3GVT

Structure and RNA binding of the mouse Pumilio-2 Puf Domain

• PDB DOI: https://doi.org/10.2210/pdb3GVT/pdb

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


• Deposited: 2009-03-31 Released: 2009-06-30 
• Deposition Author(s): Jenkins, H.T., Edwards, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.253 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 

Starting Model: experimental

Literature

Structure and RNA binding of the mouse Pumilio-2 Puf domain

Jenkins, H.T., Baker-Wilding, R., Edwards, T.A.

(2009) J Struct Biol 167: 271-276

• PubMed: 19540345 
• DOI: https://doi.org/10.1016/j.jsb.2009.06.007
• Primary Citation of Related Structures:  
  3GVO, 3GVT


• PubMed Abstract: 
  

  Puf proteins control translation through the interaction of a C-terminal Puf domain with specific sequences present in the 3' untranslated region of messenger RNAs. In Drosophila, binding of the protein Pumilio to mRNA leads to translational repression which is required for anterior/posterior patterning during embryogenesis. The vertebrate Pumilio homologue 2 (Pum2) has been implicated in controlling germ cell development through interactions with the RNA binding proteins deleted in azoospermia (DAZ), DAZ-like (DAZL) and BOULE. We present the 1.6A resolution X-ray crystal structure of the Puf domain from murine Pum2 and demonstrate that this domain is capable of binding with nanomolar affinity to RNA sequences from the hunchback Nanos response element (NRE) and a previously identified Pum2 binding element (PBE).

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Organizational Affiliation: 

Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.

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: 81.24 kDa 
• Atom Count: 5,658 
• Modelled Residue Count: 684 
• Deposited Residue Count: 702 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pumilio homolog 2	A, B	351	Mus musculus	Mutation(s): 0  Gene Names: Pum2
UniProt & NIH Common Fund Data Resources
Find proteins for Q80U58 (Mus musculus) Explore Q80U58  Go to UniProtKB:  Q80U58
IMPC:  MGI:1931751

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTT	C [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.253 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.54	α = 90
b = 150.54	β = 90
c = 77.22	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-30 
Deposition Author(s): Jenkins, H.T., Edwards, T.A.

Revision History  

• Version 1.0: 2009-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description