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Yorodumi- EMDB-25214: Cryo-EM structure of Drosophila Integrator cleavage module (IntS4... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25214 | ||||||||||||
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Title | Cryo-EM structure of Drosophila Integrator cleavage module (IntS4-IntS9-IntS11) in complex with IP6 | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | integrator / inositol hexakisphosphate / NUCLEASE | ||||||||||||
Function / homology | Function and homology information RNA polymerase II transcribes snRNA genes / snRNA 3'-end processing / snRNA processing / integrator complex / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.74 Å | ||||||||||||
Authors | Lin M / Tong L | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Inositol hexakisphosphate is required for Integrator function. Authors: Min-Han Lin / Madeline K Jensen / Nathan D Elrod / Kai-Lieh Huang / Kevin A Welle / Eric J Wagner / Liang Tong / Abstract: Integrator is a multi-subunit protein complex associated with RNA polymerase II (Pol II), with critical roles in noncoding RNA 3'-end processing and transcription attenuation of a broad collection of ...Integrator is a multi-subunit protein complex associated with RNA polymerase II (Pol II), with critical roles in noncoding RNA 3'-end processing and transcription attenuation of a broad collection of mRNAs. IntS11 is the endonuclease for RNA cleavage, as a part of the IntS4-IntS9-IntS11 Integrator cleavage module (ICM). Here we report a cryo-EM structure of the Drosophila ICM, at 2.74 Å resolution, revealing stable association of an inositol hexakisphosphate (IP) molecule. The IP binding site is located in a highly electropositive pocket at an interface among all three subunits of ICM, 55 Å away from the IntS11 active site and generally conserved in other ICMs. We also confirmed IP association with the same site in human ICM. IP binding is not detected in ICM samples harboring mutations in this binding site. Such mutations or disruption of IP biosynthesis significantly reduced Integrator function in snRNA 3'-end processing and mRNA transcription attenuation. Our structural and functional studies reveal that IP is required for Integrator function in Drosophila, humans, and likely other organisms. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25214.map.gz | 58.3 MB | EMDB map data format | |
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Header (meta data) | emd-25214-v30.xml emd-25214.xml | 14.5 KB 14.5 KB | Display Display | EMDB header |
Images | emd_25214.png | 78.2 KB | ||
Filedesc metadata | emd-25214.cif.gz | 6.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25214 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25214 | HTTPS FTP |
-Validation report
Summary document | emd_25214_validation.pdf.gz | 537.5 KB | Display | EMDB validaton report |
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Full document | emd_25214_full_validation.pdf.gz | 537.1 KB | Display | |
Data in XML | emd_25214_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_25214_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25214 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25214 | HTTPS FTP |
-Related structure data
Related structure data | 7sn8MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25214.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.083 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Integrator cleavage module with inositol hexakisphosphate
Entire | Name: Integrator cleavage module with inositol hexakisphosphate |
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Components |
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-Supramolecule #1: Integrator cleavage module with inositol hexakisphosphate
Supramolecule | Name: Integrator cleavage module with inositol hexakisphosphate type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
-Macromolecule #1: Integrator complex subunit 4
Macromolecule | Name: Integrator complex subunit 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 114.728875 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MHHHHHHGSG MALAIKKRVG TYVETVDGSP PVKKLRLQTL AADAKGGKSG KVGNVERKLT ALNQLDAYVG NLPAGALVLP TGTPVASTG APSTGVIGNP PAAATGAPPM TAANSRELLE LLVKITDEIS YEDVEMGELK EVASKIFQLY QLQERDSDTS I RVKLLELL ...String: MHHHHHHGSG MALAIKKRVG TYVETVDGSP PVKKLRLQTL AADAKGGKSG KVGNVERKLT ALNQLDAYVG NLPAGALVLP TGTPVASTG APSTGVIGNP PAAATGAPPM TAANSRELLE LLVKITDEIS YEDVEMGELK EVASKIFQLY QLQERDSDTS I RVKLLELL SGLGCECATE QALTMIIDYF IFLLRKEVSQ KVLAQGMMCL FRIGERRKHM LPISYKTQVA HLAKEQLRSG SA HTQKNAM LVIGRFATKM EGERHYVWKL AFYIDSQDSS VRAQALHALL TLGERGSQLP AVLYKRAVEA MKDDYECVRK EAL QLVFML GNRHPDYILP SDRQQEELRM IDAAFSKVCE ALCDLSLQIR VLAAELLGGM TAVSREFLHQ TLDKKLMSNL RRKR TAHER GARLVASGEW SSGKRWADDA PQEHLDAQSI SIIASGACGA LIHGLEDEFL EVRTAAVASM CKLALSRPDF AVTSL DFLV DMFNDEIEDV RLKAIYSLTA IAKHIVLRED QLEIMLGSLE DYSVDVREGL HLMLGACRVS TQTCLLMVVQ KLLDVL AKY PQDRNSTYAC MRKIGQKHPH LVMAVAVHLL YVHPFFETPE RDVEDPAYLC VLILVFNAAE HLVPIISLLP TATHRHY AY LRDSMPNLVP QLPIEGASSA SATHRIDSAM HQAGSSAEYL QMILSHIEEI FTMTDERLEL LQTAQSNLQR LGSIDAGM Y GTSNFLETFL AAQIQIEQMQ RCASTQRSRV PLKESLAALI RNCLKLQHTF SGLNYGDILQ VKQLRLRACA LHLVLVVRD RSQSALGPCQ MLLQTAGDIS EFIKANTKDE EEKPPVVETD MPMKESVSRD AQPDSFTRQL LIKLDGISDP KPGRVFREIL PLVQQAPPL ALPPANDKIR RCVANILEPC PLQSQDNVIK VTAGLIAAVP FVAEIDNLLE SQKADMRIKI KYPDQHMHTV V PKQSDFKP IMTEQGEHKT NVRLRTTILL SHSVWTESSL VEIQLCLAVR PGSELELCKP AKVLFAPKPV RRGI UniProtKB: Integrator complex subunit 4 |
-Macromolecule #2: Integrator complex subunit 11
Macromolecule | Name: Integrator complex subunit 11 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 67.683922 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MPDIKITPLG AGQDVGRSCL LLSMGGKNIM LDCGMHMGYN DERRFPDFSY IVPEGPITSH IDCVIISHFH LDHCGALPYM SEIVGYTGP IYMTHPTKAI APILLEDMRK VAVERKGESN FFTTQMIKDC MKKVIPVTLH QSMMVDTDLE IKAYYAGHVL G AAMFWIKV ...String: MPDIKITPLG AGQDVGRSCL LLSMGGKNIM LDCGMHMGYN DERRFPDFSY IVPEGPITSH IDCVIISHFH LDHCGALPYM SEIVGYTGP IYMTHPTKAI APILLEDMRK VAVERKGESN FFTTQMIKDC MKKVIPVTLH QSMMVDTDLE IKAYYAGHVL G AAMFWIKV GSQSVVYTGD YNMTPDRHLG AAWIDKCRPD LLISESTYAT TIRDSKRCRE RDFLKKVHEC VAKGGKVLIP VF ALGRAQE LCILLETYWE RMNLKYPIYF ALGLTEKANT YYKMFITWTN QKIRKTFVHR NMFDFKHIKP FDKAYIDNPG AMV VFATPG MLHAGLSLQI FKKWAPNENN MVIMPGYCVQ GTVGNKILGG AKKVEFENRQ VVEVKMAVEY MSFSAHADAK GIMQ LIQNC EPKNVMLVHG EAGKMKFLRS KIKDEFNLET YMPANGETCV ISTPVKIPVD ASVSLLKAEA RSYNAQPPDP KRRRL IHGV LVMKDNRIML QNLTDALKEI GINRHVMRFT SKVKMDDSGP VIRTSERLKT LLEEKLAGWT VTMQENGSIA IESVEV KVE EDEKDPKQKN ILISWTNQDE DIGAYILNVL QNMC UniProtKB: Integrator complex subunit 11 |
-Macromolecule #3: Integrator complex subunit 9
Macromolecule | Name: Integrator complex subunit 9 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 73.351531 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MRLYCLSGDL AKPCYIITFK GLRIMLDCGL TEQTVLNFLP LPFVQSLKWS NLPNFVPSRD HDPQMDGELK DCCGRVFVDS TPEFNLPMD KMLDFSEVDV ILISNYLNML ALPYITENTG FKGKVYATEP TLQIGRFFLE ELVDYIEVSP KACTARLWKE K LHLLPSPL ...String: MRLYCLSGDL AKPCYIITFK GLRIMLDCGL TEQTVLNFLP LPFVQSLKWS NLPNFVPSRD HDPQMDGELK DCCGRVFVDS TPEFNLPMD KMLDFSEVDV ILISNYLNML ALPYITENTG FKGKVYATEP TLQIGRFFLE ELVDYIEVSP KACTARLWKE K LHLLPSPL SEAFRAKKWR TIFSLKDVQG SLSKVTIMGY DEKLDILGAF IATPVSSGYC LGSSNWVLST AHEKICYVSG SS TLTTHPR PINQSALKHA DVLIMTGLTQ APTVNPDTKL GELCMNVALT IRNNGSALIP CYPSGVVYDL FECLTQNLEN AGL NNVPMF FISPVADSSL AYSNILAEWL SSAKQNKVYL PDDPFPHAFY LRNNKLKHYN HVFSEGFSKD FRQPCVVFCG HPSL RFGDA VHFIEMWGNN PNNSIIFTEP DFPYLQVLAP FQPLAMKAFY CPIDTSLNYQ QANKLIKELK PNVLVIPEAY TKPHP SAPN LFIEQPDKKI ITFKCGEIIR LPLKRKLDRI YITSELAQKI SPKEVAAGVT FSTLTGVLQV KDKVHCIQPC ADSVKD ETI SSNSAPTKED VLKNVKYEYG SIDVDAVMKK LAQDGFSNIK LDRTGGALTL NLVNEDTVIK FEDNETHIIC GGKPTTR LK LRDTIMKCLQ SF UniProtKB: Integrator complex subunit 9 |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #5: INOSITOL HEXAKISPHOSPHATE
Macromolecule | Name: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: IHP |
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Molecular weight | Theoretical: 660.035 Da |
Chemical component information | ChemComp-IHP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 4395 / Average electron dose: 51.35 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 620438 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |