4H79

Crystal structure of CasB from Thermobifida fusca

• PDB DOI: https://doi.org/10.2210/pdb4H79/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Thermobifida fusca YX
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-09-20 Released: 2012-10-03 
• Deposition Author(s): Ke, A., Nam, K.H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.196 
• R-Value Work: 0.148 
• R-Value Observed: 0.150 

Starting Model: experimental

Literature

Nucleic acid binding surface and dimer interface revealed by CRISPR-associated CasB protein structures.

Nam, K.H., Huang, Q., Ke, A.

(2012) FEBS Lett 586: 3956-3961

• PubMed: 23079036 
• DOI: https://doi.org/10.1016/j.febslet.2012.09.041
• Primary Citation of Related Structures:  
  4H79, 4H7A


• PubMed Abstract: 
  

  The CRISPR system is an adaptive RNA-based microbial immune system against invasive genetic elements. CasB is an essential protein component in Type I-E Cascade. Here, we characterize CasB proteins from three different organisms as non-specific nucleic acid binding proteins. The Thermobifida fusca CasB crystal structure reveals conserved positive surface charges, which we show are important for its nucleic acid binding function. EM docking reveals that CasB dimerization aligns individual nucleic acid binding surfaces into a curved, elongated binding surface inside Type I-E Cascade, consistent with the putative functions of CasB in ds-DNA recruitment and crRNA-DNA duplex formation steps.

---

Organizational Affiliation: 

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.81 kDa 
• Atom Count: 1,538 
• Modelled Residue Count: 177 
• Deposited Residue Count: 216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated protein, Cse2 family	A	216	Thermobifida fusca YX	Mutation(s): 0  Gene Names: Tfu_1599
UniProt
Find proteins for Q47PI5 (Thermobifida fusca (strain YX)) Explore Q47PI5  Go to UniProtKB:  Q47PI5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.196 
• R-Value Work: 0.148 
• R-Value Observed: 0.150 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.749	α = 90
b = 86.749	β = 90
c = 70.016	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-03 
Deposition Author(s): Ke, A., Nam, K.H.

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release
  
• Version 1.1: 2012-11-28
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description