Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.47 kDa 
• Atom Count: 3200 
• Modelled Residue Count: 336 
• Deposited Residue Count: 390 
• Unique protein chains: 1

4TXD

Crystal structure of Thermofilum pendens Csc2

• PDB DOI: 10.2210/pdb4TXD/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Thermofilum pendens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-07-03 Released: 2014-08-27 
• Deposition Author(s): Hrle, A., Conti, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.212 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Structural analyses of the CRISPR protein Csc2 reveal the RNA-binding interface of the type I-D Cas7 family.

Hrle, A., Maier, L.K., Sharma, K., Ebert, J., Basquin, C., Urlaub, H., Marchfelder, A., Conti, E.

(2014) RNA Biol 11: 1072-1082

• PubMed: 25483036 
• DOI: 10.4161/rna.29893
• Primary Citation of Related Structures:  
  4TXD


• PubMed Abstract: 
  

Upon pathogen invasion, bacteria and archaea activate an RNA-interference-like mechanism termed CRISPR (clustered regularly interspaced short palindromic repeats). A large family of Cas (CRISPR-associated) proteins mediates the different stages of this sophisticated immune response. Bioinformatic studies have classified the Cas proteins into families, according to their sequences and respective functions. These range from the insertion of the foreign genetic elements into the host genome to the activation of the interference machinery as well as target degradation upon attack. Cas7 family proteins are central to the type I and type III interference machineries as they constitute the backbone of the large interference complexes. Here we report the crystal structure of Thermofilum pendens Csc2, a Cas7 family protein of type I-D. We found that Csc2 forms a core RRM-like domain, flanked by three peripheral insertion domains: a lid domain, a Zinc-binding domain and a helical domain. Comparison with other Cas7 family proteins reveals a set of similar structural features both in the core and in the peripheral domains, despite the absence of significant sequence similarity. T. pendens Csc2 binds single-stranded RNA in vitro in a sequence-independent manner. Using a crosslinking - mass-spectrometry approach, we mapped the RNA-binding surface to a positively charged surface patch on T. pendens Csc2. Thus our analysis of the key structural and functional features of T. pendens Csc2 highlights recurring themes and evolutionary relationships in type I and type III Cas proteins.

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Organizational Affiliation: 

a Structural Cell Biology Department; Max Planck Institute of Biochemistry ; Martinsried , Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Csc2	A	390	Thermofilum pendens	Mutation(s): 0  Gene Names: Tpen_1325
UniProt
Find proteins for A1RZU2 (Thermofilum pendens (strain DSM 2475 / Hrk 5)) Explore A1RZU2  Go to UniProtKB:  A1RZU2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.212 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.951	α = 90
b = 112.591	β = 90
c = 60.465	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-07-03 
• Released Date: 2014-08-27 
Deposition Author(s): Hrle, A., Conti, E.

Revision History  

• Version 1.0: 2014-08-27
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection