Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

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

Macromolecule Content

• Total Structure Weight: 13.82 kDa 
• Atom Count: 978 
• Modelled Residue Count: 114 
• Deposited Residue Count: 115 
• Unique protein chains: 1

5M48

Coiled coil domain of Rtt103p

• PDB DOI: 10.2210/pdb5M48/pdb

• Classification: TRANSCRIPTION
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-10-18 Released: 2017-10-11 
• Deposition Author(s): Jasnovidova, O., Kalynych, S., Plevka, P., Stefl, R.
• Funding Organization(s): European Union, European Molecular Biology Organization, European Research Council, Czech Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.264 
• R-Value Work: 0.245 
• R-Value Observed: 0.247 

Literature

Structure and dynamics of the RNAPII CTDsome with Rtt103.

Jasnovidova, O., Klumpler, T., Kubicek, K., Kalynych, S., Plevka, P., Stefl, R.

(2017) Proc Natl Acad Sci U S A 114: 11133-11138

• PubMed: 29073019 
• DOI: 10.1073/pnas.1712450114
• Primary Citation of Related Structures:  
  5M48, 5M9D


• PubMed Abstract: 
  

RNA polymerase II contains a long C-terminal domain (CTD) that regulates interactions at the site of transcription. The CTD architecture remains poorly understood due to its low sequence complexity, dynamic phosphorylation patterns, and structural variability. We used integrative structural biology to visualize the architecture of the CTD in complex with Rtt103, a 3'-end RNA-processing and transcription termination factor. Rtt103 forms homodimers via its long coiled-coil domain and associates densely on the repetitive sequence of the phosphorylated CTD via its N-terminal CTD-interacting domain. The CTD-Rtt103 association opens the compact random coil structure of the CTD, leading to a beads-on-a-string topology in which the long rod-shaped Rtt103 dimers define the topological and mobility restraints of the entire assembly. These findings underpin the importance of the structural plasticity of the CTD, which is templated by a particular set of CTD-binding proteins.

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Organizational Affiliation: 

CEITEC-Central European Institute of Technology, Masaryk University, CZ-62500 Brno, Czech Republic [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Regulator of Ty1 transposition protein 103	A	115	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RTT103, YDR289C
UniProt
Find proteins for Q05543 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05543  Go to UniProtKB:  Q05543

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.264 
• R-Value Work: 0.245 
• R-Value Observed: 0.247 
• Space Group: F 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 217.141	α = 90
b = 217.141	β = 90
c = 217.141	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-10-18 
• Released Date: 2017-10-11 
Deposition Author(s): Jasnovidova, O., Kalynych, S., Plevka, P., Stefl, R.

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Funding Organization	Location	Grant Number
European Union		355855
European Molecular Biology Organization		3041
European Research Council		649030
Czech Science Foundation	Czech Republic	13-18344S

Revision History  

• Version 1.0: 2017-10-11
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Database references