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- PDB-8r23: INTS9-INTS11-BRAT1 complex -

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Basic information

Entry
Database: PDB / ID: 8r23
TitleINTS9-INTS11-BRAT1 complex
Components
  • BRCA1-associated ATM activator 1
  • Integrator complex subunit 11
  • Integrator complex subunit 9
KeywordsTRANSCRIPTION / Chaperone / Integrator complex / nuclear import
Function / homology
Function and homology information


snRNA 3'-end processing / snRNA processing / mitochondrion localization / integrator complex / regulation of transcription elongation by RNA polymerase II / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / response to ionizing radiation / RNA polymerase II transcribes snRNA genes / RNA endonuclease activity / negative regulation of transforming growth factor beta receptor signaling pathway ...snRNA 3'-end processing / snRNA processing / mitochondrion localization / integrator complex / regulation of transcription elongation by RNA polymerase II / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / response to ionizing radiation / RNA polymerase II transcribes snRNA genes / RNA endonuclease activity / negative regulation of transforming growth factor beta receptor signaling pathway / glucose metabolic process / cell migration / positive regulation of cell growth / cell population proliferation / blood microparticle / positive regulation of protein phosphorylation / apoptotic process / DNA damage response / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
BRCA1-associated ATM activator 1 / : / : / Integrator IntS9, C-terminal domain / Integrator IntS11, C-terminal domain / Integrator complex subunit 9 / Integrator complex subunit 11, MBL-fold / Metallo-beta-lactamase superfamily domain / Beta-Casp domain / Beta-Casp domain ...BRCA1-associated ATM activator 1 / : / : / Integrator IntS9, C-terminal domain / Integrator IntS11, C-terminal domain / Integrator complex subunit 9 / Integrator complex subunit 11, MBL-fold / Metallo-beta-lactamase superfamily domain / Beta-Casp domain / Beta-Casp domain / Beta-Casp domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / HEAT repeat / HEAT repeat / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Integrator complex subunit 11 / BRCA1-associated ATM activator 1 / Integrator complex subunit 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSabath, K. / Qiu, C. / Jonas, S.
Funding support Switzerland, European Union, 8items
OrganizationGrant numberCountry
Swiss National Science Foundation141735 Switzerland
Swiss National Science Foundation182880 Switzerland
Swiss National Science Foundation205601 Switzerland
Swiss National Science Foundation31003A_179498 Switzerland
Other governmentMB22.00064
European Molecular Biology Organization (EMBO)4918European Union
Other governmentETH-31 18-1
OthKevin Sabath
CitationJournal: Mol Cell / Year: 2024
Title: Assembly mechanism of Integrator's RNA cleavage module.
Authors: Kevin Sabath / Chunhong Qiu / Stefanie Jonas /
Abstract: The modular Integrator complex is a transcription regulator that is essential for embryonic development. It attenuates coding gene expression via premature transcription termination and performs 3'- ...The modular Integrator complex is a transcription regulator that is essential for embryonic development. It attenuates coding gene expression via premature transcription termination and performs 3'-processing of non-coding RNAs. For both activities, Integrator requires endonuclease activity that is harbored by an RNA cleavage module consisting of INTS4-9-11. How correct assembly of Integrator modules is achieved remains unknown. Here, we show that BRAT1 and WDR73 are critical biogenesis factors for the human cleavage module. They maintain INTS9-11 inactive during maturation by physically blocking the endonuclease active site and prevent premature INTS4 association. Furthermore, BRAT1 facilitates import of INTS9-11 into the nucleus, where it is joined by INTS4. Final BRAT1 release requires locking of the mature cleavage module conformation by inositol hexaphosphate (IP). Our data explain several neurodevelopmental disorders caused by BRAT1, WDR73, and INTS11 mutations as Integrator assembly defects and reveal that IP is an essential co-factor for cleavage module maturation.
History
DepositionNov 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BRCA1-associated ATM activator 1
B: Integrator complex subunit 9
C: Integrator complex subunit 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,7865
Polymers231,6553
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein BRCA1-associated ATM activator 1


Mass: 88766.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRAT1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6PJG6
#2: Protein Integrator complex subunit 9 / Int9 / Protein related to CPSF subunits of 74 kDa / RC-74


Mass: 73891.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS9, RC74 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NV88
#3: Protein Integrator complex subunit 11


Mass: 68997.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS11 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5TA45
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: INTS9-INTS11-BRAT1 complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3400 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 63.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 255744 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00312244
ELECTRON MICROSCOPYf_angle_d0.52416635
ELECTRON MICROSCOPYf_dihedral_angle_d6.6957373
ELECTRON MICROSCOPYf_chiral_restr0.0391932
ELECTRON MICROSCOPYf_plane_restr0.0052121

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