5M9D | pdb_00005m9d

Solution structure of Rtt103 CTD-interacting domain bound to a Ser2Ser7 phosphorylated CTD peptide


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 5M9D

This is version 1.3 of the entry. See complete history

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

  • DOI: https://doi.org/10.1073/pnas.1712450114
  • Primary Citation 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.


  • Organizational Affiliation
    • CEITEC-Central European Institute of Technology, Masaryk University, CZ-62500 Brno, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 18.53 kDa 
  • Atom Count: 1,257 
  • Modeled Residue Count: 154 
  • Deposited Residue Count: 158 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Regulator of Ty1 transposition protein 103142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RTT103YDR289C
UniProt
Find proteins for Q05543 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q05543 
Go to UniProtKB:  Q05543
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05543
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER16Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P04050 
Go to UniProtKB:  P04050
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04050
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
B
L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council649030
Czech Science FoundationCzech Republic13-18344S

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Structure summary