5I30 | pdb_00005i30

Crystal structure of the human astrovirus 2 neutralizing monoclonal antibody PL-2 Fab fragment at 1.9 A resolution

• PDB DOI: https://doi.org/10.2210/pdb5I30/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2016-02-09 Released: 2016-04-13 
• Deposition Author(s): Bogdanoff, W.A., DuBois, R.M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.221 (Depositor) 
• R-Value Work: 
  0.180 (Depositor) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

De Novo Sequencing and Resurrection of a Human Astrovirus-Neutralizing Antibody.

Bogdanoff, W.A., Morgenstern, D., Bern, M., Ueberheide, B.M., Sanchez-Fauquier, A., DuBois, R.M.

(2016) ACS Infect Dis 2: 313-321

• PubMed: 27213181 
• DOI: https://doi.org/10.1021/acsinfecdis.6b00026
• Primary Citation Related Structures: 
  5I30


• PubMed Abstract: 
  

  Monoclonal antibody (mAb) therapeutics targeting cancer, autoimmune diseases, inflammatory diseases, and infectious diseases are growing exponentially. Although numerous panels of mAbs targeting infectious disease agents have been developed, their progression into clinically useful mAbs is often hindered by the lack of sequence information and/or loss of hybridoma cells that produce them. Here we combine the power of crystallography and mass spectrometry to determine the amino acid sequence and glycosylation modification of the Fab fragment of a potent human astrovirus-neutralizing mAb. We used this information to engineer a recombinant antibody single-chain variable fragment that has the same specificity as the parent monoclonal antibody to bind to the astrovirus capsid protein. This antibody can now potentially be developed as a therapeutic and diagnostic agent.

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Organizational Affiliation: 
• Department of Biomolecular Engineering, University of California Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States.
Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine , New York, New York 10016, United States.
Protein Metrics , San Carlos, California 94070, United States.
Viral Gastroenteritis Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III , Madrid, Spain.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 47.48 kDa 
• Atom Count: 3,425 
• Modeled Residue Count: 424 
• Deposited Residue Count: 435 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab PL-2 light chain	A [auth L]	214	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab PL-2 heavy chain	B [auth H]	221	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.221 (Depositor) 
• R-Value Work:  0.180 (Depositor) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.22	α = 90
b = 170.47	β = 90
c = 78.27	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
Coot	model building
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-04-13 
Deposition Author(s): Bogdanoff, W.A., DuBois, R.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI095369

Revision History  

• Version 1.0: 2016-04-13
  Type: Initial release
  
• Version 1.1: 2016-06-08
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence, Database references
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.6: 2024-10-23
  Changes: Structure summary