+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33741 | |||||||||||||||||||||
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Title | The structure of INTAC-PEC complex | |||||||||||||||||||||
Map data | the overall map of INATC-PEC | |||||||||||||||||||||
Sample |
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Keywords | INTAC-PEC / Transcription termination / Endonuclease / Phosphatase / TRANSCRIPTION | |||||||||||||||||||||
Function / homology | Function and homology information U2 snRNA 3'-end processing / NELF complex / positive regulation of protein modification process / snRNA processing / integrator complex / snRNA 3'-end processing / microfibril binding / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors ...U2 snRNA 3'-end processing / NELF complex / positive regulation of protein modification process / snRNA processing / integrator complex / snRNA 3'-end processing / microfibril binding / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / NTRK3 as a dependence receptor / regulation of microtubule binding / negative regulation of DNA-templated transcription, elongation / MASTL Facilitates Mitotic Progression / mitotic sister chromatid separation / regulation of meiotic cell cycle process involved in oocyte maturation / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / peptidyl-serine dephosphorylation / DSIF complex / regulation of transcription elongation by RNA polymerase II / peptidyl-threonine dephosphorylation / : / positive regulation of microtubule binding / negative regulation of tyrosine phosphorylation of STAT protein / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / female meiotic nuclear division / protein antigen binding / protein phosphatase regulator activity / ceramide metabolic process / GABA receptor binding / negative regulation of epithelial to mesenchymal transition / nuclear DNA-directed RNA polymerase complex / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Initiation of Nuclear Envelope (NE) Reformation / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major Pathway / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / ERKs are inactivated / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / negative regulation of stem cell differentiation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / regulation of Wnt signaling pathway / positive regulation of DNA-templated transcription, elongation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / regulation of growth / MicroRNA (miRNA) biogenesis / transcription elongation-coupled chromatin remodeling / Viral Messenger RNA Synthesis / inner cell mass cell proliferation / negative regulation of glycolytic process through fructose-6-phosphate / positive regulation of NLRP3 inflammasome complex assembly / Signaling by FGFR2 IIIa TM / myosin phosphatase activity / protein serine/threonine phosphatase activity / CTLA4 inhibitory signaling / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Platelet sensitization by LDL / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / negative regulation of MAPK cascade / protein-serine/threonine phosphatase Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) / synthetic construct (others) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.18 Å | |||||||||||||||||||||
Authors | Zheng H / Jin Q / Wang X / Qi Y / Liu W / Ren Y / Zhao D / Chen FX / Cheng J / Chen X / Xu Y | |||||||||||||||||||||
Funding support | China, 6 items
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Citation | Journal: Protein Cell / Year: 2023 Title: Structural basis of INTAC-regulated transcription. Authors: Hai Zheng / Qianwei Jin / Xinxin Wang / Yilun Qi / Weida Liu / Yulei Ren / Dan Zhao / Fei Xavier Chen / Jingdong Cheng / Xizi Chen / Yanhui Xu / | |||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33741.map.gz | 159.1 MB | EMDB map data format | |
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Header (meta data) | emd-33741-v30.xml emd-33741.xml | 82.7 KB 82.7 KB | Display Display | EMDB header |
Images | emd_33741.png | 229.1 KB | ||
Others | emd_33741_additional_1.map.gz emd_33741_additional_2.map.gz emd_33741_additional_3.map.gz emd_33741_additional_4.map.gz emd_33741_additional_5.map.gz emd_33741_additional_6.map.gz emd_33741_half_map_1.map.gz emd_33741_half_map_2.map.gz | 159.2 MB 159.2 MB 159.1 MB 158.7 MB 158.7 MB 158.7 MB 225.5 MB 225.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33741 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33741 | HTTPS FTP |
-Related structure data
Related structure data | 7ycxMC 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_33741.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | the overall map of INATC-PEC | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.054 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #6
File | emd_33741_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #5
File | emd_33741_additional_2.map | ||||||||||||
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Density Histograms |
-Additional map: #4
File | emd_33741_additional_3.map | ||||||||||||
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Density Histograms |
-Additional map: #3
File | emd_33741_additional_4.map | ||||||||||||
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Density Histograms |
-Additional map: #2
File | emd_33741_additional_5.map | ||||||||||||
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Density Histograms |
-Additional map: #1
File | emd_33741_additional_6.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33741_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33741_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : INTAC-PEC
+Supramolecule #1: INTAC-PEC
+Supramolecule #2: INTAC
+Supramolecule #3: DNA-directed RNA polymerase II subunit
+Supramolecule #4: DNA/RNA
+Macromolecule #1: Integrator complex subunit 1
+Macromolecule #2: Integrator complex subunit 2
+Macromolecule #3: Integrator complex subunit 4
+Macromolecule #4: Integrator complex subunit 5
+Macromolecule #5: Integrator complex subunit 6
+Macromolecule #6: Integrator complex subunit 7
+Macromolecule #7: Integrator complex subunit 8
+Macromolecule #8: Integrator complex subunit 9
+Macromolecule #9: Integrator complex subunit 11
+Macromolecule #10: Unknown2
+Macromolecule #11: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit...
+Macromolecule #12: Serine/threonine-protein phosphatase 2A catalytic subunit alpha i...
+Macromolecule #13: Unknown
+Macromolecule #14: DNA-directed RNA polymerase II subunit RPB1,DNA-directed RNA poly...
+Macromolecule #15: DNA-directed RNA polymerase subunit beta
+Macromolecule #16: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #17: DNA-directed RNA polymerase II subunit E
+Macromolecule #18: DNA-directed RNA polymerase II subunit F
+Macromolecule #19: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #20: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #21: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #22: RNA_pol_L_2 domain-containing protein
+Macromolecule #23: RPB12
+Macromolecule #27: Negative elongation factor A
+Macromolecule #28: Negative elongation factor B
+Macromolecule #29: Negative elongation factor C/D
+Macromolecule #30: Negative elongation factor E
+Macromolecule #31: Transcription elongation factor SPT4
+Macromolecule #32: Transcription elongation factor SPT5
+Macromolecule #33: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #34: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #24: non-template DNA
+Macromolecule #26: template DNA
+Macromolecule #25: RNA
+Macromolecule #35: ZINC ION
+Macromolecule #36: MANGANESE (II) ION
+Macromolecule #37: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41201 |