+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35712 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | human RNA polymerase III pre-initiation complex closed DNA 1 | |||||||||
Map data | closed complex 1 | |||||||||
Sample |
| |||||||||
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 / calcitonin gene-related peptide receptor activity / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly ...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 / calcitonin gene-related peptide receptor activity / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / 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 / RNA polymerase transcription factor SL1 complex / snRNA transcription by RNA polymerase II / regulation of transcription by RNA polymerase III / RPAP3/R2TP/prefoldin-like complex / DNA polymerase III complex / Cytosolic sensors of pathogen-associated DNA / RNA polymerase III general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / 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 / RNA polymerase II general transcription initiation factor binding / nucleobase-containing compound metabolic process / RNA Polymerase I Transcription Termination / transcription preinitiation complex / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / Signaling by FGFR2 IIIa TM / Viral Messenger RNA Synthesis / 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 / PIWI-interacting RNA (piRNA) biogenesis / termination of RNA polymerase III transcription / 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 / RNA polymerase III activity / transcription initiation at RNA polymerase III promoter / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / transcription by RNA polymerase I / aryl hydrocarbon receptor binding / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Processing of Capped Intron-Containing Pre-mRNA / TFIIB-class transcription factor binding / transcription by RNA polymerase III / RNA polymerase II transcribes snRNA genes / neuropeptide signaling pathway / Tat-mediated elongation of the HIV-1 transcript / transcription elongation by RNA polymerase I / positive regulation of transcription initiation by RNA polymerase II / Formation of HIV-1 elongation complex containing HIV-1 Tat / tRNA transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / core promoter sequence-specific DNA binding / Formation of RNA Pol II elongation complex / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere / TBP-class protein binding / positive regulation of interferon-beta production / mRNA Splicing - Major Pathway / acrosomal vesicle / SIRT1 negatively regulates rRNA expression / protein-DNA complex / male germ cell nucleus / DNA-templated transcription initiation / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Hou H / Jin Q / Ren Y / Wang Q / Xu Y | |||||||||
Funding support | China, 1 items
| |||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_35712.map.gz | 113.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-35712-v30.xml emd-35712.xml | 60.1 KB 60.1 KB | Display Display | EMDB header |
Images | emd_35712.png | 120.5 KB | ||
Filedesc metadata | emd-35712.cif.gz | 15.1 KB | ||
Others | emd_35712_additional_1.map.gz emd_35712_half_map_1.map.gz emd_35712_half_map_2.map.gz | 56.2 MB 98.5 MB 98.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35712 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35712 | HTTPS FTP |
-Validation report
Summary document | emd_35712_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_35712_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_35712_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | emd_35712_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35712 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35712 | HTTPS FTP |
-Related structure data
Related structure data | 8ityMC 8iueC 8iuhC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_35712.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | closed complex 1 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.334 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: TFIIIB-SNAPC masked
File | emd_35712_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | TFIIIB-SNAPC masked | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map1
File | emd_35712_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map2
File | emd_35712_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : RNA polymerase III pre-initiation complex closed complex 1
+Supramolecule #1: RNA polymerase III pre-initiation complex closed complex 1
+Supramolecule #2: RNA polymerase III pre-initiation complex closed complex 1
+Supramolecule #3: RNA polymerase III pre-initiation complex closed complex 1
+Supramolecule #4: DNA
+Macromolecule #1: snRNA-activating protein complex subunit 1
+Macromolecule #2: snRNA-activating protein complex subunit 3
+Macromolecule #3: snRNA-activating protein complex subunit 4
+Macromolecule #4: DNA-directed RNA polymerase III subunit RPC1
+Macromolecule #5: DNA-directed RNA polymerase III subunit RPC2
+Macromolecule #6: DNA-directed RNA polymerases I and III subunit RPAC1
+Macromolecule #7: DNA-directed RNA polymerase III subunit RPC9
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #9: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #10: DNA-directed RNA polymerase III subunit RPC8
+Macromolecule #11: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #12: DNA-directed RNA polymerase III subunit RPC10
+Macromolecule #13: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #14: DNA-directed RNA polymerases I and III subunit RPAC2
+Macromolecule #15: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #16: DNA-directed RNA polymerase III subunit RPC5
+Macromolecule #17: DNA-directed RNA polymerase III subunit RPC4
+Macromolecule #18: DNA-directed RNA polymerase III subunit RPC3
+Macromolecule #19: DNA-directed RNA polymerase III subunit RPC6
+Macromolecule #20: DNA-directed RNA polymerase III subunit RPC7
+Macromolecule #21: TATA-box-binding protein
+Macromolecule #22: Transcription factor IIIB 50 kDa subunit
+Macromolecule #23: Transcription factor TFIIIB component B'' homolog
+Macromolecule #24: DNA (82-MER)
+Macromolecule #25: DNA (82-MER)
+Macromolecule #26: ZINC ION
+Macromolecule #27: MAGNESIUM ION
+Macromolecule #28: IRON/SULFUR CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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 |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 70361 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |