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- EMDB-19851: Structure of the Integrator arm module containing INTS10/13/14 su... -

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Basic information

Entry
Database: EMDB / ID: EMD-19851
TitleStructure of the Integrator arm module containing INTS10/13/14 subunits
Map data
Sample
  • Complex: INTS10/13/14 complex of the Integrator's Arm module
    • Protein or peptide: Integrator complex subunit 13
    • Protein or peptide: Integrator complex subunit 14
    • Protein or peptide: Integrator complex subunit 10
  • Ligand: MAGNESIUM ION
KeywordsIntegrator complex assembly / RNA polymerase II transcription termination / transcription factors / TRANSCRIPTION
Function / homology
Function and homology information


regulation of fertilization / snRNA 3'-end processing / snRNA processing / flagellated sperm motility / protein localization to nuclear envelope / integrator complex / regulation of transcription elongation by RNA polymerase II / centrosome localization / RNA polymerase II transcribes snRNA genes / regulation of mitotic cell cycle ...regulation of fertilization / snRNA 3'-end processing / snRNA processing / flagellated sperm motility / protein localization to nuclear envelope / integrator complex / regulation of transcription elongation by RNA polymerase II / centrosome localization / RNA polymerase II transcribes snRNA genes / regulation of mitotic cell cycle / mitotic spindle organization / nuclear body / cell division / intracellular membrane-bounded organelle / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Integrator complex subunit 10 / Integrator complex subunit 14 / Integrator complex subunit 14, beta-barrel domain / Integrator complex subunit 14, C-terminal / Integrator complex subunit 14, beta-barrel domain / Integrator complex subunit 14, alpha-helical domain / Integrator subunit 10 / Cell cycle regulator Mat89Bb / Cell cycle and development regulator Mat89Bb / von Willebrand factor type A domain ...Integrator complex subunit 10 / Integrator complex subunit 14 / Integrator complex subunit 14, beta-barrel domain / Integrator complex subunit 14, C-terminal / Integrator complex subunit 14, beta-barrel domain / Integrator complex subunit 14, alpha-helical domain / Integrator subunit 10 / Cell cycle regulator Mat89Bb / Cell cycle and development regulator Mat89Bb / von Willebrand factor type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Integrator complex subunit 14 / Integrator complex subunit 13 / Integrator complex subunit 10
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsRazew M / Galej WP
Funding support Germany, 1 items
OrganizationGrant numberCountry
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND Germany
CitationJournal: Mol Cell / Year: 2024
Title: Structural basis of the Integrator complex assembly and association with transcription factors.
Authors: Michal Razew / Angelique Fraudeau / Moritz M Pfleiderer / Romain Linares / Wojciech P Galej /
Abstract: Integrator is a multi-subunit protein complex responsible for premature transcription termination of coding and non-coding RNAs. This is achieved via two enzymatic activities, RNA endonuclease and ...Integrator is a multi-subunit protein complex responsible for premature transcription termination of coding and non-coding RNAs. This is achieved via two enzymatic activities, RNA endonuclease and protein phosphatase, acting on the promoter-proximally paused RNA polymerase Ⅱ (RNAPⅡ). Yet, it remains unclear how Integrator assembly and recruitment are regulated and what the functions of many of its core subunits are. Here, we report the structures of two human Integrator sub-complexes: INTS10/13/14/15 and INTS5/8/10/15, and an integrative model of the fully assembled Integrator bound to the RNAPⅡ paused elongating complex (PEC). An in silico protein-protein interaction screen of over 1,500 human transcription factors (TFs) identified ZNF655 as a direct interacting partner of INTS13 within the fully assembled Integrator. We propose a model wherein INTS13 acts as a platform for the recruitment of TFs that could modulate the stability of the Integrator's association at specific loci and regulate transcription attenuation of the target genes.
History
DepositionMar 14, 2024-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19851.png

Downloads & links

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Map

FileDownload / File: emd_19851.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 600 pix.
= 492. Å		0.82 Å/pix.
x 600 pix.
= 492. Å		0.82 Å/pix.
x 600 pix.
= 492. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.397
Minimum - Maximum-2.9024558 - 4.439541
Average (Standard dev.)0.0005023011 (±0.026505731)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 492.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19851_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_19851_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 : INTS10/13/14 complex of the Integrator's Arm module

EntireName: INTS10/13/14 complex of the Integrator's Arm module
Components
  • Complex: INTS10/13/14 complex of the Integrator's Arm module
    • Protein or peptide: Integrator complex subunit 13
    • Protein or peptide: Integrator complex subunit 14
    • Protein or peptide: Integrator complex subunit 10
  • Ligand: MAGNESIUM ION

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Supramolecule #1: INTS10/13/14 complex of the Integrator's Arm module

SupramoleculeName: INTS10/13/14 complex of the Integrator's Arm module / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Integrator complex subunit 13

MacromoleculeName: Integrator complex subunit 13 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.34518 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKIFSESHKT VFVVDHCPYM AESCRQHVEF DMLVKNRTQG IIPLAPISKS LWTCSVESSM EYCRIMYDIF PFKKLVNFIV SDSGAHVLN SWTQEDQNLQ ELMAALAAVG PPNPRADPEC CSILHGLVAA VETLCKITEY QHEARTLLME NAERVGNRGR I ICITNAKS ...String:
MKIFSESHKT VFVVDHCPYM AESCRQHVEF DMLVKNRTQG IIPLAPISKS LWTCSVESSM EYCRIMYDIF PFKKLVNFIV SDSGAHVLN SWTQEDQNLQ ELMAALAAVG PPNPRADPEC CSILHGLVAA VETLCKITEY QHEARTLLME NAERVGNRGR I ICITNAKS DSHVRMLEDC VQETIHEHNK LAANSDHLMQ IQKCELVLIH TYPVGEDSLV SDRSKKELSP VLTSEVHSVR AG RHLATKL NILVQQHFDL ASTTITNIPM KEEQHANTSA NYDVELLHHK DAHVDFLKSG DSHLGGGSRE GSFKETITLK WCT PRTNNI ELHYCTGAYR ISPVDVNSRP SSCLTNFLLN GRSVLLEQPR KSGSKVISHM LSSHGGEIFL HVLSSSRSIL EDPP SISEG CGGRVTDYRI TDFGEFMREN RLTPFLDPRY KIDGSLEVPL ERAKDQLEKH TRYWPMIISQ TTIFNMQAVV PLASV IVKE SLTEEDVLNC QKTIYNLVDM ERKNDPLPIS TVGTRGKGPK RDEQYRIMWN ELETLVRAHI NNSEKHQRVL ECLMAC RSK PPEEEERKKR GRKREDKEDK SEKAVKDYEQ EKSWQDSERL KGILERGKEE LAEAEIIKDS PDSPEPPNKK PLVEMDE TP QVEKSKGPVS LLSLWSNRIN TANSRKHQEF AGRLNSVNNR AELYQHLKEE NGMETTENGK ASRQ

UniProtKB: Integrator complex subunit 13

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Macromolecule #2: Integrator complex subunit 14

MacromoleculeName: Integrator complex subunit 14 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.526547 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MPTVVVMDVS LSMTRPVSIE GSEEYQRKHL AAHGLTMLFE HMATNYKLEF TALVVFSSLW ELMVPFTRDY NTLQEALSNM DDYDKTCLE SALVGVCNIV QQEWGGAIPC QVVLVTDGCL GIGRGSLRHS LATQNQRSES NRFPLPFPFP SKLYIMCMAN L EELQSTDS ...String:
MPTVVVMDVS LSMTRPVSIE GSEEYQRKHL AAHGLTMLFE HMATNYKLEF TALVVFSSLW ELMVPFTRDY NTLQEALSNM DDYDKTCLE SALVGVCNIV QQEWGGAIPC QVVLVTDGCL GIGRGSLRHS LATQNQRSES NRFPLPFPFP SKLYIMCMAN L EELQSTDS LECLERLIDL NNGEGQIFTI DGPLCLKNVQ SMFGKLIDLA YTPFHAVLKC GHLTADVQVF PRPEPFVVDE EI DPIPKVI NTDLEIVGFI DIADISSPPV LSRHLVLPIA LNKEGDEVGT GITDDNEDEN SANQIAGKIP NFCVLLHGSL KVE GMVAIV QLGPEWHGML YSQADSKKKS NLMMSLFEPG PEPLPWLGKM AQLGPISDAK ENPYGEDDNK SPFPLQPKNK RSYA QNVTV WIKPSGLQTD VQKILRNARK LPEKTQTFYK ELNRLRKAAL AFGFLDLLKG VADMLERECT LLPETAHPDA AFQLT HAAQ QLKLASTGTS EYAAYDQNIT PLHTDFSGSS TERI

UniProtKB: Integrator complex subunit 14

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Macromolecule #3: Integrator complex subunit 10

MacromoleculeName: Integrator complex subunit 10 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.339867 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSAQGDCEFL VQRARELVPQ DLWAAKAWLI TARSLYPADF NIQYEMYTIE RNAERTATAG RLLYDMFVNF PDQPVVWREI SIITSALRN DSQDKQTQFL RSLFETLPGR VQCEMLLKVT EQCFNTLERS EMLLLLLRRF PETVVQHGVG LGEALLEAET I EEQESPVN ...String:
MSAQGDCEFL VQRARELVPQ DLWAAKAWLI TARSLYPADF NIQYEMYTIE RNAERTATAG RLLYDMFVNF PDQPVVWREI SIITSALRN DSQDKQTQFL RSLFETLPGR VQCEMLLKVT EQCFNTLERS EMLLLLLRRF PETVVQHGVG LGEALLEAET I EEQESPVN CFRKLFVCDV LPLIINNHDV RLPANLLYKY LNKAAEFYIN YVTRSTQIEN QHQGAQDTSD LMSPSKRSSQ KY IIEGLTE KSSQIVDPWE RLFKILNVVG MRCEWQMDKG RRSYGDILHR MKDLCRYMNN FDSEAHAKYK NQVVYSTMLV FFK NAFQYV NSIQPSLFQG PNAPSQVPLV LLEDVSNVYG DVEIDRNKHI HKKRKLAEGR EKTMSSDDED CSAKGRNRHI VVNK AELAN STEVLESFKL ARESWELLYS LEFLDKEFTR ICLAWKTDTW LWLRIFLTDM IIYQGQYKKA IASLHHLAAL QGSIS QPQI TGQGTLEHQR ALIQLATCHF ALGEYRMTCE KVLDLMCYMV LPIQDGGKSQ EEPSKVKPKF RKGSDLKLLP CTSKAI MPY CLHLMLACFK LRAFTDNRDD MALGHVIVLL QQEWPRGENL FLKAVNKICQ QGNFQYENFF NYVTNIDMLE EFAYLRT QE GGKIHLELLP NQGMLIKHHT VTRGITKGVK EDFRLAMERQ VSRCGENLMV VLHRFCINEK ILLLQTLT

UniProtKB: Integrator complex subunit 10

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 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: 7.8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6sn1

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 258952
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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