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- EMDB-12163: Integrator cleavage module with focused classification on the INT... -

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Basic information

Entry
Database: EMDB / ID: EMD-12163
TitleIntegrator cleavage module with focused classification on the INTS9/11 CTD
Map data
Sample
  • Complex: Terneray complex of the Integrator cleavage module containing Integrator subunit 4, 9 and 11
    • Complex: Integrator subunit 4
      • Protein or peptide: Integrator subunit 4
    • Complex: Integrator subunit 9
      • Protein or peptide: Integrator subunit 9
    • Complex: Integrator subunit 11
      • Protein or peptide: Integrator subunit 11
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: 6.5 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) releaseFeb 24, 2021-
Map releaseFeb 24, 2021-
UpdateApr 7, 2021-
Current statusApr 7, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00809
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.00809
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12163.png

Downloads & links

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Map

FileDownload / File: emd_12163.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: 0.00809 / Movie #1: 0.00809
Minimum - Maximum-0.01009272 - 0.03178021
Average (Standard dev.)3.1547446e-05 (±0.0010294348)
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
start NX/NY/NZ000
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS348348348
D min/max/mean-0.0100.0320.000

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Supplemental data

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Mask #1

Fileemd_12163_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_12163_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_12163_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Terneray complex of the Integrator cleavage module containing Int...

EntireName: Terneray complex of the Integrator cleavage module containing Integrator subunit 4, 9 and 11
Components
  • Complex: Terneray complex of the Integrator cleavage module containing Integrator subunit 4, 9 and 11
    • Complex: Integrator subunit 4
      • Protein or peptide: Integrator subunit 4
    • Complex: Integrator subunit 9
      • Protein or peptide: Integrator subunit 9
    • Complex: Integrator subunit 11
      • Protein or peptide: Integrator subunit 11

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Supramolecule #1: Terneray complex of the Integrator cleavage module containing Int...

SupramoleculeName: Terneray complex of the Integrator cleavage module containing Integrator subunit 4, 9 and 11
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Integrator subunit 4

SupramoleculeName: Integrator subunit 4 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant strain: Hi5 / Recombinant plasmid: pBIG1a

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Supramolecule #3: Integrator subunit 9

SupramoleculeName: Integrator subunit 9 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant strain: Hi5 / Recombinant plasmid: pBIG1a

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Supramolecule #4: Integrator subunit 11

SupramoleculeName: Integrator subunit 11 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant strain: Hi5 / Recombinant plasmid: pBIG1a

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Macromolecule #1: Integrator subunit 4

MacromoleculeName: Integrator subunit 4 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MHHHHHHHHP PSGADPMAAH LKKRVYEEFT KVVQPQEEIA TKKLRLTKPS KSAALHIDLC KATSPADALQ YLLQFARKPV EAESVEGVVR ILLEHYYKEN DPSVRLKIAS LLGLLSKTAG FSPDCIMDDA INILQNEKSH QVLAQLLDTL LAIGTKLPEN QAIQMRLVDV ...String:
MHHHHHHHHP PSGADPMAAH LKKRVYEEFT KVVQPQEEIA TKKLRLTKPS KSAALHIDLC KATSPADALQ YLLQFARKPV EAESVEGVVR ILLEHYYKEN DPSVRLKIAS LLGLLSKTAG FSPDCIMDDA INILQNEKSH QVLAQLLDTL LAIGTKLPEN QAIQMRLVDV ACKHLTDTSH GVRNKCLQL LGNLGSLEKS VTKDAEGLAA RDVQKIIGDY FSDQDPRVRT AAIKAMLQLH ERGLKLHQTI YNQACKLLSD DYEQVRSAAV QLIWVVSQLY PESIVPIPSS NEEIRLVDDA F GKICHMVS DGSWVVRVQA AKLLGSMEQV SSHFLEQTLD KKLMSDLRRK RTAHERAKEL YSSGEFSSGR KWGDDAPKEE VDTGAVNLIE SGACGAFVHG LEDEMYEVRI AAVEALCMLA QSSPSFAEKC LDFLVDMFND EIEEVRLQSI HTMRKISNNI TLREDQLDTV LAVLEDSSRD IREALHELLC CTNVSTKEGI HLALVELLKN LTKYPTDRDS IWKCLKFLGS RHPTLVLPLV PELLSTHPFF DTAEPDMDDP AYIAVLVLIF NAAKTCPTMP ALFSDHTFRH YAYLRDSLSH LVPALRLPGR KLVSSAVSPS IIPQEDPSQQ FLQQSLERVY SLQHLDPQGA QELLEFTIRD LQRLGELQSE LAGVADFSAT YLRCQLLLIK ALQEKLWNVA APLYLKQSDL ASAAAKQIME ETYKMEFMYS GVENKQVVII HHMRLQAKAL QLIVTARTTR GLDPLFGMCE KFLQEVDFFQ RYFIADLPHL QDSFVDKLLD LMPRLMTSKP AEVVKILQTM LRQSAFLHLP LPEQIHKASA TIIEPAGESD NPLRFTSGLV VALDVDATLE HVQDPQNTVK VQVLYPDGQA QMIHPKPADF RNPGPGRHRL ITQVYLSHTA WTEACQVEVR LLLAYNSSAR IPKCPWMEGG EMSPQVETSI EGTIPFSKPV KVYIMPKPAR R

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Macromolecule #2: Integrator subunit 9

MacromoleculeName: Integrator subunit 9 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MKLYCLSGHP TLPCNVLKFK STTIMLDCGL DMTSTLNFLP LPLVQSPRLS NLPGWSLKDG NAFLDKELKE CSGHVFVDSV PEFCLPETEL IDLSTVDVIL ISNYHCMMAL PYITEHTGFT GTVYATEPTV QIGRLLMEEL VNFIERVPKA QSASLWKNKD IQRLLPSPLK ...String:
MKLYCLSGHP TLPCNVLKFK STTIMLDCGL DMTSTLNFLP LPLVQSPRLS NLPGWSLKDG NAFLDKELKE CSGHVFVDSV PEFCLPETEL IDLSTVDVIL ISNYHCMMAL PYITEHTGFT GTVYATEPTV QIGRLLMEEL VNFIERVPKA QSASLWKNKD IQRLLPSPLK DAVEVSTWRR CYTMQEVNSA LSKIQLVGYS QKIELFGAVQ VTPLSSGYAL GSSNWIIQSH YEKVSYVSGS SLLTTHPQPM DQASLKNSDV LVLTGLTQIP TANPDGMVGE FCSNLALTVR NGGNVLVPCY PSGVIYDLLE CLYQYIDSAG LSSVPLYFIS PVANSSLEFS QIFAEWLCHN KQSKVYLPEP PFPHAELIQT NKLKHYPSIH GDFSNDFRQP CVVFTGHPSL RFGDVVHFME LWGKSSLNTV IFTEPDFSYL EALAPYQPLA MKCIYCPIDT RLNFIQVSKL LKEVQPLHVV CPEQYTQPPP AQSHRMDLMI DCQPPAMSYR RAEVLALPFK RRYEKIEIMP ELADSLVPME IKPGISLATV SAVLHTKDNK HLLQPPPRPA QPTSGKKRKR VSDDVPDCKV LKPLLSGSIP VEQFVQTLEK HGFSDIKVED TAKGHIVLLQ EAETLIQIEE DSTHIICDND EMLRVRLRDL VLKFLQKF

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Macromolecule #3: Integrator subunit 11

MacromoleculeName: Integrator subunit 11 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MDEKTTGWRG GHVVEGLAGE LEQLRARLEH HPQGQREPPP SGADPMPEIR VTPLGAGQDV GRSCILVSIA GKNVMLDCGM HMGFNDDRRF PDFSYITQNG RLTDFLDCVI ISHFHLDHCG ALPYFSEMVG YDGPIYMTHP TQAICPILLE DYRKIAVDKK GEANFFTSQM ...String:
MDEKTTGWRG GHVVEGLAGE LEQLRARLEH HPQGQREPPP SGADPMPEIR VTPLGAGQDV GRSCILVSIA GKNVMLDCGM HMGFNDDRRF PDFSYITQNG RLTDFLDCVI ISHFHLDHCG ALPYFSEMVG YDGPIYMTHP TQAICPILLE DYRKIAVDKK GEANFFTSQM IKDCMKKVVA VHLHQTVQVD DELEIKAYYA GHVLGAAMFQ IKVGSESVVY TGDYNMTPDR HLGAAWIDKC RPNLLITEST YATTIRDSKR CRERDFLKKV HETVERGGKV LIPVFALGRA QELCILLETF WERMNLKVPI YFSTGLTEKA NHYYKLFIPW TNQKIRKTFV QRNMFEFKHI KAFDRAFADN PGPMVVFATP GMLHAGQSLQ IFRKWAGNEK NMVIMPGYCV QGTVGHKILS GQRKLEMEGR QVLEVKMQVE YMSFSAHADA KGIMQLVGQA EPESVLLVHG EAKKMEFLKQ KIEQELRVNC YMPANGETVT LLTSPSIPVG ISLGLLKREM AQGLLPEAKK PRLLHGTLIM KDSNFRLVSS EQALKELGLA EHQLRFTCRV HLHDTRKEQE TALRVYSHLK SVLKDHCVQH LPDGSVTVES VLLQAAAPSE DPGTKVLLVS WTYQDEELGS FLTSLLKKGL PQAPS

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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
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
CTF correctionSoftware - Name: RELION (ver. 3.0)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19938
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: OTHER

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