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- EMDB-12165: Structure of the Integrator cleavage module with INTS4/9/11 -

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Basic information

Entry
Database: EMDB / ID: EMD-12165
TitleStructure of the Integrator cleavage module with INTS4/9/11
Map data
Sample
  • Complex: Heterotrimeric cleavage module of the Integrator complex
    • Protein or peptide: Integrator complex subunit 9
    • Protein or peptide: Integrator complex subunit 4
    • Protein or peptide: Integrator complex subunit 11
    • Protein or peptide: Unknown
KeywordsNuclease / Integrator / 3'-end processing / NUCLEAR PROTEIN
Function / homology
Function and homology information


snRNA 3'-end processing / snRNA processing / integrator complex / regulation of transcription elongation by RNA polymerase II / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA polymerase II transcribes snRNA genes / RNA endonuclease activity / negative regulation of transforming growth factor beta receptor signaling pathway / blood microparticle / nucleolus ...snRNA 3'-end processing / snRNA processing / integrator complex / regulation of transcription elongation by RNA polymerase II / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA polymerase II transcribes snRNA genes / RNA endonuclease activity / negative regulation of transforming growth factor beta receptor signaling pathway / blood microparticle / nucleolus / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Sister chromatid cohesion protein PDS5 protein / 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 ...Sister chromatid cohesion protein PDS5 protein / 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 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 / Integrator complex subunit 4 / Integrator complex subunit 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsPfleiderer MM / Galej WP
CitationJournal: Mol Cell / Year: 2021
Title: Structure of the catalytic core of the Integrator complex.
Authors: Moritz M Pfleiderer / Wojciech P Galej /
Abstract: The Integrator is a specialized 3' end-processing complex involved in cleavage and transcription termination of a subset of nascent RNA polymerase II transcripts, including small nuclear RNAs (snRNAs) ...The Integrator is a specialized 3' end-processing complex involved in cleavage and transcription termination of a subset of nascent RNA polymerase II transcripts, including small nuclear RNAs (snRNAs). We provide evidence of the modular nature of the Integrator complex by biochemically characterizing its two subcomplexes, INTS5/8 and INTS10/13/14. Using cryoelectron microscopy (cryo-EM), we determined a 3.5-Å-resolution structure of the INTS4/9/11 ternary complex, which constitutes Integrator's catalytic core. Our structure reveals the spatial organization of the catalytic nuclease INTS11, bound to its catalytically impaired homolog INTS9 via several interdependent interfaces. INTS4, a helical repeat protein, plays a key role in stabilizing nuclease domains and other components. In this assembly, all three proteins form a composite electropositive groove, suggesting a putative RNA binding path within the complex. Comparison with other 3' end-processing machineries points to distinct features and a unique architecture of the Integrator's catalytic module.
History
DepositionJan 4, 2021-
Header (metadata) releaseMar 24, 2021-
Map releaseMar 24, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bfp
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7bfp
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12165.png

Downloads & links

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Map

FileDownload / File: emd_12165.map.gz / Format: CCP4 / Size: 160.8 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 348 pix.
= 288.84 Å		0.83 Å/pix.
x 348 pix.
= 288.84 Å		0.83 Å/pix.
x 348 pix.
= 288.84 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: 0.0186 / Movie #1: 0.015
Minimum - Maximum-0.06619282 - 0.093836114
Average (Standard dev.)0.0000028168486 (±0.0026706725)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions348348348
Spacing348348348
CellA=B=C: 288.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z348348348
origin x/y/z0.0000.0000.000
length x/y/z288.840288.840288.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS348348348
D min/max/mean-0.0660.0940.000

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Supplemental data

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Mask #1

Fileemd_12165_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_12165_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_12165_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Heterotrimeric cleavage module of the Integrator complex

EntireName: Heterotrimeric cleavage module of the Integrator complex
Components
  • Complex: Heterotrimeric cleavage module of the Integrator complex
    • Protein or peptide: Integrator complex subunit 9
    • Protein or peptide: Integrator complex subunit 4
    • Protein or peptide: Integrator complex subunit 11
    • Protein or peptide: Unknown

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Supramolecule #1: Heterotrimeric cleavage module of the Integrator complex

SupramoleculeName: Heterotrimeric cleavage module of the Integrator complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 257 kDa/nm

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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 4

MacromoleculeName: Integrator complex subunit 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 110.164773 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHHHP PSGADPMAAH LKKRVYEEFT KVVQPQEEIA TKKLRLTKPS KSAALHIDLC KATSPADALQ YLLQFARKPV EAESVEGVV RILLEHYYKE NDPSVRLKIA SLLGLLSKTA GFSPDCIMDD AINILQNEKS HQVLAQLLDT LLAIGTKLPE N QAIQMRLV ...String:
MHHHHHHHHP PSGADPMAAH LKKRVYEEFT KVVQPQEEIA TKKLRLTKPS KSAALHIDLC KATSPADALQ YLLQFARKPV EAESVEGVV RILLEHYYKE NDPSVRLKIA SLLGLLSKTA GFSPDCIMDD AINILQNEKS HQVLAQLLDT LLAIGTKLPE N QAIQMRLV DVACKHLTDT SHGVRNKCLQ LLGNLGSLEK SVTKDAEGLA ARDVQKIIGD YFSDQDPRVR TAAIKAMLQL HE RGLKLHQ TIYNQACKLL SDDYEQVRSA AVQLIWVVSQ LYPESIVPIP SSNEEIRLVD DAFGKICHMV SDGSWVVRVQ AAK LLGSME QVSSHFLEQT LDKKLMSDLR RKRTAHERAK ELYSSGEFSS GRKWGDDAPK EEVDTGAVNL IESGACGAFV HGLE DEMYE VRIAAVEALC MLAQSSPSFA EKCLDFLVDM FNDEIEEVRL QSIHTMRKIS NNITLREDQL DTVLAVLEDS SRDIR EALH ELLCCTNVST KEGIHLALVE LLKNLTKYPT DRDSIWKCLK FLGSRHPTLV LPLVPELLST HPFFDTAEPD MDDPAY IAV LVLIFNAAKT CPTMPALFSD HTFRHYAYLR DSLSHLVPAL RLPGRKLVSS AVSPSIIPQE DPSQQFLQQS LERVYSL QH LDPQGAQELL EFTIRDLQRL GELQSELAGV ADFSATYLRC QLLLIKALQE KLWNVAAPLY LKQSDLASAA AKQIMEET Y KMEFMYSGVE NKQVVIIHHM RLQAKALQLI VTARTTRGLD PLFGMCEKFL QEVDFFQRYF IADLPHLQDS FVDKLLDLM PRLMTSKPAE VVKILQTMLR QSAFLHLPLP EQIHKASATI IEPAGESDNP LRFTSGLVVA LDVDATLEHV QDPQNTVKVQ VLYPDGQAQ MIHPKPADFR NPGPGRHRLI TQVYLSHTAW TEACQVEVRL LLAYNSSARI PKCPWMEGGE MSPQVETSIE G TIPFSKPV KVYIMPKPAR R

UniProtKB: Integrator complex subunit 4

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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
EC number: Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72.690008 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDEKTTGWRG GHVVEGLAGE LEQLRARLEH HPQGQREPPP SGADPMPEIR VTPLGAGQDV GRSCILVSIA GKNVMLDCGM HMGFNDDRR FPDFSYITQN GRLTDFLDCV IISHFHLDHC GALPYFSEMV GYDGPIYMTH PTQAICPILL EDYRKIAVDK K GEANFFTS ...String:
MDEKTTGWRG GHVVEGLAGE LEQLRARLEH HPQGQREPPP SGADPMPEIR VTPLGAGQDV GRSCILVSIA GKNVMLDCGM HMGFNDDRR FPDFSYITQN GRLTDFLDCV IISHFHLDHC GALPYFSEMV GYDGPIYMTH PTQAICPILL EDYRKIAVDK K GEANFFTS QMIKDCMKKV VAVHLHQTVQ VDDELEIKAY YAGHVLGAAM FQIKVGSESV VYTGDYNMTP DRHLGAAWID KC RPNLLIT ESTYATTIRD SKRCRERDFL KKVHETVERG GKVLIPVFAL GRAQELCILL ETFWERMNLK VPIYFSTGLT EKA NHYYKL FIPWTNQKIR KTFVQRNMFE FKHIKAFDRA FADNPGPMVV FATPGMLHAG QSLQIFRKWA GNEKNMVIMP GYCV QGTVG HKILSGQRKL EMEGRQVLEV KMQVEYMSFS AHADAKGIMQ LVGQAEPESV LLVHGEAKKM EFLKQKIEQE LRVNC YMPA NGETVTLLTS PSIPVGISLG LLKREMAQGL LPEAKKPRLL HGTLIMKDSN FRLVSSEQAL KELGLAEHQL RFTCRV HLH DTRKEQETAL RVYSHLKSVL KDHCVQHLPD GSVTVESVLL QAAAPSEDPG TKVLLVSWTY QDEELGSFLT SLLKKGL PQ APS

UniProtKB: Integrator complex subunit 11

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Macromolecule #4: Unknown

MacromoleculeName: Unknown / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.08179 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)

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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

Concentration0.5 mg/mL
BufferpH: 7.8 / Details: 150 mM KCl, 20 mM HEPES-KOH pH 7.8
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 2 / Number real images: 19268 / Average exposure time: 5.0 sec. / Average electron dose: 44.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 9124445
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26358
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: OTHER
Output model

PDB-7bfp:
Structure of the Integrator cleavage module with INTS4/9/11

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