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Orientation of RNA polymerase II within the human VP16-Mediator-pol II-TFIIF assembly
by single particle reconstruction, at 36 A resolution
#1: Depositted structure unit, Made by Jmol
#2: Superimposing with simplified surface model of EM map, EMDB-5343, Made by Jmol
#3: Superimposing with EM 3D map: EMDB-5343, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 3j0k |
|---|---|
| Title | Orientation of RNA polymerase II within the human VP16-Mediator-pol II-TFIIF assembly |
| Descriptor | DNA-directed RNA polymerase II largest subunit DNA-directed RNA polymerase II 140 kDa polypeptide DNA-directed RNA polymerase II 45 kDa polypeptide DNA-directed RNA polymerase II 32 kDa polypeptide DNA-directed RNA polymerases I II and III 27 kDa polypeptide DNA-directed RNA polymerases I II and III 23 kDa polypeptide DNA-directed RNA polymerase II 19 kDa polypeptide
DNA-directed RNA polymerases I II and III 14.5 kDa polypeptide DNA-directed RNA polymerase II subunit 9 DNA-directed RNA polymerases I/II/III subunit 10 DNA-directed RNA polymerase II 13.6 kDa polypeptide DNA-directed RNA polymerases I II and III 7.7 kDa polypeptide |
| Keywords |  TRANSFERASE/TRANSCRIPTION, TRANSFERASE-TRANSCRIPTION complex |
| PDBj Mine pages |  Summary, Structural Details, Experimental Details, Functional Details |
| Other databases | RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST |
| Sequence details | THIS ENTRY WAS MODELED WITH HOMOLOGOUS PROTEIN SEQUENCES FROM SACCHAROMYCES CEREVISIAE. |
| Structure Visualization | |
| Movies |  Movie Page#1: Depositted structure unit, Made by Jmol #2: Superimposing with simplified surface model of EM map, EMDB-5343, Made by Jmol #3: Superimposing with EM 3D map: EMDB-5343, Made by UCSF CHIMERA |
| Structure viewers |  Yorodumi, jV4, Jmol,  Biological unit (Images, jV) |
| Related Structure Data | |
| Related Entries |
Fit: target map of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - primary | |
| Article | Plos Biol., Vol. 9, Page: e1000603 - e1000603, Year: 2011, |
|---|---|
| Title | Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. |
| Authors | Bernecky, C., Grob, P., Ebmeier, C.C., Nogales, E., Taatjes, D.J. |
| Links | DOI: 10.1371/journal.pbio.1000603 |
 Components | |
| ID 1 : DNA-directed RNA polymerase II largest subunit | |
| Image |   |
|---|---|
| Description | DNA-directed RNA polymerase II largest subunit |
| Type | polypeptide(L) |
| Formula weight | 163180.906 Da |
| Number of molecules | 1 |
| ID | 1 |
| Ec | 2.7.7.6 |
| Source | Method: Isolated from a natural source Common name: human Cell line: HeLa NCBI taxonomy: ID:9606Organelle: nucleus Organism scientific: Homo sapiens |
| Links | Sequence view |
| ID 2 : DNA-directed RNA polymerase II 140 kDa polypeptide | |
| Image |   |
| Description | DNA-directed RNA polymerase II 140 kDa polypeptide |
| Type | polypeptide(L) |
| Formula weight | 138938.062 Da |
| Number of molecules | 1 |
| ID | 2 |
| Ec | 2.7.7.6 |
| Source | Method: Isolated from a natural source Common name: human Cell line: HeLa NCBI taxonomy: ID:9606Organelle: nucleus Organism scientific: Homo sapiens |
| Links | Sequence view |
| ID 3 : DNA-directed RNA polymerase II 45 kDa polypeptide | |
| Image |   |
| Description | DNA-directed RNA polymerase II 45 kDa polypeptide |
| Type | polypeptide(L) |
| Formula weight | 30140.277 Da |
| Number of molecules | 1 |
| ID | 3 |
| Ec | 2.7.7.6 |
| Source | Method: Isolated from a natural source Common name: human Cell line: HeLa NCBI taxonomy: ID:9606Organelle: nucleus Organism scientific: Homo sapiens |
| Links | Sequence view |
| ID 4 : DNA-directed RNA polymerase II 32 kDa polypeptide | |
| Image |   |
| Description | DNA-directed RNA polymerase II 32 kDa polypeptide |
| Type | polypeptide(L) |
| Formula weight | 25451.395 Da |
| Number of molecules | 1 |
| ID | 4 |
| Ec | 2.7.7.6 |
| Source | Method: Isolated from a natural source Common name: human Cell line: HeLa NCBI taxonomy: ID:9606Organelle: nucleus Organism scientific: Homo sapiens |
| Links | Sequence view |
| ID 5 : DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide | |
| Image |   |
| Description | DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide |
| Type | polypeptide(L) |
| Formula weight | 25117.262 Da |
| Number of molecules | 1 |
| ID | 5 |
| Ec | 2.7.7.6 |
| Source | Method: Isolated from a natural source Common name: human Cell line: HeLa NCBI taxonomy: ID:9606Organelle: nucleus Organism scientific: Homo sapiens |
| Links | Sequence view |
| ID 6 : DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide | |
| Image |   |
| Description | DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide |
| Type | polypeptide(L) |
| Formula weight | 9675.320 Da |
| Number of molecules | 1 |
| ID | 6 |
| Ec | 2.7.7.6 |
| Source | Method: Isolated from a natural source Common name: human Cell line: HeLa NCBI taxonomy: ID:9606Organelle: nucleus Organism scientific: Homo sapiens |
| Links | Sequence view |
| ID 7 : DNA-directed RNA polymerase II 19 kDa polypeptide | |
| Image |   |
| Description | DNA-directed RNA polymerase II 19 kDa polypeptide |
| Type | polypeptide(L) |
| Formula weight | 19081.186 Da |
| Number of molecules | 1 |
| ID | 7 |
| Ec | 2.7.7.6 |
| Source | Method: Isolated from a natural source Common name: human Cell line: HeLa NCBI taxonomy: ID:9606Organelle: nucleus Organism scientific: Homo sapiens |
| Links | Sequence view |
| ID 8 : DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide | |
| Image |   |
| Description | DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide |
| Type | polypeptide(L) |
| Formula weight | 16525.500 Da |
| Number of molecules | 1 |
| ID | 8 |
| Ec | 2.7.7.6 |
| Source | Method: Isolated from a natural source Common name: human Cell line: HeLa NCBI taxonomy: ID:9606Organelle: nucleus Organism scientific: Homo sapiens |
| Links | Sequence view |
| ID 9 : DNA-directed RNA polymerase II subunit 9 | |
| Image |   |
| Description | DNA-directed RNA polymerase II subunit 9 |
| Type | polypeptide(L) |
| Formula weight | 14308.247 Da |
| Number of molecules | 1 |
| ID | 9 |
| Ec | 2.7.7.6 |
| Source | Method: Isolated from a natural source Common name: human Cell line: HeLa NCBI taxonomy: ID:9606Organelle: nucleus Organism scientific: Homo sapiens |
| Links | Sequence view |
| ID 10 : DNA-directed RNA polymerases I/II/III subunit 10 | |
| Image |   |
| Description | DNA-directed RNA polymerases I/II/III subunit 10 |
| Type | polypeptide(L) |
| Formula weight | 8290.787 Da |
| Number of molecules | 1 |
| ID | 10 |
| Ec | 2.7.7.6 |
| Source | Method: Isolated from a natural source Common name: human Cell line: HeLa NCBI taxonomy: ID:9606Organelle: nucleus Organism scientific: Homo sapiens |
| Links | Sequence view |
| ID 11 : DNA-directed RNA polymerase II 13.6 kDa polypeptide | |
| Image |   |
| Description | DNA-directed RNA polymerase II 13.6 kDa polypeptide |
| Type | polypeptide(L) |
| Formula weight | 13633.628 Da |
| Number of molecules | 1 |
| ID | 11 |
| Ec | 2.7.7.6 |
| Source | Method: Isolated from a natural source Common name: human Cell line: HeLa NCBI taxonomy: ID:9606Organelle: nucleus Organism scientific: Homo sapiens |
| Links | Sequence view |
| ID 12 : DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide | |
| Image |   |
| Description | DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide |
| Type | polypeptide(L) |
| Formula weight | 5252.292 Da |
| Number of molecules | 1 |
| ID | 12 |
| Ec | 2.7.7.6 |
| Source | Method: Isolated from a natural source Common name: human Cell line: HeLa NCBI taxonomy: ID:9606Organelle: nucleus Organism scientific: Homo sapiens |
| Links | Sequence view |
| ID 13 : MAGNESIUM ION | |
| Image |    |
| Description | MAGNESIUM ION |
| Type | non-polymer |
| Formula weight | 24.305 Da |
| Number of molecules | 1 |
| ID | 13 |
| Source | Method: Obtained synthetically |
| ID 14 : ZINC ION | |
| Image |    |
| Description | ZINC ION |
| Type | non-polymer |
| Formula weight | 65.380 Da |
| Number of molecules | 9 |
| ID | 14 |
| Source | Method: Obtained synthetically |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Composition | one Mediator complex binds one pol II-TFIIF |
| Theoretical Mass | 1.9 |
| Num components | 3 |
| Entity assembly | |
| Assembly-ID | 1 |
| Ebi cell | HeLa |
| Ebi organelle | Nucleus |
| Ebi organism common | human |
| Ebi organism scientific | Homo sapiens |
| Mutant flag | NO |
| Name | core Mediator |
| Oligomeric details | 26 subunit complex |
| Synonym | Mediator |
| Type | PROTEIN |
| Entity assembly | |
| Assembly-ID | 1 |
| Ebi cell | HeLa |
| Ebi organelle | Nucleus |
| Ebi organism common | Human |
| Ebi organism scientific | Homo sapiens |
| Mutant flag | NO |
| Name | RNA polymerase II |
| Oligomeric details | 12-subunit complex |
| Synonym | pol II |
| Type | PROTEIN |
| Entity assembly | |
| Assembly-ID | 1 |
| Ebi expression system | Escherichia coli |
| Ebi organism common | Human |
| Ebi organism scientific | Homo sapiens |
| Mutant flag | YES |
| Name | TFIIF |
| Oligomeric details | Dimer |
| Synonym | TFIIF |
| Type | PROTEIN |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | VITREOUS ICE (CRYO EM) |
| Sample preparation | |
| Details | 20 mM HEPES, 0.10 mM EDTA, 150 mM KCl, 0.02% NP-40, 35% glycerol |
| pH | 7.9 |
| Sample support | |
| Details | thin carbon-coated holey carbon 400 mesh copper grid |
| Vitrification | |
| Cryogen name | ETHANE |
| Method | blot for 2 seconds, dry for 3 seconds before plunging |
| Temp | 90 Kelvin |
| Experiment | |
| Method | ELECTRON MICROSCOPY |
 Electron Microscopy | |
| Imaging | |
| Microscope | Model: FEI TECNAI F20 |
|---|---|
| Electron gun | |
| Electron source | FIELD EMISSION GUN |
| Accelerating voltage | 200 kV |
| Electron dose | 15 e/A**2 |
| Illumination mode | FLOOD BEAM |
| Lens | |
| Mode | BRIGHT FIELD |
| Magnification | Nominal: 29000 X |
| Cs | Nominal: 2.0 mm |
| Detector distance | 0.0 |
| Nominal defocus | Max: 4500 nm, Min: 1000 nm |
| Specimen holder | |
| Specimen holder | Model: GATAN LIQUID NITROGEN, Type: side entry |
| Tilt angle | Min: 0.0 degrees, Max: 0.0 degrees |
| Detector | |
| Type | Kodak SO-163 film |
| Image scans | |
| Number digital images | 106 |
| Od range | 1.0 |
| Quant bit size | 16 |
| Sampling size | 12.9 |
| Scanner model | OTHER |
 Processing | |
| 2D projection selection | |
| Software name | Situs |
|---|---|
| Single particle entity | |
| Symmetry type | ASYMMETRIC |
| 3D reconstruction | |
| CTF correction method | each micrograph |
| Details | The particles were selected interactively. |
| Method | multi-reference projection matching |
| Number of particles | 3146 |
| Resolution | 36 A |
| Resolution method | FSC at 0.5 cut-off |
| Software | Spider |
| 3D fitting | |
| Details | the TFIIS chain S was removed before fitting |
| Refinement Protocol | rigid body |
| Refinement Space | REAL |
| Software name | Situs |
| Target criteria | contour-based Laplacian correlation |
| 3D fitting list | |
| 3D fitting id | 1 |
| PDB entry ID | 1Y1V |
| Refine hist | |
| Cycle id | LAST |
| Refine id | ELECTRON MICROSCOPY |
| Total atoms | 31137 |
| Ligand atoms | 10 |
| Protein atoms | 31127 |
 Download | |||
| PDB format | |||
| All | pdb3j0k.ent.gzpdb3j0k.ent (uncompressed file) | ||
|---|---|---|---|
| Header only | pdb3j0k.ent.gz | ||
| mmCIF format | |||
| mmCIF | 3j0k.cif.gz | ||
| XML format | |||
| All | 3j0k.xml.gz | ||
| No-atom | 3j0k-noatom.xml.gz | ||
| Ext-atom | 3j0k-extatom.xml.gz | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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| movie #3 |
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