3V71

Crystal structure of PUF-6 in complex with 5BE13 RNA

• PDB DOI: https://doi.org/10.2210/pdb3V71/pdb
• NAKB: 3V71

• 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): Qiu, C., Kershner, A., Wang, Y., Holley, C.H., Wilinski, D., Keles, S., Kimble, J., Wickens, M., Hall, T.M.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.241 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 

Starting Model: experimental

Literature

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

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

(2012) J Biol 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: 47.97 kDa 
• Atom Count: 3,089 
• Modelled Residue Count: 371 
• Deposited Residue Count: 395 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Puf (Pumilio/fbf) domain-containing protein 7, confirmed by transcript evidence	A	382	Caenorhabditis elegans	Mutation(s): 0  Gene Names: puf-7, B0273.2
UniProt
Find proteins for O44169 (Caenorhabditis elegans) Explore O44169  Go to UniProtKB:  O44169

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	C [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.241 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.806	α = 90
b = 87.836	β = 90
c = 129.782	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-04 
Deposition Author(s): Qiu, C., Kershner, A., Wang, Y., Holley, C.H., 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: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description