+
Open data
-
Basic information
Entry | Database: PDB / ID: 3gto | ||||||
---|---|---|---|---|---|---|---|
Title | Backtracked RNA polymerase II complex with 15mer RNA | ||||||
![]() |
| ||||||
![]() | TRANSCRIPTION / TRANSFERASE/DNA-RNA HYBRID / TRANSFERASE / DNA-RNA HYBRID / Backtrack / DNA-directed RNA polymerase / DNA binding / Isopeptide bond / Magnesium / Metal binding / Nucleotidyltransferase / Nucleus / Phosphoprotein / Zinc-finger / DNA damage / DNA repair / TRANSFERASE-DNA-RNA HYBRID COMPLEX | ||||||
Function / homology | ![]() RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening ...RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / 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 / termination of RNA polymerase II transcription / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / Dual incision in TC-NER / transcription elongation by RNA polymerase I / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / translesion synthesis / RNA polymerase II activity / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / cytoplasmic stress granule / DNA-directed RNA polymerase / peroxisome / ribosome biogenesis / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, D. / Bushnell, D.A. / Huang, X. / Westover, K.D. / Levitt, M. / Kornberg, R.D. | ||||||
![]() | ![]() Title: Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution. Authors: Wang, D. / Bushnell, D.A. / Huang, X. / Westover, K.D. / Levitt, M. / Kornberg, R.D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 760.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 592.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 584 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 816.2 KB | Display | |
Data in XML | ![]() | 146.5 KB | Display | |
Data in CIF | ![]() | 199.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gtgSC ![]() 3gtjC ![]() 3gtkC ![]() 3gtlC ![]() 3gtmC ![]() 3gtpC ![]() 3gtqC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | ASYMMETRIC UNIT IS THE BIOLOGICAL UNIT |
-
Components
-DNA-directed RNA polymerase II subunit ... , 5 types, 5 molecules ABCIK
#1: Protein | Mass: 191821.578 Da / Num. of mol.: 1 / Fragment: DNA-directed RNA polymerase II largest subunit / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#2: Protein | Mass: 138937.297 Da / Num. of mol.: 1 Fragment: DNA-directed RNA polymerase II 140 kDa polypeptide Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 35330.457 Da / Num. of mol.: 1 / Fragment: DNA-directed RNA polymerase II 45 kDa polypeptide / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 14308.161 Da / Num. of mol.: 1 / Fragment: DNA-directed RNA polymerase II subunit 9 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 13633.493 Da / Num. of mol.: 1 Fragment: DNA-directed RNA polymerase II 13.6 kDa polypeptide Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL
#4: Protein | Mass: 25117.094 Da / Num. of mol.: 1 Fragment: DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#5: Protein | Mass: 17931.834 Da / Num. of mol.: 1 Fragment: DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: Protein | Mass: 16525.363 Da / Num. of mol.: 1 Fragment: DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 8290.732 Da / Num. of mol.: 1 / Fragment: DNA-directed RNA polymerases I/II/III subunit 10 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 7729.969 Da / Num. of mol.: 1 Fragment: DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-RNA chain , 1 types, 1 molecules R
#11: RNA chain | Mass: 4854.977 Da / Num. of mol.: 1 / Fragment: RNA strand / Source method: obtained synthetically / Details: Synthetic RNA |
---|
-DNA chain , 2 types, 2 molecules TN
#12: DNA chain | Mass: 8534.519 Da / Num. of mol.: 1 / Fragment: DNA template strand / Source method: obtained synthetically / Details: Synthetic template DNA |
---|---|
#13: DNA chain | Mass: 4286.789 Da / Num. of mol.: 1 / Fragment: DNA non-template strand / Source method: obtained synthetically / Details: Synthetic non-template DNA |
-Non-polymers , 2 types, 9 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#14: Chemical | ChemComp-ZN / #15: Chemical | ChemComp-MG / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.72 Å3/Da / Density % sol: 66.98 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM Dioxane, 10mM DTT, 9-11% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| |||||||||||||||
Detector |
| |||||||||||||||
Radiation |
| |||||||||||||||
Radiation wavelength |
| |||||||||||||||
Reflection | Resolution: 4→50 Å / Num. obs: 54082 / % possible obs: 90.4 % / Redundancy: 3.6 % / Net I/σ(I): 7.7 | |||||||||||||||
Reflection shell | Resolution: 4→4.1 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2 / % possible all: 77.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 3GTG Resolution: 4→50 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.874 / SU B: 135.474 / SU ML: 0.8 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.894 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 125.304 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 4→4.11 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|