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Yorodumi- EMDB-12795: Cryo-EM structure of human RNA Polymerase I in elongation state -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12795 | |||||||||
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Title | Cryo-EM structure of human RNA Polymerase I in elongation state | |||||||||
Map data | Elongating human RNA Polymerase I, Map A, unsharpened | |||||||||
Sample |
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Keywords | RNA polymerase I / human / rRNA transcription / DNA-dependent RNA polymerase / elongation state / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information RNA polymerase I transcription regulator complex / negative regulation of protein localization to nucleolus / nucleologenesis / neural crest formation / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / DNA/RNA hybrid binding / regulation of transcription by RNA polymerase I / RNA polymerase I general transcription initiation factor binding / RPAP3/R2TP/prefoldin-like complex ...RNA polymerase I transcription regulator complex / negative regulation of protein localization to nucleolus / nucleologenesis / neural crest formation / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / DNA/RNA hybrid binding / regulation of transcription by RNA polymerase I / RNA polymerase I general transcription initiation factor binding / RPAP3/R2TP/prefoldin-like complex / 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 / RNA polymerase I preinitiation complex assembly / nucleobase-containing compound metabolic process / Abortive elongation of HIV-1 transcript in the absence of Tat / MicroRNA (miRNA) biogenesis / RNA Polymerase I Transcription Termination / FGFR2 alternative splicing / 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 / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / PIWI-interacting RNA (piRNA) biogenesis / 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 / termination of RNA polymerase I transcription / mRNA Splicing - Minor Pathway / nucleolar large rRNA transcription by RNA polymerase I / 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 / transcription initiation at RNA polymerase I promoter / rRNA transcription / Processing of Capped Intron-Containing Pre-mRNA / transcription by RNA polymerase III / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / Tat-mediated elongation of the HIV-1 transcript / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / Formation of HIV-1 elongation complex containing HIV-1 Tat / 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 / Formation of RNA Pol II elongation complex / cell surface receptor protein tyrosine kinase signaling pathway / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere / embryo implantation / mRNA Splicing - Major Pathway / cellular response to leukemia inhibitory factor / DNA-templated transcription initiation / protein-DNA complex / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / fibrillar center / ribonucleoside binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / chromosome / single-stranded DNA binding / Estrogen-dependent gene expression / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / protein stabilization / chromatin binding / nucleolus / magnesium ion binding / mitochondrion / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Misiaszek AD / Girbig M | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2021 Title: Cryo-EM structures of human RNA polymerase I. Authors: Agata D Misiaszek / Mathias Girbig / Helga Grötsch / Florence Baudin / Brice Murciano / Aleix Lafita / Christoph W Müller / Abstract: RNA polymerase I (Pol I) specifically synthesizes ribosomal RNA. Pol I upregulation is linked to cancer, while mutations in the Pol I machinery lead to developmental disorders. Here we report the ...RNA polymerase I (Pol I) specifically synthesizes ribosomal RNA. Pol I upregulation is linked to cancer, while mutations in the Pol I machinery lead to developmental disorders. Here we report the cryo-EM structure of elongating human Pol I at 2.7 Å resolution. In the exit tunnel, we observe a double-stranded RNA helix that may support Pol I processivity. Our structure confirms that human Pol I consists of 13 subunits with only one subunit forming the Pol I stalk. Additionally, the structure of human Pol I in complex with the initiation factor RRN3 at 3.1 Å resolution reveals stalk flipping upon RRN3 binding. We also observe an inactivated state of human Pol I bound to an open DNA scaffold at 3.3 Å resolution. Lastly, the high-resolution structure of human Pol I allows mapping of disease-related mutations that can aid understanding of disease etiology. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12795.map.gz | 65.2 MB | EMDB map data format | |
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Header (meta data) | emd-12795-v30.xml emd-12795.xml | 61.1 KB 61.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12795_fsc.xml | 10 KB | Display | FSC data file |
Images | emd_12795.png | 62.1 KB | ||
Masks | emd_12795_msk_1.map emd_12795_msk_2.map emd_12795_msk_3.map | 83.7 MB 83.7 MB 83.7 MB | Mask map | |
Filedesc metadata | emd-12795.cif.gz | 11.5 KB | ||
Others | emd_12795_additional_1.map.gz emd_12795_additional_2.map.gz emd_12795_additional_3.map.gz emd_12795_additional_4.map.gz emd_12795_additional_5.map.gz emd_12795_additional_6.map.gz emd_12795_additional_7.map.gz emd_12795_additional_8.map.gz emd_12795_additional_9.map.gz emd_12795_half_map_1.map.gz emd_12795_half_map_2.map.gz | 75.3 MB 64.9 MB 73.5 MB 66.8 MB 62.3 MB 73.9 MB 76.1 MB 67.2 MB 74.8 MB 65.4 MB 65.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12795 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12795 | HTTPS FTP |
-Validation report
Summary document | emd_12795_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_12795_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_12795_validation.xml.gz | 17 KB | Display | |
Data in CIF | emd_12795_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12795 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12795 | HTTPS FTP |
-Related structure data
Related structure data | 7ob9MC 7obaC 7obbC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10965 (Title: Cryo-EM structure of human RNA polymerase I in elongation state Data size: 1.8 TB Data #1: Unaligned multi-frame micrographs of human RNA polymerase I in elongating state [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12795.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Elongating human RNA Polymerase I, Map A, unsharpened | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.822 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
+Mask #1
+Mask #2
+Mask #3
+Additional map: Elongating human RNA Polymerase I, Map B1, RELION...
+Additional map: Elongating human RNA Polymerase I, Map A, locally...
+Additional map: Elongating human RNA Polymerase I, Map B, RELION...
+Additional map: Elongating human RNA Polymerase I, Map B2, RELION...
+Additional map: Elongating human RNA Polymerase I, Map B1, RELION...
+Additional map: Elongating human RNA Polymerase I, Map B, RELION...
+Additional map: Elongating human RNA Polymerase I, Map B2, RELION...
+Additional map: Elongating human RNA Polymerase I, Map C, Phenix...
+Additional map: Elongating human RNA Polymerase I, Map C, Phenix...
+Half map: Elongating human RNA Polymerase I, Map A, half map 2
+Half map: Elongating human RNA Polymerase I, Map A, half map 2
-Sample components
+Entire : RNA polymerase I
+Supramolecule #1: RNA polymerase I
+Supramolecule #2: RNA polymerase I
+Supramolecule #3: RNA and DNA
+Macromolecule #1: DNA-directed RNA polymerase I subunit RPA1
+Macromolecule #2: DNA-directed RNA polymerase I subunit RPA2
+Macromolecule #3: DNA-directed RNA polymerases I and III subunit RPAC1
+Macromolecule #4: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #6: DNA-directed RNA polymerase I subunit RPA43
+Macromolecule #7: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #8: DNA-directed RNA polymerase I subunit RPA12
+Macromolecule #9: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #10: DNA-directed RNA polymerases I and III subunit RPAC2
+Macromolecule #11: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #12: DNA-directed RNA polymerase I subunit RPA34
+Macromolecule #13: DNA-directed RNA polymerase I subunit RPA49
+Macromolecule #14: RNA
+Macromolecule #15: DNA non-template strand
+Macromolecule #16: DNA template strand
+Macromolecule #17: ZINC ION
+Macromolecule #18: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.7 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER Details: NanoClean plasma cleaner (Fischione Instruments, Model 1070) | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 3, blot time 0 s, wait time 0 s. | |||||||||||||||
Details | Human RNA Polymerase I with 1.5 molar excess of the synthetic nucleic acid template |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 10053 / Average electron dose: 50.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Details | Initial rigid body fitting with UCSF Chimera followed by manual model fitting in Coot. | ||||||||||||||||
Output model | PDB-7ob9: |