+
Open data
-
Basic information
Entry | Database: PDB / ID: 1i6h | ||||||
---|---|---|---|---|---|---|---|
Title | RNA POLYMERASE II ELONGATION COMPLEX | ||||||
![]() |
| ||||||
![]() | TRANSCRIPTION/DNA-RNA HYBRID / TRANSCRIPTION / MRNA / MULTIPROTEIN COMPLEX / MOLECULAR MACHINE / DNA / TRANSCRIPTION-DNA-RNA COMPLEX / TRANSCRIPTION-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 / termination of RNA polymerase II transcription / RNA Polymerase II Promoter Escape ...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 / termination of RNA polymerase II transcription / 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 II Pre-transcription Events / RNA-templated transcription / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase III transcription / RNA Polymerase I Promoter Escape / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription by RNA polymerase I / transcription by RNA polymerase III / Dual incision in TC-NER / RNA polymerase I complex / tRNA transcription by RNA polymerase III / translesion synthesis / RNA polymerase III complex / transcription elongation by RNA polymerase I / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / : / DNA-directed RNA polymerase activity / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / cytoplasmic stress granule / 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 | ![]() ![]() ![]() | ||||||
![]() | Gnatt, A.L. / Cramer, P. / Kornberg, R.D. | ||||||
![]() | ![]() Title: Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution. Authors: Gnatt, A.L. / Cramer, P. / Fu, J. / Bushnell, D.A. / Kornberg, R.D. #1: ![]() Title: Structural Basis of Transcription: RNA Polymerase II at 2.8 A Resolution Authors: Cramer, P. / Bushnell, D.A. / Kornberg, R.D. #2: ![]() Title: Architecture of RNA Polymerase II and Implications for the Transcription Mechanism Authors: Cramer, P. / Bushnell, D.A. / Fu, J. / Gnatt, A.L. / Maier-Davis, B. / Thompson, N.E. / Burgess, R.R. / Edwards, A.M. / David, P.R. / Kornberg, R.D. | ||||||
History |
| ||||||
Remark 650 | HELIX REMOVAL OF THE SECONDARY STRUCTURE WAS REQUESTED BY THE AUTHOR. Secondary structure was ...HELIX REMOVAL OF THE SECONDARY STRUCTURE WAS REQUESTED BY THE AUTHOR. Secondary structure was assigned by visual inspection, see reference 1. | ||||||
Remark 700 | SHEET REMOVAL OF THE SECONDARY STRUCTURE WAS REQUESTED BY THE AUTHOR. Secondary structure was ...SHEET REMOVAL OF THE SECONDARY STRUCTURE WAS REQUESTED BY THE AUTHOR. Secondary structure was assigned by visual inspection, see reference 1. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 737.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 577.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 502.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 740.4 KB | Display | |
Data in XML | ![]() | 100.1 KB | Display | |
Data in CIF | ![]() | 148.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1i3qS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-DNA-DIRECTED RNA POLYMERASE II ... , 10 types, 10 molecules ABCEFHIJKL
#3: Protein | Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#4: Protein | Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: Protein | Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: Protein | Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-DNA chain / RNA chain , 2 types, 2 molecules DR
#1: DNA chain | Mass: 3966.596 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: TEMPLATE Source: (gene. exp.) ![]() ![]() |
---|---|
#2: RNA chain | Mass: 2893.823 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The RNA was synthesized by the polymerase before the crystal was formed. |
-Non-polymers , 2 types, 9 molecules 


#13: Chemical | ChemComp-MG / |
---|---|
#14: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.37 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, sitting drop / pH: 6 Details: PEG 6000, AMMONIUM HYDROGEN PHOSPHATE, SODIUM DIHYDROGEN PHOSPHATE, DIOXANE, DTT, pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 100K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 17, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.998 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→40 Å / Num. obs: 96867 / % possible obs: 100 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.111 |
Reflection shell | Resolution: 3.3→3.4 Å / Rmerge(I) obs: 0.317 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 40 Å |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1I3Q Resolution: 3.3→40 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.51 Å2
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→40 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rwork: 0.25 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|