3V74 | pdb_00003v74

crystal structure of FBF-2 in complex with gld-1 FBEa13 RNA

• PDB DOI: https://doi.org/10.2210/pdb3V74/pdb
• NAKB: 3V74

• Classification: RNA binding protein/RNA
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-12-20 Released: 2012-01-04 
• Deposition Author(s): Wang, Y., Qiu, C., Kershner, A., Holley, C.P., Wilinski, D., Keles, S., Kimble, J., Wickens, M., Hall, T.M.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.227 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.171 (DCC) 

Starting Model: experimental

Literature

Divergence of PUF protein specificity through variations in an RNA-binding pocket

Wang, Y., Qiu, C., Kershner, A., Holley, C.P., Wilinski, D., Keles, S., Kimble, J., Wickens, M., Hall, T.M.T.

(2012) J Biological Chem 

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 51.1 kDa 
• Atom Count: 3,689 
• Modeled Residue Count: 405 
• Deposited Residue Count: 426 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fem-3 mRNA-binding factor 2	A	413	Caenorhabditis elegans	Mutation(s): 0  Gene Names: F21H12.5, fbf-2
UniProt
Find proteins for Q09312 (Caenorhabditis elegans) Explore Q09312  Go to UniProtKB:  Q09312

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*CP*AP*UP*GP*UP*GP*CP*CP*AP*UP*AP*C)-3')	B	13	Caenorhabditis elegans

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.227 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.171 (DCC) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.465	α = 90
b = 98.465	β = 90
c = 107.982	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-04 
Deposition Author(s): Wang, Y., Qiu, C., Kershner, A., Holley, C.P., Wilinski, D., Keles, S., Kimble, J., Wickens, M., Hall, T.M.T.

Revision History  

• Version 1.0: 2012-01-04
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.2: 2019-08-14
  Changes: Data collection
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Refinement description