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- EMDB-18834: INTS9-INTS11-BRAT1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-18834
TitleINTS9-INTS11-BRAT1 complex
Map dataOverall map
Sample
  • Complex: INTS9-INTS11-BRAT1 complex
    • Protein or peptide: BRCA1-associated ATM activator 1
    • Protein or peptide: Integrator complex subunit 9
    • Protein or peptide: Integrator complex subunit 11
  • Ligand: ZINC ION
KeywordsChaperone / Integrator complex / nuclear import / TRANSCRIPTION
Function / homology
Function and homology information


snRNA 3'-end processing / snRNA processing / mitochondrion localization / regulation of transcription elongation by RNA polymerase II / integrator complex / 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 / regulation of transcription elongation by RNA polymerase II / integrator complex / 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 protein phosphorylation / positive regulation of cell growth / blood microparticle / cell population proliferation / apoptotic process / DNA damage response / nucleoplasm / nucleus / membrane / 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 / Integrator complex assembly factor BRAT1 / Integrator complex subunit 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSabath K / Qiu C / Jonas S
Funding support Switzerland, European Union, 8 items
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, 2023-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18834.png

Downloads & links

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Map

FileDownload / File: emd_18834.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOverall map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 220 pix.
= 290.4 Å		1.32 Å/pix.
x 220 pix.
= 290.4 Å		1.32 Å/pix.
x 220 pix.
= 290.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0171
Minimum - Maximum-0.06447115 - 0.114050046
Average (Standard dev.)0.0001171448 (±0.0021618048)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 290.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1

Fileemd_18834_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_18834_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : INTS9-INTS11-BRAT1 complex

EntireName: INTS9-INTS11-BRAT1 complex
Components
  • Complex: INTS9-INTS11-BRAT1 complex
    • Protein or peptide: BRCA1-associated ATM activator 1
    • Protein or peptide: Integrator complex subunit 9
    • Protein or peptide: Integrator complex subunit 11
  • Ligand: ZINC ION

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Supramolecule #1: INTS9-INTS11-BRAT1 complex

SupramoleculeName: INTS9-INTS11-BRAT1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: BRCA1-associated ATM activator 1

MacromoleculeName: BRCA1-associated ATM activator 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.766328 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPSQSNMDPE CAQLLPALCA VLVDPRQPVA DDTCLEKLLD WFKTVTEGES SVVLLQEHPC LVELLSHVLK VQDLSSGVLS FSLRLAGTF AAQENCFQYL QQGELLPGLF GEPGPLGRAT WAVPTVRSGW IQGLRSLAQH PSALRFLADH GAVDTIFSLQ G DSSLFVAS ...String:
GPSQSNMDPE CAQLLPALCA VLVDPRQPVA DDTCLEKLLD WFKTVTEGES SVVLLQEHPC LVELLSHVLK VQDLSSGVLS FSLRLAGTF AAQENCFQYL QQGELLPGLF GEPGPLGRAT WAVPTVRSGW IQGLRSLAQH PSALRFLADH GAVDTIFSLQ G DSSLFVAS AASQLLVHVL ALSMRGGAEG QPCLPGGDWP ACAQKIMDHV EESLCSAATP KVTQALNVLT TTFGRCQSPW TE ALWVRLS PRVACLLERD PIPAAHSFVD LLLCVARSPV FSSSDGSLWE TVARALSCLG PTHMGPLALG ILKLEHCPQA LRT QAFQVL LQPLACVLKA TVQAPGPPGL LDGTADDATT VDTLLASKSS CAGLLCRTLA HLEELQPLPQ RPSPWPQASL LGAT VTVLR LCDGSAAPAS SVGGHLCGTL AGCVRVQRAA LDFLGTLSQG TGPQELVTQA LAVLLECLES PGSSPTVLKK AFQAT LRWL LSSPKTPGCS DLGPLIPQFL RELFPVLQKR LCHPCWEVRD SALEFLTQLS RHWGGQADFR CALLASEVPQ LALQLL QDP ESYVRASAVT AMGQLSSQGL HAPTSPEHAE ARQSLFLELL HILSVDSEGF PRRAVMQVFT EWLRDGHADA AQDTEQF VA TVLQAASRDL DWEVRAQGLE LALVFLGQTL GPPRTHCPYA VALPEVAPAQ PLTEALRALC HVGLFDFAFC ALFDCDRP V AQKSCDLLLF LRDKIASYSS LREARGSPNT ASAEATLPRW RAGEQAQPPG DQEPEAVLAM LRSLDLEGLR STLAESSDH VEKSPQSLLQ DMLATGGFLQ GDEADCY

UniProtKB: Integrator complex assembly factor BRAT1

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Macromolecule #2: Integrator complex subunit 9

MacromoleculeName: Integrator complex subunit 9 / type: protein_or_peptide / ID: 2 / 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 #3: Integrator complex subunit 11

MacromoleculeName: Integrator complex subunit 11 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.997906 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPSDPGPKRA EFMPEIRVTP LGAGQDVGRS CILVSIAGKN VMLDCGMHMG FNDDRRFPDF SYITQNGRLT DFLDCVIISH FHLDHCGAL PYFSEMVGYD GPIYMTHPTQ AICPILLEDY RKIAVDKKGE ANFFTSQMIK DCMKKVVAVH LHQTVQVDDE L EIKAYYAG ...String:
GPSDPGPKRA EFMPEIRVTP LGAGQDVGRS CILVSIAGKN VMLDCGMHMG FNDDRRFPDF SYITQNGRLT DFLDCVIISH FHLDHCGAL PYFSEMVGYD GPIYMTHPTQ AICPILLEDY RKIAVDKKGE ANFFTSQMIK DCMKKVVAVH LHQTVQVDDE L EIKAYYAG HVLGAAMFQI KVGSESVVYT GDYNMTPDRH LGAAWIDKCR PNLLITESTY ATTIRDSKRC RERDFLKKVH ET VERGGKV LIPVFALGRA QELCILLETF WERMNLKVPI YFSTGLTEKA NHYYKLFIPW TNQKIRKTFV QRNMFEFKHI KAF DRAFAD NPGPMVVFAT PGMLHAGQSL QIFRKWAGNE KNMVIMPGYC VQGTVGHKIL SGQRKLEMEG RQVLEVKMQV EYMS FSAHA DAKGIMQLVG QAEPESVLLV HGEAKKMEFL KQKIEQELRV NCYMPANGET VTLPTSPSIP VGISLGLLKR EMAQG LLPE AKKPRLLHGT LIMKDSNFRL VSSEQALKEL GLAEHQLRFT CRVHLHDTRK EQETALRVYS HLKSVLKDHC VQHLPD GSV TVESVLLQAA APSEDPGTKV LLVSWTYQDE ELGSFLTSLL KKGLPQAPS

UniProtKB: Integrator complex subunit 11

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 63.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.4 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 255744
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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