3MD3

Crystal Structure of the First Two RRM Domains of Yeast Poly(U) Binding Protein (Pub1)

• PDB DOI: https://doi.org/10.2210/pdb3MD3/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2010-03-29 Released: 2010-05-05 
• Deposition Author(s): Li, H., Shi, H., Zhu, Z., Wang, H., Niu, L., Teng, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.268 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 

Literature

Crystal Structure of the First Two RRM Domains of Yeast Poly(U) Binding Protein (Pub1)

Li, H., Shi, H., Zhu, Z., Wang, H., Niu, L., Teng, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 20.3 kDa 
• Atom Count: 1,485 
• Modelled Residue Count: 165 
• Deposited Residue Count: 166 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1	A	166	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32588 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32588  Go to UniProtKB:  P32588

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.268 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.615	α = 90
b = 57.615	β = 90
c = 237.082	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-05 
Deposition Author(s): Li, H., Shi, H., Zhu, Z., Wang, H., Niu, L., Teng, M.

Revision History  

• Version 1.0: 2010-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations