+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37352 | |||||||||
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Title | human co-transcriptional RNA capping enzyme RNGTT | |||||||||
Map data | RNGTT-pol II-NELF overall | |||||||||
Sample |
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Keywords | RNA polymerase II / capping / pausing / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information RNA guanylyltransferase activity / NELF complex / positive regulation of protein modification process / inorganic triphosphate phosphatase activity / NTRK3 as a dependence receptor / negative regulation of DNA-templated transcription, elongation / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / DSIF complex ...RNA guanylyltransferase activity / NELF complex / positive regulation of protein modification process / inorganic triphosphate phosphatase activity / NTRK3 as a dependence receptor / negative regulation of DNA-templated transcription, elongation / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / DSIF complex / regulation of transcription elongation by RNA polymerase II / protein tyrosine/serine/threonine phosphatase activity / nuclear DNA-directed RNA polymerase 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 / 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 / negative regulation of stem cell differentiation / nuclear lumen / Abortive elongation of HIV-1 transcript in the absence of Tat / positive regulation of DNA-templated transcription, elongation / 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 / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase II complex binding / negative regulation of transcription elongation by RNA polymerase II / 7-methylguanosine mRNA capping / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II activity / organelle membrane / positive regulation of macroautophagy / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / transcription-coupled nucleotide-excision repair / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / RNA polymerase III complex / Formation of HIV elongation complex in the absence of HIV Tat / RNA processing / localization / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / dephosphorylation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / DNA-directed RNA polymerase complex / stem cell differentiation / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / TP53 Regulates Transcription of DNA Repair Genes / ribonucleoside binding / fibrillar center / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / mRNA guanylyltransferase activity / chromatin organization / mRNA guanylyltransferase / cell population proliferation / transcription by RNA polymerase II / nucleic acid binding / positive regulation of ERK1 and ERK2 cascade / molecular adaptor activity / nuclear body / protein dimerization activity / protein heterodimerization activity / nucleotide binding / mRNA binding / DNA-templated transcription Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Li Y / Wang Q / Xu Y / Li Z | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: Strcutures of co-transcriptional RNA capping enzymes on paused transcription complex Authors: Li Y / Wang Q / Xu Y / Li Z | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37352.map.gz | 4.6 MB | EMDB map data format | |
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Header (meta data) | emd-37352-v30.xml emd-37352.xml | 49 KB 49 KB | Display Display | EMDB header |
Images | emd_37352.png | 99.7 KB | ||
Filedesc metadata | emd-37352.cif.gz | 12.4 KB | ||
Others | emd_37352_additional_1.map.gz emd_37352_additional_2.map.gz emd_37352_half_map_1.map.gz emd_37352_half_map_2.map.gz | 927.6 KB 416.3 KB 116.2 MB 116.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37352 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37352 | HTTPS FTP |
-Related structure data
Related structure data | 8w8eMC 8w8fC 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_37352.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | RNGTT-pol II-NELF overall | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.334 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: halfRNGTT-pol II stalk-RNA exit channel local map
File | emd_37352_additional_1.map | ||||||||||||
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Annotation | halfRNGTT-pol II stalk-RNA exit channel local map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: RNGTT local map
File | emd_37352_additional_2.map | ||||||||||||
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Annotation | RNGTT local map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_37352_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_37352_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : human co-transcriptional RNA capping enzyme RNGTT
+Supramolecule #1: human co-transcriptional RNA capping enzyme RNGTT
+Supramolecule #2: DNA-directed RNA polimerase
+Supramolecule #3: DNA,RNA
+Supramolecule #4: Negative elongation factor, transcription elongation factor, mRNA...
+Macromolecule #1: DNA-directed RNA polymerase subunit
+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 RPB4
+Macromolecule #5: DNA-directed RNA polymerase II subunit E
+Macromolecule #6: DNA-directed RNA polymerase II subunit F
+Macromolecule #7: DNA-directed RNA polymerase II subunit RPB7
+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: RPB12
+Macromolecule #16: Negative elongation factor A
+Macromolecule #17: Negative elongation factor B
+Macromolecule #18: Negative elongation factor C/D
+Macromolecule #19: Negative elongation factor E
+Macromolecule #20: Transcription elongation factor SPT4
+Macromolecule #21: Transcription elongation factor SPT5
+Macromolecule #22: mRNA-capping enzyme
+Macromolecule #13: DNA (36-MER)
+Macromolecule #15: DNA (45-MER)
+Macromolecule #14: RNA (5'-D(*(GTP))-R(P*AP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*C...
+Macromolecule #23: MAGNESIUM ION
+Macromolecule #24: ZINC ION
+Macromolecule #25: GUANOSINE-5'-TRIPHOSPHATE
-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-PROPANE |
-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: FLOOD BEAM / 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 K3 (6k 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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69000 |