5I2T | pdb_00005i2t

Domain characterization of the WD protein Pwp2 and their relevance in ribosome biogenesis

• PDB DOI: https://doi.org/10.2210/pdb5I2T/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-02-09 Released: 2017-06-21 
• Deposition Author(s): Fribourg, S., Boissier, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 
  0.252 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Pwp2 mediates UTP-B assembly via two structurally independent domains.

Boissier, F., Schmidt, C.M., Linnemann, J., Fribourg, S., Perez-Fernandez, J.

(2017) Sci Rep 7: 3169-3169

• PubMed: 28600509 
• DOI: https://doi.org/10.1038/s41598-017-03034-y
• Primary Citation Related Structures: 
  5I2T


• PubMed Abstract: 
  

  The SSU processome constitutes a large ribonucleoprotein complex involved in the early steps of ribosome biogenesis. UTP-B is one of the first multi-subunit protein complexes that associates with the pre-ribosomal RNA to form the SSU processome. To understand the molecular basis of the hierarchical assembly of the SSU-processome, we have undergone a structural and functional analysis of the UTP-B subunit Pwp2p. We show that Pwp2p is required for the proper assembly of UTP-B and for a productive association of UTP-B with pre-rRNA. These two functions are mediated by two distinct structural domains. The N-terminal domain of Pwp2p folds into a tandem WD-repeat (tWD) that associates with Utp21p, Utp18p, and Utp6p to form a core complex. The CTDs of Pwp2p and Utp21p mediate the assembly of the heterodimer Utp12p:Utp13p that is required for the stable incorporation of the UTP-B complex in the SSU processome. Finally, we provide evidence suggesting a role of UTP-B as a platform for the binding of assembly factors during the maturation of 20S rRNA precursors.

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Organizational Affiliation: 
• Université de Bordeaux, INSERM U1212, CNRS 5320, Bordeaux, France.
Universität Regensburg, Biochemie-Zentrum Regensburg (BZR), Lehrstuhl Biochemie III, D-93053, Regensburg, Germany.
Université de Bordeaux, INSERM U1212, CNRS 5320, Bordeaux, France. [e-mail].
Universität Regensburg, Biochemie-Zentrum Regensburg (BZR), Lehrstuhl Biochemie III, D-93053, Regensburg, Germany. [e-mail].

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: 83.42 kDa 
• Atom Count: 4,839 
• Modeled Residue Count: 606 
• Deposited Residue Count: 742 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periodic tryptophan protein 2	A	742	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: PWP2, UTP1, YCR057C, YCR55C/YCR57C/YCR58C
UniProt
Find proteins for P25635 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25635  Go to UniProtKB:  P25635

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free:  0.252 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.83	α = 90
b = 76.04	β = 90
c = 191.35	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-21 
Deposition Author(s): Fribourg, S., Boissier, F.

Revision History  

• Version 1.0: 2017-06-21
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description