed: 33823129 
• DOI: https://doi.org/10.1016/j.immuni.2021.03.004
• Primary Citation Related Structures: 
  7LUC, 7LUD, 7LUE


• PubMed Abstract: 
  

  An effective vaccine for respiratory syncytial virus (RSV) is an unrealized public health goal. A single dose of the prefusion-stabilized fusion (F) glycoprotein subunit vaccine (DS-Cav1) substantially increases serum-neutralizing activity in healthy adults. We sought to determine whether DS-Cav1 vaccination induces a repertoire mirroring the pre-existing diversity from natural infection or whether antibody lineages targeting specific epitopes predominate. We evaluated RSV F-specific B cell responses before and after vaccination in six participants using complementary B cell sequencing methodologies and identified 555 clonal lineages. DS-Cav1-induced lineages recognized the prefusion conformation of F (pre-F) and were genetically diverse. Expressed antibodies recognized all six antigenic sites on the pre-F trimer. We identified 34 public clonotypes, and structural analysis of two antibodies from a predominant clonotype revealed a common mode of recognition. Thus, vaccination with DS-Cav1 generates a diverse polyclonal response targeting the antigenic sites on pre-F, supporting the development and advanced testing of pre-F-based vaccines against RSV.

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Organizational Affiliation: 
• Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute for Biomedical Sciences, George Washington University, Washington, DC 20052, USA.
Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66045, USA; Department of Chemical Engineering, The University of Kansas, Lawrence, KS 66045, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. 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 Evidence: gel filtration

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: 96.2 kDa 
• Atom Count: 6,699 
• Modeled Residue Count: 881 
• Deposited Residue Count: 888 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADI-14442 Fab Heavy chain	A [auth H], C [auth A]	225	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ADI-14442 Fab Light chain	B [auth L], D [auth B]	219	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth L], F [auth L], G [auth L], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.195 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.879	α = 90
b = 158.669	β = 104.8
c = 60.18	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-16 
Deposition Author(s): Rush, S.A., McLellan, J.S.

Revision History  

• Version 1.0: 2021-06-16
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary