+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35719 | |||||||||
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Title | RNA polymerase III pre-initiation complex melting complex 1 | |||||||||
Map data | RNA polymerase III pre-initiation complex melting complex 1 | |||||||||
Sample |
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Keywords | RNA polymerase III / SNAPc complex / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information transcription preinitiation complex assembly / snRNA-activating protein complex / snRNA transcription / snRNA transcription by RNA polymerase III / bent DNA binding / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / calcitonin gene-related peptide receptor activity ...transcription preinitiation complex assembly / snRNA-activating protein complex / snRNA transcription / snRNA transcription by RNA polymerase III / bent DNA binding / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / calcitonin gene-related peptide receptor activity / TFIIIC-class transcription factor complex binding / DNA/RNA hybrid binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / regulation of transcription by RNA polymerase I / regulation of transcription by RNA polymerase III / RPAP3/R2TP/prefoldin-like complex / snRNA transcription by RNA polymerase II / RNA polymerase transcription factor SL1 complex / RNA polymerase III general transcription initiation factor activity / DNA polymerase III complex / RNA polymerase I core promoter sequence-specific DNA binding / Cytosolic sensors of pathogen-associated DNA / 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 Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / female germ cell nucleus / positive regulation of innate immune response / male pronucleus / female pronucleus / Abortive elongation of HIV-1 transcript in the absence of Tat / nucleobase-containing compound metabolic process / RNA polymerase II general transcription initiation factor binding / MicroRNA (miRNA) biogenesis / FGFR2 alternative splicing / transcription preinitiation complex / RNA Polymerase I Transcription Termination / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription factor TFIID complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / RNA polymerase II general transcription initiation factor activity / mRNA Capping / termination of RNA polymerase III transcription / PIWI-interacting RNA (piRNA) biogenesis / RNA polymerase III activity / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / transcription initiation at RNA polymerase III promoter / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / transcription by RNA polymerase I / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / aryl hydrocarbon receptor binding / transcription by RNA polymerase III / Processing of Capped Intron-Containing Pre-mRNA / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / TFIIB-class transcription factor binding / RNA polymerase II transcribes snRNA genes / neuropeptide signaling pathway / transcription elongation by RNA polymerase I / Tat-mediated elongation of the HIV-1 transcript / positive regulation of transcription initiation by RNA polymerase II / tRNA transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I activity / 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 / male germ cell nucleus / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / Inhibition of DNA recombination at telomere / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / positive regulation of interferon-beta production / mRNA Splicing - Major Pathway / SIRT1 negatively regulates rRNA expression / acrosomal vesicle / DNA-templated transcription initiation / mRNA transcription by RNA polymerase II / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / transcription initiation at RNA polymerase II promoter / protein-DNA complex Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Hou H / Jin Q / Ren Y / Wang Q / Xu Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Res / Year: 2023 Title: Structure of the SNAPc-bound RNA polymerase III preinitiation complex. Authors: Haifeng Hou / Qianwei Jin / Yulei Ren / Zhenguo Chen / Qianmin Wang / Yanhui Xu / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35719.map.gz | 116.7 MB | EMDB map data format | |
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Header (meta data) | emd-35719-v30.xml emd-35719.xml | 60.4 KB 60.4 KB | Display Display | EMDB header |
Images | emd_35719.png | 133.5 KB | ||
Filedesc metadata | emd-35719.cif.gz | 15.2 KB | ||
Others | emd_35719_additional_1.map.gz emd_35719_half_map_1.map.gz emd_35719_half_map_2.map.gz | 56.2 MB 98.4 MB 98.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35719 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35719 | HTTPS FTP |
-Validation report
Summary document | emd_35719_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_35719_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_35719_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | emd_35719_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35719 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35719 | HTTPS FTP |
-Related structure data
Related structure data | 8iueMC 8ityC 8iuhC 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_35719.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | RNA polymerase III pre-initiation complex melting complex 1 | ||||||||||||||||||||
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: TFIIIB-SNAPC masked
File | emd_35719_additional_1.map | ||||||||||||
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Annotation | TFIIIB-SNAPC masked | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map-1
File | emd_35719_half_map_1.map | ||||||||||||
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Annotation | half map-1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map-2
File | emd_35719_half_map_2.map | ||||||||||||
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Annotation | half map-2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : RNA polymerase III pre-initiation complex melting complex 1
+Supramolecule #1: RNA polymerase III pre-initiation complex melting complex 1
+Supramolecule #2: DNA-directed RNA polymerase
+Supramolecule #3: DNA
+Supramolecule #4: transcription factor
+Macromolecule #1: DNA-directed RNA polymerase III subunit RPC1
+Macromolecule #2: DNA-directed RNA polymerase III subunit RPC2
+Macromolecule #3: DNA-directed RNA polymerases I and III subunit RPAC1
+Macromolecule #4: DNA-directed RNA polymerase III subunit RPC9
+Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #7: DNA-directed RNA polymerase III subunit RPC8
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #9: DNA-directed RNA polymerase III subunit RPC10
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #11: DNA-directed RNA polymerases I and III subunit RPAC2
+Macromolecule #12: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #13: DNA-directed RNA polymerase III subunit RPC5
+Macromolecule #14: DNA-directed RNA polymerase III subunit RPC4
+Macromolecule #15: DNA-directed RNA polymerase III subunit RPC3
+Macromolecule #16: DNA-directed RNA polymerase III subunit RPC6
+Macromolecule #17: DNA-directed RNA polymerase III subunit RPC7
+Macromolecule #20: snRNA-activating protein complex subunit 1
+Macromolecule #21: snRNA-activating protein complex subunit 3
+Macromolecule #22: snRNA-activating protein complex subunit 4
+Macromolecule #23: TATA-box-binding protein
+Macromolecule #24: Transcription factor IIIB 50 kDa subunit
+Macromolecule #25: Transcription factor TFIIIB component B'' homolog
+Macromolecule #18: Human gene for U 6 RNA
+Macromolecule #19: DNA (74-MER)
+Macromolecule #26: ZINC ION
+Macromolecule #27: MAGNESIUM ION
+Macromolecule #28: IRON/SULFUR CLUSTER
-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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Image recording | Film or detector model: GATAN K3 (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: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 37656 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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Output model | PDB-8iue: |