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- EMDB-42292: Structure of the Drosophila IntS11-CG7044(dBRAT1) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-42292
TitleStructure of the Drosophila IntS11-CG7044(dBRAT1) complex
Map data
Sample
  • Complex: Complex of Drosophila IntS11 and CG7044
    • Protein or peptide: Integrator complex subunit 11
    • Protein or peptide: FI02071p
  • Ligand: ZINC ION
KeywordsComplex / Chaperone / Nuclease / RNA BINDING PROTEIN
Function / homology
Function and homology information


RNA polymerase II transcribes snRNA genes / snRNA 3'-end processing / snRNA processing / integrator complex / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / cell population proliferation / DNA damage response / nucleus / cytosol / cytoplasm
Similarity search - Function
BRCA1-associated ATM activator 1 / 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 ...BRCA1-associated ATM activator 1 / 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 / 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 / FI02071p
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 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-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42292.png

Downloads & links

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Map

FileDownload / File: emd_42292.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 277.248 Å		1.08 Å/pix.
x 256 pix.
= 277.248 Å		1.08 Å/pix.
x 256 pix.
= 277.248 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.82
Minimum - Maximum-3.3000658 - 4.507874
Average (Standard dev.)-0.00007382852 (±0.10851145)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 277.248 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_42292_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_42292_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Drosophila IntS11 and CG7044

EntireName: Complex of Drosophila IntS11 and CG7044
Components
  • Complex: Complex of Drosophila IntS11 and CG7044
    • Protein or peptide: Integrator complex subunit 11
    • Protein or peptide: FI02071p
  • Ligand: ZINC ION

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Supramolecule #1: Complex of Drosophila IntS11 and CG7044

SupramoleculeName: Complex of Drosophila IntS11 and CG7044 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 180 KDa

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Macromolecule #1: Integrator complex subunit 11

MacromoleculeName: Integrator complex subunit 11 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 67.683922 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MPDIKITPLG AGQDVGRSCL LLSMGGKNIM LDCGMHMGYN DERRFPDFSY IVPEGPITSH IDCVIISHFH LDHCGALPYM SEIVGYTGP IYMTHPTKAI APILLEDMRK VAVERKGESN FFTTQMIKDC MKKVIPVTLH QSMMVDTDLE IKAYYAGHVL G AAMFWIKV ...String:
MPDIKITPLG AGQDVGRSCL LLSMGGKNIM LDCGMHMGYN DERRFPDFSY IVPEGPITSH IDCVIISHFH LDHCGALPYM SEIVGYTGP IYMTHPTKAI APILLEDMRK VAVERKGESN FFTTQMIKDC MKKVIPVTLH QSMMVDTDLE IKAYYAGHVL G AAMFWIKV GSQSVVYTGD YNMTPDRHLG AAWIDKCRPD LLISESTYAT TIRDSKRCRE RDFLKKVHEC VAKGGKVLIP VF ALGRAQE LCILLETYWE RMNLKYPIYF ALGLTEKANT YYKMFITWTN QKIRKTFVHR NMFDFKHIKP FDKAYIDNPG AMV VFATPG MLHAGLSLQI FKKWAPNENN MVIMPGYCVQ GTVGNKILGG AKKVEFENRQ VVEVKMAVEY MSFSAHADAK GIMQ LIQNC EPKNVMLVHG EAGKMKFLRS KIKDEFNLET YMPANGETCV ISTPVKIPVD ASVSLLKAEA RSYNAQPPDP KRRRL IHGV LVMKDNRIML QNLTDALKEI GINRHVMRFT SKVKMDDSGP VIRTSERLKT LLEEKLAGWT VTMQENGSIA IESVEV KVE EDEKDPKQKN ILISWTNQDE DIGAYILNVL QNMC

UniProtKB: Integrator complex subunit 11

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Macromolecule #2: FI02071p

MacromoleculeName: FI02071p / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 113.151703 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MQKQEETLSR LRTIFDIFLR ENFSTTNNVY FEKLLTHLQA KENAFVLQAP FVVEWVDRCI TAVTEDFKKI HPKVISFMLN LTSFLANNE WMIVRLRELD IVNRAVKLLQ REHNLSPSIK LGGIRLMKAI TVYSMGLAFL RMHRIWTLLI QYSNNDHTLY V VREARQVL ...String:
MQKQEETLSR LRTIFDIFLR ENFSTTNNVY FEKLLTHLQA KENAFVLQAP FVVEWVDRCI TAVTEDFKKI HPKVISFMLN LTSFLANNE WMIVRLRELD IVNRAVKLLQ REHNLSPSIK LGGIRLMKAI TVYSMGLAFL RMHRIWTLLI QYSNNDHTLY V VREARQVL YNMVYKSCDK LHDKAVTLEI LSEIMQPIHD NLYKNTDGVE RIHVKVDDNE MLHKISSTLD LLSYILQQTL VL EERTTLI ILLKEHHDFE ITVWKLIDMT HNPYFTEKIF TTLSSYNFAL LLHEKLLNPN ATEPSEEFTE FGLAFFNLMK FLI TRKDGL SFVKLAELNH VLWKKLGPRA PKEIVIQQER VTFENQLICF HMLPLLFSMK YAQKIADEES KIELFDAYVV KLLE ISCEQ TLRLCYTMRD NFFSADGMAV GLVTAGLANK CIHSLLALEN VLDREQAVTV CQALLYVLRE AVAMSVITNN GEDDC HSVS SAGSSYLKLY PRGTEQVVND PQVLHSVMVG LRTLIERFKI TWKESVETIG LVNCLAFVLE NTSMDARCTV QALKLV QLA VEHFLSPNMA LLVDNLQGSA LVCLGPIIVK RMHDTMWEVR DTTLELTTSI ASISRIKFPA FQRFLIDSKI PPIVYEM AK NDSEVYVRAS AFQCLSQMVS INLLWENGLS QLDLVDHLLF VMYRETNDIV RSEAVITLMK IYEHRKIHEK YKNTLFST L NYCVIGDHHT EVKLNALNFW RREFYRQFSN QGMIDGSFPT VTFSKEQKKI VTLTEKEIQT SIAKVFGEVQ QYGYFGILL KCLREETSME VLEFLIKGVK TMTEKFERYK GIMEEIEMRS PLSDRERPRF DFPSQPQPTP IPQQPPVNPT EADEVIESIL NSQDAQLLE KAFETQMQIN AQGKTAEKRH IDEFYYKQFA VPLRQFFEEL KTIDLDQLVK QHQEWFECKE NFTSLLDDIL G ALKRDDEN MISDCY

UniProtKB: FI02071p

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / 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

Concentration0.18 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: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2028174
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AlphaFold prediction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 406222
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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