4GKF | pdb_00004gkf

Crystal structure and characterization of Cmr5 protein from Pyrococcus furiosus

• PDB DOI: https://doi.org/10.2210/pdb4GKF/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-08-11 Released: 2013-01-23 
• Deposition Author(s): Park, J., Sun, J., Park, S., Hwang, H., Park, M., Shin, M.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.276 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Cmr5 from Pyrococcus furiosus and its functional implications

Park, J.H., Sun, J., Park, S.Y., Hwang, H.J., Park, M.Y., Shin, M., Kim, J.S.

(2013) FEBS Lett 587: 562-568

• PubMed: 23370277 
• DOI: https://doi.org/10.1016/j.febslet.2013.01.029
• Primary Citation Related Structures: 
  4GKF


• PubMed Abstract: 
  

  The bacterial acquired immune system consists of clustered regularly interspaced short palindromic repeats (CRISPRs) and CRIPSR-associated (Cas) genes, which include Cas-module repeat-associated mysterious proteins (Cmr). The six Cmr proteins of Pyrococcus furiosus (pfCmr1-pfCmr6) form a Cmr effector complex that functions against exogenous nucleic acid. Among the Cmr proteins, the role of pfCmr5 and its involvement in the complex's cleavage activity have been obscure. The elucidated pfCmr5 structure has two inserted α-helices compared with the other trimeric Cmr5 structure. However, pfCmr5 exists as a monomeric protein both in the crystalline state and in solution. In vitro assays indicate that pfCmr5 interacts with pfCmr4. These structural and biophysical data might help in understanding the complicated and ill-characterized Cmr effector complex.

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Organizational Affiliation: 
• Department of Chemistry and Institute of Basic Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757, Republic of Korea.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.43 kDa 
• Atom Count: 2,605 
• Modeled Residue Count: 293 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR system Cmr subunit Cmr5	A, B	169	Pyrococcus furiosus DSM 3638	Mutation(s): 0  Gene Names: cmr5, PF1125
UniProt
Find proteins for Q8U1T0 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U1T0  Go to UniProtKB:  Q8U1T0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.276 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.944	α = 90
b = 53.944	β = 90
c = 235.987	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-23 
Deposition Author(s): Park, J., Sun, J., Park, S., Hwang, H., Park, M., Shin, M.S.

Revision History  

• Version 1.0: 2013-01-23
  Type: Initial release
  
• Version 1.1: 2013-07-10
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description