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- PDB-8uib: Structure of the human INTS9-INTS11-BRAT1 complex -

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Basic information

Entry
Database: PDB / ID: 8uib
TitleStructure of the human INTS9-INTS11-BRAT1 complex
Components
  • BRCA1-associated ATM activator 1
  • Integrator complex subunit 11
  • Integrator complex subunit 9
KeywordsRNA BINDING PROTEIN / Complex / Chaperone / Nuclease
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 / blood microparticle / cell population proliferation / positive regulation of protein phosphorylation / DNA damage response / apoptotic process / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
BRCA1-associated ATM activator 1 / Integrator complex subunit 9 / : / Integrator IntS9, C-terminal domain / Integrator complex subunit 11, MBL-fold / : / Integrator IntS11, C-terminal domain / Metallo-beta-lactamase superfamily domain / : / Beta-Casp domain ...BRCA1-associated ATM activator 1 / Integrator complex subunit 9 / : / Integrator IntS9, C-terminal domain / Integrator complex subunit 11, MBL-fold / : / Integrator IntS11, C-terminal domain / 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: 3.21 Å
AuthorsLin, M. / Tong, L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM134539 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118093 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP170593 United States
CitationJournal: Mol Cell / Year: 2024
Title: Cytoplasmic binding partners of the Integrator endonuclease INTS11 and its paralog CPSF73 are required for their nuclear function.
Authors: Min-Han Lin / Madeline K Jensen / Nathan D Elrod / Hsu-Feng Chu / MaryClaire Haseley / Alissa C Beam / Kai-Lieh Huang / Wesley Chiang / William K Russell / Kelsey Williams / Christoph ...Authors: Min-Han Lin / Madeline K Jensen / Nathan D Elrod / Hsu-Feng Chu / MaryClaire Haseley / Alissa C Beam / Kai-Lieh Huang / Wesley Chiang / William K Russell / Kelsey Williams / Christoph Pröschel / Eric J Wagner / Liang Tong /
Abstract: INTS11 and CPSF73 are metal-dependent endonucleases for Integrator and pre-mRNA 3'-end processing, respectively. Here, we show that the INTS11 binding partner BRAT1/CG7044, a factor important for ...INTS11 and CPSF73 are metal-dependent endonucleases for Integrator and pre-mRNA 3'-end processing, respectively. Here, we show that the INTS11 binding partner BRAT1/CG7044, a factor important for neuronal fitness, stabilizes INTS11 in the cytoplasm and is required for Integrator function in the nucleus. Loss of BRAT1 in neural organoids leads to transcriptomic disruption and precocious expression of neurogenesis-driving transcription factors. The structures of the human INTS9-INTS11-BRAT1 and Drosophila dIntS11-CG7044 complexes reveal that the conserved C terminus of BRAT1/CG7044 is captured in the active site of INTS11, with a cysteine residue directly coordinating the metal ions. Inspired by these observations, we find that UBE3D is a binding partner for CPSF73, and UBE3D likely also uses a conserved cysteine residue to directly coordinate the active site metal ions. Our studies have revealed binding partners for INTS11 and CPSF73 that behave like cytoplasmic chaperones with a conserved impact on the nuclear functions of these enzymes.
History
DepositionOct 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Integrator complex subunit 9
K: Integrator complex subunit 11
T: BRCA1-associated ATM activator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,9745
Polymers229,8443
Non-polymers1312
Water00
1


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

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Components

#1: Protein Integrator complex subunit 9


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


Mass: 67756.562 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
#3: Protein BRCA1-associated ATM activator 1


Mass: 88195.781 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
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: Complex of BRAT1-IntS9-IntS11 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.230 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 1300 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 58.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1112411
3D reconstructionResolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 185172 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00612129
ELECTRON MICROSCOPYf_angle_d0.84816467
ELECTRON MICROSCOPYf_dihedral_angle_d14.8311616
ELECTRON MICROSCOPYf_chiral_restr0.0511911
ELECTRON MICROSCOPYf_plane_restr0.0062094

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