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- EMDB-42291: Structure of the human INTS9-INTS11-BRAT1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-42291
TitleStructure of the human INTS9-INTS11-BRAT1 complex
Map data
Sample
  • Complex: Complex of BRAT1-IntS9-IntS11
    • Protein or peptide: Integrator complex subunit 9
    • Protein or peptide: Integrator complex subunit 11
    • Protein or peptide: BRCA1-associated ATM activator 1
  • Ligand: ZINC ION
KeywordsComplex / Chaperone / Nuclease / RNA BINDING PROTEIN
Function / homology
Function and homology information


integrator complex assembly / ribonuclease inhibitor activity / snRNA 3'-end processing / snRNA processing / INTAC complex / regulation of transcription elongation by RNA polymerase II / mitochondrion localization / integrator complex / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA polymerase II transcription initiation surveillance ...integrator complex assembly / ribonuclease inhibitor activity / snRNA 3'-end processing / snRNA processing / INTAC complex / regulation of transcription elongation by RNA polymerase II / mitochondrion localization / integrator complex / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA polymerase II transcription initiation surveillance / response to ionizing radiation / RNA polymerase II transcribes snRNA genes / protein localization to nucleus / RNA endonuclease activity / negative regulation of transforming growth factor beta receptor signaling pathway / positive regulation of protein phosphorylation / glucose metabolic process / cell migration / positive regulation of cell growth / blood microparticle / cell population proliferation / apoptotic process / DNA damage response / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
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 / Integrator complex assembly factor BRAT1 / Integrator complex subunit 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsLin M / Tong L
Funding support United States, 3 items
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, 2023-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42291.png

Downloads & links

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Map

FileDownload / File: emd_42291.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 280 pix.
= 232.4 Å		0.83 Å/pix.
x 280 pix.
= 232.4 Å		0.83 Å/pix.
x 280 pix.
= 232.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.1749716 - 3.273075
Average (Standard dev.)0.008435485 (±0.0927113)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 232.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_42291_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_42291_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of BRAT1-IntS9-IntS11

EntireName: Complex of BRAT1-IntS9-IntS11
Components
  • Complex: Complex of BRAT1-IntS9-IntS11
    • Protein or peptide: Integrator complex subunit 9
    • Protein or peptide: Integrator complex subunit 11
    • Protein or peptide: BRCA1-associated ATM activator 1
  • Ligand: ZINC ION

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Supramolecule #1: Complex of BRAT1-IntS9-IntS11

SupramoleculeName: Complex of BRAT1-IntS9-IntS11 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 230 KDa

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Macromolecule #1: Integrator complex subunit 9

MacromoleculeName: Integrator complex subunit 9 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 73.891219 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKLYCLSGHP TLPCNVLKFK STTIMLDCGL DMTSTLNFLP LPLVQSPRLS NLPGWSLKDG NAFLDKELKE CSGHVFVDSV PEFCLPETE LIDLSTVDVI LISNYHCMMA LPYITEHTGF TGTVYATEPT VQIGRLLMEE LVNFIERVPK AQSASLWKNK D IQRLLPSP ...String:
MKLYCLSGHP TLPCNVLKFK STTIMLDCGL DMTSTLNFLP LPLVQSPRLS NLPGWSLKDG NAFLDKELKE CSGHVFVDSV PEFCLPETE LIDLSTVDVI LISNYHCMMA LPYITEHTGF TGTVYATEPT VQIGRLLMEE LVNFIERVPK AQSASLWKNK D IQRLLPSP LKDAVEVSTW RRCYTMQEVN SALSKIQLVG YSQKIELFGA VQVTPLSSGY ALGSSNWIIQ SHYEKVSYVS GS SLLTTHP QPMDQASLKN SDVLVLTGLT QIPTANPDGM VGEFCSNLAL TVRNGGNVLV PCYPSGVIYD LLECLYQYID SAG LSSVPL YFISPVANSS LEFSQIFAEW LCHNKQSKVY LPEPPFPHAE LIQTNKLKHY PSIHGDFSND FRQPCVVFTG HPSL RFGDV VHFMELWGKS SLNTVIFTEP DFSYLEALAP YQPLAMKCIY CPIDTRLNFI QVSKLLKEVQ PLHVVCPEQY TQPPP AQSH RMDLMIDCQP PAMSYRRAEV LALPFKRRYE KIEIMPELAD SLVPMEIKPG ISLATVSAVL HTKDNKHLLQ PPPRPA QPT SGKKRKRVSD DVPDCKVLKP LLSGSIPVEQ FVQTLEKHGF SDIKVEDTAK GHIVLLQEAE TLIQIEEDST HIICDND EM LRVRLRDLVL KFLQKF

UniProtKB: Integrator complex subunit 9

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Macromolecule #2: Integrator complex subunit 11

MacromoleculeName: Integrator complex subunit 11 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.756562 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MPEIRVTPLG AGQDVGRSCI LVSIAGKNVM LDCGMHMGFN DDRRFPDFSY ITQNGRLTDF LDCVIISHFH LDHCGALPYF SEMVGYDGP IYMTHPTQAI CPILLEDYRK IAVDKKGEAN FFTSQMIKDC MKKVVAVHLH QTVQVDDELE IKAYYAGHVL G AAMFQIKV ...String:
MPEIRVTPLG AGQDVGRSCI LVSIAGKNVM LDCGMHMGFN DDRRFPDFSY ITQNGRLTDF LDCVIISHFH LDHCGALPYF SEMVGYDGP IYMTHPTQAI CPILLEDYRK IAVDKKGEAN FFTSQMIKDC MKKVVAVHLH QTVQVDDELE IKAYYAGHVL G AAMFQIKV GSESVVYTGD YNMTPDRHLG AAWIDKCRPN LLITESTYAT TIRDSKRCRE RDFLKKVHET VERGGKVLIP VF ALGRAQE LCILLETFWE RMNLKVPIYF STGLTEKANH YYKLFIPWTN QKIRKTFVQR NMFEFKHIKA FDRAFADNPG PMV VFATPG MLHAGQSLQI FRKWAGNEKN MVIMPGYCVQ GTVGHKILSG QRKLEMEGRQ VLEVKMQVEY MSFSAHADAK GIMQ LVGQA EPESVLLVHG EAKKMEFLKQ KIEQELRVNC YMPANGETVT LPTSPSIPVG ISLGLLKREM AQGLLPEAKK PRLLH GTLI MKDSNFRLVS SEQALKELGL AEHQLRFTCR VHLHDTRKEQ ETALRVYSHL KSVLKDHCVQ HLPDGSVTVE SVLLQA AAP SEDPGTKVLL VSWTYQDEEL GSFLTSLLKK GLPQAPS

UniProtKB: Integrator complex subunit 11

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Macromolecule #3: BRCA1-associated ATM activator 1

MacromoleculeName: BRCA1-associated ATM activator 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.195781 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDPECAQLLP ALCAVLVDPR QPVADDTCLE KLLDWFKTVT EGESSVVLLQ EHPCLVELLS HVLKVQDLSS GVLSFSLRLA GTFAAQENC FQYLQQGELL PGLFGEPGPL GRATWAVPTV RSGWIQGLRS LAQHPSALRF LADHGAVDTI FSLQGDSSLF V ASAASQLL ...String:
MDPECAQLLP ALCAVLVDPR QPVADDTCLE KLLDWFKTVT EGESSVVLLQ EHPCLVELLS HVLKVQDLSS GVLSFSLRLA GTFAAQENC FQYLQQGELL PGLFGEPGPL GRATWAVPTV RSGWIQGLRS LAQHPSALRF LADHGAVDTI FSLQGDSSLF V ASAASQLL VHVLALSMRG GAEGQPCLPG GDWPACAQKI MDHVEESLCS AATPKVTQAL NVLTTTFGRC QSPWTEALWV RL SPRVACL LERDPIPAAH SFVDLLLCVA RSPVFSSSDG SLWETVARAL SCLGPTHMGP LALGILKLEH CPQALRTQAF QVL LQPLAC VLKATVQAPG PPGLLDGTAD DATTVDTLLA SKSSCAGLLC RTLAHLEELQ PLPQRPSPWP QASLLGATVT VLRL CDGSA APASSVGGHL CGTLAGCVRV QRAALDFLGT LSQGTGPQEL VTQALAVLLE CLESPGSSPT VLKKAFQATL RWLLS SPKT PGCSDLGPLI PQFLRELFPV LQKRLCHPCW EVRDSALEFL TQLSRHWGGQ ADFRCALLAS EVPQLALQLL QDPESY VRA SAVTAMGQLS SQGLHAPTSP EHAEARQSLF LELLHILSVD SEGFPRRAVM QVFTEWLRDG HADAAQDTEQ FVATVLQ AA SRDLDWEVRA QGLELALVFL GQTLGPPRTH CPYAVALPEV APAQPLTEAL RALCHVGLFD FAFCALFDCD RPVAQKSC D LLLFLRDKIA SYSSLREARG SPNTASAEAT LPRWRAGEQA QPPGDQEPEA VLAMLRSLDL EGLRSTLAES SDHVEKSPQ SLLQDMLATG GFLQGDEADC Y

UniProtKB: Integrator complex assembly factor BRAT1

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.3 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1112411
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AlphaFold prediction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 185172
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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