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- EMDB-17404: Structural insights into human co-transcriptional capping - struc... -
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Open data
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Basic information
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Title | Structural insights into human co-transcriptional capping - structure 2 | |||||||||
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![]() | rna polymerase II / capping / TRANSCRIPTION | |||||||||
Function / homology | ![]() RNA guanylyltransferase activity / inorganic triphosphate phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / 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 ...RNA guanylyltransferase activity / inorganic triphosphate phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / 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 / mRNA 5'-phosphatase / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / polynucleotide 5'-phosphatase activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / : / : / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / organelle membrane / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / 7-methylguanosine mRNA capping / transcription elongation by RNA polymerase I / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA processing / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase II activity / dephosphorylation / translation initiation factor binding / positive regulation of RNA splicing / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / P-body / ribonucleoside binding / fibrillar center / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / mRNA guanylyltransferase activity / chromosome / single-stranded DNA binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / mRNA guanylyltransferase / transcription by RNA polymerase II / nucleic acid binding / chromosome, telomeric region / single-stranded RNA binding / protein dimerization activity / hydrolase activity / nuclear speck / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / chromatin binding / nucleolus / GTP binding / DNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Garg G / Dienemann C / Farnung L / Schwarz J / Linden A / Urlaub H / Cramer P | |||||||||
Funding support | European Union, ![]()
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![]() | ![]() 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 | ![]() | 80.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 31.7 KB 31.7 KB | Display Display | ![]() |
Images | ![]() | 116.8 KB | ||
Others | ![]() ![]() | 80.9 MB 80.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8p4bMC ![]() 8p4aC ![]() 8p4cC ![]() 8p4dC ![]() 8p4eC ![]() 8p4fC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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_17404_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17404_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Pol II - TPase complex
+Supramolecule #1: Pol II - TPase complex
+Macromolecule #1: DNA-directed RNA polymerase II subunit RPB1
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #4: DNA-directed RNA polymerase II subunit E
+Macromolecule #5: DNA-directed RNA polymerase II subunit F
+Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #7: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #9: DNA-directed RNA polymerase II subunit RPB11-a
+Macromolecule #10: RNA polymerase II subunit K
+Macromolecule #14: RNA polymerase II subunit D
+Macromolecule #15: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #16: mRNA-capping enzyme
+Macromolecule #11: DNA (5'-D(P*AP*GP*CP*GP*GP*CP*GP*GP*AP*GP*CP*CP*AP*GP*CP*AP*GP*GP...
+Macromolecule #13: DNA (35-MER)
+Macromolecule #12: RNA (5'-R(P*GP*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP...
+Macromolecule #17: ZINC ION
+Macromolecule #18: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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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: ![]() |
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 |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21150 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |