1BBD | pdb_00001bbd

THREE DIMENSIONAL STRUCTURE OF THE FAB FRAGMENT OF A NEUTRALIZING ANTIBODY TO HUMAN RHINOVIRUS SEROTYPE 2

• PDB DOI: https://doi.org/10.2210/pdb1BBD/pdb

• Classification: IMMUNOGLOBULIN
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 1992-05-05 Released: 1994-01-31 
• Deposition Author(s): Tormo, J., Blaas, D., Fita, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Three-dimensional structure of the Fab fragment of a neutralizing antibody to human rhinovirus serotype 2.

Tormo, J., Stadler, E., Skern, T., Auer, H., Kanzler, O., Betzel, C., Blaas, D., Fita, I.

(1992) Protein Sci 1: 1154-1161

• PubMed: 1338980 
• DOI: https://doi.org/10.1002/pro.5560010909
• Primary Citation Related Structures: 
  1BBD


• PubMed Abstract: 
  

  The crystal structure of the antigen-binding fragment of a monoclonal antibody (8F5) that neutralizes human rhinovirus serotype 2 has been determined by X-ray diffraction studies. Antibody 8F5, obtained by immunization with native HRV2 virions, cross-reacts with peptides of the viral capsid protein VP2, which contribute to the neutralizing immunogenic site B in this serotype. The structure was solved by the molecular replacement method and has been refined to an R-factor of 18.9% at 2.8 A resolution. The elbow angle, relating the variable and constant modules of the molecule is 127 degrees, representing the smallest elbow angle observed so far in an Fab fragment. Furthermore, the charged residues of the epitope can be well accommodated in the antigen-binding site. This is the first crystal structure reported for an antibody directed against an icosahedral virus.

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Organizational Affiliation: 
• Departament d'Enginyeria Química, Escola Tècnica Superior d'Enginyers Industrials, Barcelona, 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: 48.1 kDa 
• Atom Count: 3,342 
• Modeled Residue Count: 432 
• Deposited Residue Count: 438 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IGG2A-KAPPA 8F5 FAB (LIGHT CHAIN)	A [auth L]	220	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q52L64 (Mus musculus) Explore Q52L64  Go to UniProtKB:  Q52L64

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IGG2A-KAPPA 8F5 FAB (HEAVY CHAIN)	B [auth H]	218	Mus musculus	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.7	α = 90
b = 86.8	β = 90
c = 128	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-01-31 
Deposition Author(s): Tormo, J., Blaas, D., Fita, I.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2014-02-05
  Changes: Source and taxonomy
• Version 1.4: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.5: 2024-10-23
  Changes: Structure summary