5V8W

Crystal structure of human Integrator IntS9-IntS11 CTD complex

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli

  • Deposited: 2017-03-22 Released: 2017-04-12 
  • Deposition Author(s): Wu, Y., Tong, L.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences; National Institutes of Health/Office of the Director 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular basis for the interaction between Integrator subunits IntS9 and IntS11 and its functional importance.

Wu, Y.Albrecht, T.R.Baillat, D.Wagner, E.J.Tong, L.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 4394-4399

  • DOI: 10.1073/pnas.1616605114

  • PubMed Abstract: 
  • The metazoan Integrator complex (INT) has important functions in the 3'-end processing of noncoding RNAs, including the uridine-rich small nuclear RNA (UsnRNA) and enhancer RNA (eRNA), and in the transcription of coding genes by RNA polymerase II. Th ...

    The metazoan Integrator complex (INT) has important functions in the 3'-end processing of noncoding RNAs, including the uridine-rich small nuclear RNA (UsnRNA) and enhancer RNA (eRNA), and in the transcription of coding genes by RNA polymerase II. The INT contains at least 14 subunits, but its molecular mechanism of action is poorly understood, because currently there is little structural information about its subunits. The endonuclease activity of INT is mediated by its subunit 11 (IntS11), which belongs to the metallo-β-lactamase superfamily and is a paralog of CPSF-73, the endonuclease for pre-mRNA 3'-end processing. IntS11 forms a stable complex with Integrator complex subunit 9 (IntS9) through their C-terminal domains (CTDs). Here, we report the crystal structure of the IntS9-IntS11 CTD complex at 2.1-Å resolution and detailed, structure-based biochemical and functional studies. The complex is composed of a continuous nine-stranded β-sheet with four strands from IntS9 and five from IntS11. Highly conserved residues are located in the extensive interface between the two CTDs. Yeast two-hybrid assays and coimmunoprecipitation experiments confirm the structural observations on the complex. Functional studies demonstrate that the IntS9-IntS11 interaction is crucial for the role of INT in snRNA 3'-end processing.


    Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, NY 10027.,Department of Biological Sciences, Columbia University, New York, NY 10027; ltong@columbia.edu ejwagner@utmb.edu.,Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77550.,Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77550 ltong@columbia.edu ejwagner@utmb.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrator complex subunit 9
A, C, E, G
78Homo sapiensMutation(s): 0 
Gene Names: INTS9 (RC74)
Find proteins for Q9NV88 (Homo sapiens)
Go to Gene View: INTS9
Go to UniProtKB:  Q9NV88
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Integrator complex subunit 11
B, D, F, H
114Homo sapiensMutation(s): 0 
Gene Names: INTS11 (CPSF3L, RC68)
EC: 3.1.27.-
Find proteins for Q5TA45 (Homo sapiens)
Go to Gene View: INTS11
Go to UniProtKB:  Q5TA45
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.010α = 90.00
b = 67.780β = 100.65
c = 98.585γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
AutoSolphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-03-22 
  • Released Date: 2017-04-12 
  • Deposition Author(s): Wu, Y., Tong, L.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR35GM118093
National Institutes of Health/Office of the DirectorUnited StatesS10OD012018

Revision History 

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-04-26
    Type: Database references
  • Version 1.2: 2017-05-10
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence