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Yorodumi- EMDB-17407: Structural insights into human co-transcriptional capping - struc... -
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-Basic information
Entry | Database: EMDB / ID: EMD-17407 | |||||||||
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Title | Structural insights into human co-transcriptional capping - structure 5 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | rna polymerase II / capping / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information RNA guanylyltransferase activity / inorganic triphosphate phosphatase activity / negative regulation of DNA-templated transcription, elongation / DSIF complex / regulation of transcription elongation by RNA polymerase II / 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 guanylyltransferase activity / inorganic triphosphate phosphatase activity / negative regulation of DNA-templated transcription, elongation / DSIF complex / regulation of transcription elongation by RNA polymerase II / 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 / mRNA 5'-triphosphate monophosphatase activity / 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 / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / positive regulation of DNA-templated transcription, elongation / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription elongation-coupled chromatin remodeling / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / RNA polymerase III activity / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / phosphoprotein phosphatase activity / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / positive regulation of macroautophagy / RNA polymerase II transcribes snRNA genes / RNA polymerase II activity / 7-methylguanosine mRNA capping / transcription elongation by RNA polymerase I / Tat-mediated elongation of the HIV-1 transcript / tRNA transcription by RNA polymerase III / RNA polymerase I activity / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / Formation of HIV elongation complex in the absence of HIV Tat / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / RNA processing / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / translation initiation factor binding / RNA Polymerase II Pre-transcription Events / positive regulation of RNA splicing / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / fibrillar center / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / mRNA processing / chromosome / mRNA guanylyltransferase activity / single-stranded DNA binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / chromosome, telomeric region / mRNA guanylyltransferase / methyltransferase cap1 / methylation / mRNA (nucleoside-2'-O-)-methyltransferase activity / nucleic acid binding / transcription by RNA polymerase II / single-stranded RNA binding / protein dimerization activity / nuclear speck / hydrolase activity / protein heterodimerization activity / intracellular membrane-bounded organelle Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Garg G / Dienemann C / Farnung L / Schwarz J / Linden A / Urlaub H / Cramer P | |||||||||
Funding support | European Union, Germany, 2 items
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Citation | Journal: Mol Cell / Year: 2023 Title: Structural insights into human co-transcriptional capping. Authors: Gaurika Garg / Christian Dienemann / Lucas Farnung / Juliane Schwarz / Andreas Linden / Henning Urlaub / Patrick Cramer / Abstract: Co-transcriptional capping of the nascent pre-mRNA 5' end prevents degradation of RNA polymerase (Pol) II transcripts and suppresses the innate immune response. Here, we provide mechanistic insights ...Co-transcriptional capping of the nascent pre-mRNA 5' end prevents degradation of RNA polymerase (Pol) II transcripts and suppresses the innate immune response. Here, we provide mechanistic insights into the three major steps of human co-transcriptional pre-mRNA capping based on six different cryoelectron microscopy (cryo-EM) structures. The human mRNA capping enzyme, RNGTT, first docks to the Pol II stalk to position its triphosphatase domain near the RNA exit site. The capping enzyme then moves onto the Pol II surface, and its guanylyltransferase receives the pre-mRNA 5'-diphosphate end. Addition of a GMP moiety can occur when the RNA is ∼22 nt long, sufficient to reach the active site of the guanylyltransferase. For subsequent cap(1) methylation, the methyltransferase CMTR1 binds the Pol II stalk and can receive RNA after it is grown to ∼29 nt in length. The observed rearrangements of capping factors on the Pol II surface may be triggered by the completion of catalytic reaction steps and are accommodated by domain movements in the elongation factor DRB sensitivity-inducing factor (DSIF). | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17407.map.gz | 80.6 MB | EMDB map data format | |
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Header (meta data) | emd-17407-v30.xml emd-17407.xml | 35.4 KB 35.4 KB | Display Display | EMDB header |
Images | emd_17407.png | 97.5 KB | ||
Filedesc metadata | emd-17407.cif.gz | 11.1 KB | ||
Others | emd_17407_half_map_1.map.gz emd_17407_half_map_2.map.gz | 80.5 MB 80.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17407 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17407 | HTTPS FTP |
-Validation report
Summary document | emd_17407_validation.pdf.gz | 895.5 KB | Display | EMDB validaton report |
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Full document | emd_17407_full_validation.pdf.gz | 895.1 KB | Display | |
Data in XML | emd_17407_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | emd_17407_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17407 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17407 | HTTPS FTP |
-Related structure data
Related structure data | 8p4eMC 8p4aC 8p4bC 8p4cC 8p4dC 8p4fC 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_17407.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_17407_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17407_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Pol II - TPase complex
+Supramolecule #1: Pol II - TPase complex
+Macromolecule #1: Transcription elongation factor SPT5
+Macromolecule #2: mRNA-capping enzyme
+Macromolecule #3: DNA-directed RNA polymerase II subunit RPB1
+Macromolecule #4: DNA-directed RNA polymerase subunit beta
+Macromolecule #5: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #6: DNA-directed RNA polymerase II subunit E
+Macromolecule #7: DNA-directed RNA polymerase II subunit F
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #9: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #11: DNA-directed RNA polymerase II subunit RPB11-a
+Macromolecule #12: RNA polymerase II subunit K
+Macromolecule #13: RNA polymerase II subunit D
+Macromolecule #14: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #15: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1
+Macromolecule #16: RNA (5'-D(*(MGT))-R(P*GP*AP*CP*AP*UP*AP*CP*AP*UP*AP*AP*AP*GP*AP*C...
+Macromolecule #17: DNA (26-MER)
+Macromolecule #18: DNA (35-MER)
+Macromolecule #19: MAGNESIUM ION
+Macromolecule #20: ZINC 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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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 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: 2.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48148 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |