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- EMDB-18839: Integrator cleavage module assembly intermediate -

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Basic information

Entry
Database: EMDB / ID: EMD-18839
TitleIntegrator cleavage module assembly intermediate
Map data
Sample
  • Complex: INTS4-INTS9-INTS11-BRAT1 complex
    • Protein or peptide: BRCA1-associated ATM activator 1
    • Protein or peptide: Integrator complex subunit 11
    • Protein or peptide: Integrator complex subunit 4
    • Protein or peptide: Integrator complex subunit 9
  • Ligand: ZINC ION
Keywordschaperone / Integrator complex / nuclear import / TRANSCRIPTION
Function / homology
Function and homology information


intercellular transport / 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 ...intercellular transport / 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 / endosome / positive regulation of protein phosphorylation / apoptotic process / DNA damage response / nucleolus / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
BRCA1-associated ATM activator 1 / : / : / Sister chromatid cohesion protein PDS5 protein / 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 ...BRCA1-associated ATM activator 1 / : / : / Sister chromatid cohesion protein PDS5 protein / 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 / HEAT repeats / 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 4 / Integrator complex subunit 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsSabath K / Qiu C / Jonas S
Funding support Switzerland, European Union, Germany, 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
Swiss State Secretariat for Education, Research and InnovationMB22.00064 Switzerland
European Molecular Biology Organization (EMBO)4918European Union
ETH ZurichETH-31 18-1 Switzerland
German Academic Scholarship FoundationKevin Sabath Germany
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 3, 2023-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_18839.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 230 pix.
= 298.08 Å
1.3 Å/pix.
x 230 pix.
= 298.08 Å
1.3 Å/pix.
x 230 pix.
= 298.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.296 Å
Density
Contour LevelBy AUTHOR: 0.324
Minimum - Maximum-1.934148 - 3.117966
Average (Standard dev.)0.002553418 (±0.056045085)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions230230230
Spacing230230230
CellA=B=C: 298.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Locally refined cryo-EM map around INTS4-INTS9

Fileemd_18839_additional_1.map
AnnotationLocally refined cryo-EM map around INTS4-INTS9
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_18839_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_18839_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : INTS4-INTS9-INTS11-BRAT1 complex

EntireName: INTS4-INTS9-INTS11-BRAT1 complex
Components
  • Complex: INTS4-INTS9-INTS11-BRAT1 complex
    • Protein or peptide: BRCA1-associated ATM activator 1
    • Protein or peptide: Integrator complex subunit 11
    • Protein or peptide: Integrator complex subunit 4
    • Protein or peptide: Integrator complex subunit 9
  • Ligand: ZINC ION

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Supramolecule #1: INTS4-INTS9-INTS11-BRAT1 complex

SupramoleculeName: INTS4-INTS9-INTS11-BRAT1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3-#4, #2
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: BRCA1-associated ATM activator 1

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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: Integrator complex subunit 4

MacromoleculeName: Integrator complex subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 109.271836 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPSDPGPKRA MAAHLKKRVY EEFTKVVQPQ EEIATKKLRL TKPSKSAALH IDLCKATSPA DALQYLLQFA RKPVEAESVE GVVRILLEH YYKENDPSVR LKIASLLGLL SKTAGFSPDC IMDDAINILQ NEKSHQVLAQ LLDTLLAIGT KLPENQAIQM R LVDVACKH ...String:
GPSDPGPKRA MAAHLKKRVY EEFTKVVQPQ EEIATKKLRL TKPSKSAALH IDLCKATSPA DALQYLLQFA RKPVEAESVE GVVRILLEH YYKENDPSVR LKIASLLGLL SKTAGFSPDC IMDDAINILQ NEKSHQVLAQ LLDTLLAIGT KLPENQAIQM R LVDVACKH LTDTSHGVRN KCLQLLGNLG SLEKSVTKDA EGLAARDVQK IIGDYFSDQD PRVRTAAIKA MLQLHERGLK LH QTIYNQA CKLLSDDYEQ VRSAAVQLIW VVSQLYPESI VPIPSSNEEI RLVDDAFGKI CHMVSDGSWV VRVQAAKLLG SME QVSSHF LEQTLDKKLM SDLRRKRTAH ERAKELYSSG EFSSGRKWGD DAPKEEVDTG AVNLIESGAC GAFVHGLEDE MYEV RIAAV EALCMLAQSS PSFAEKCLDF LVDMFNDEIE EVRLQSIHTM RKISNNITLR EDQLDTVLAV LEDSSRDIRE ALHEL LCCT NVSTKEGIHL ALVELLKNLT KYPTDRDSIW KCLKFLGSRH PTLVLPLVPE LLSTHPFFDT AEPDMDDPAY IAVLVL IFN AAKTCPTMPA LFSDHTFRHY AYLRDSLSHL VPALRLPGRK LVSSAVSPSI IPQEDPSQQF LQQSLERVYS LQHLDPQ GA QELLEFTIRD LQRLGELQSE LAGVADFSAT YLRCQLLLIK ALQEKLWNVA APLYLKQSDL ASAAAKQIME ETYKMEFM Y SGVENKQVVI IHHMRLQAKA LQLIVTARTT RGLDPLFGMC EKFLQEVDFF QRYFIADLPH LQDSFVDKLL DLMPRLMTS KPAEVVKILQ TMLRQSAFLH LPLPEQIHKA SATIIEPAGE SDNPLRFTSG LVVALDVDAT LEHVQDPQNT VKVQVLYPDG QAQMIHPKP ADFRNPGPGR HRLITQVYLS HTAWTEACQV EVRLLLAYNS SARIPKCPWM EGGEMSPQVE TSIEGTIPFS K PVKVYIMP KPARR

UniProtKB: Integrator complex subunit 4

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / 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: 59.5 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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97185
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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