5I30

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

  • 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)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


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

  • DOI: 10.1021/acsinfecdis.6b00026
  • Structures With Same Primary Citation

  • 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 pr ...

    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.


    Organizational Affiliation

    Department of Biomolecular Engineering, University of California Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab PL-2 light chainL214Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab PL-2 heavy chainH221Mus musculusMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
H
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.22α = 90
b = 170.47β = 90
c = 78.27γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI095369

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