Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 51140.48 
• Atom Count: 3562 
• Residue Count: 489 
• Unique protein chains: 2

5E99

Bovine Fab fragment F08_B11

• DOI: 10.2210/pdb5E99/pdb

• Classification: IMMUNE SYSTEM
• Expression System: Homo sapiens


• 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 

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
• Primary Citation of Related Structures:  
  5ILT, 5IJV, 5IHU


• 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 Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Fab F08_B11 light chain	L	216	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Fab F08_B11 heavy chain	H	273	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length (Å)	Angle (°)
a = 78.410	α = 90.00
b = 71.460	β = 97.27
c = 88.320	γ = 90.00

Software Package:

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

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
  Type: Database references