Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

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

Macromolecule Content

• Total Structure Weight: 51.14 kDa 
• Atom Count: 3617 
• Residue Count: 486 
• Unique protein chains: 2

5E99

Bovine Fab fragment F08_B11

• DOI: 10.2210/pdb5E99/pdb

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


• Deposited: 2015-10-14 Released: 2016-08-24 
• Deposition Author(s): Stanfield, R.L., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.235 
• R-Value Work: 0.194 
• R-Value Observed: 0.198 

Literature

Conservation and diversity in the ultralong third heavy-chain complementarity-determining region of bovine antibodies.

Stanfield, R.L., Wilson, I.A., Smider, V.V.

(2016) Sci Immunol 1

• PubMed: 27574710 
• DOI: 10.1126/sciimmunol.aaf7962
• Structures With Same Primary Citation


• PubMed Abstract: 
  

A subset of bovine antibodies have an exceptionally long third heavy-chain complementarity determining region (CDR H3) that is highly variable in sequence and includes multiple cysteines. These long CDR H3s (up to 69 residues) fold into a long stalk atop which sits a knob domain that is located far from the antibody surface. Three new bovine Fab crystal structures have been determined to decipher the conserved and variable features of ultralong CDR H3s that lead to diversity in antigen recognition. Despite high sequence variability, the stalks adopt a conserved β-ribbon structure, while the knob regions share a conserved β-sheet that serves as a scaffold for two connecting loops of variable length and conformation, as well as one conserved disulfide. Variation in patterns and connectivity of the remaining disulfides contribute to the knob structural diversity. The unusual architecture of these ultralong bovine CDR H3s for generating diversity is unique in adaptive immune systems.

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Organizational Affiliation: 

Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California, 92037, USA; Fabrus Inc., A Division of Sevion Therapeutics, San Diego, CA 92121, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Fab F08_B11 light chain	L	216	Bos taurus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Fab F08_B11 heavy chain	H	273	Bos taurus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.235 
• R-Value Work: 0.194 
• R-Value Observed: 0.198 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.41	α = 90
b = 71.46	β = 97.27
c = 88.32	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
XDS	data reduction
Coot	model building
Blu-Ice	data collection
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-10-14 
• Released Date: 2016-08-24 
Deposition Author(s): Stanfield, R.L., Wilson, I.A.

Revision History 

• Version 1.0: 2016-08-24
  Type: Initial release
  
• Version 1.1: 2016-09-14
  Changes: Database references