+Open data
-Basic information
Entry | Database: PDB / ID: 6xp5 | ||||||
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Title | Head-Middle module of Mediator | ||||||
Components |
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Keywords | TRANSCRIPTION | ||||||
Function / homology | Function and homology information meiotic gene conversion / meiotic sister chromatid segregation / core mediator complex / mediator complex / transcription coregulator activity / transcription by RNA polymerase II / DNA repair / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||
Authors | Zhang, H.Q. / Chen, D.C. / Kornberg, R.D. | ||||||
Citation | Journal: Mol Cell / Year: 2021 Title: Mediator structure and conformation change. Authors: Heqiao Zhang / Dong-Hua Chen / Rayees U H Mattoo / David A Bushnell / Yannan Wang / Chao Yuan / Lin Wang / Chunnian Wang / Ralph E Davis / Yan Nie / Roger D Kornberg / Abstract: Mediator is a universal adaptor for transcription control. It serves as an interface between gene-specific activator or repressor proteins and the general RNA polymerase II (pol II) transcription ...Mediator is a universal adaptor for transcription control. It serves as an interface between gene-specific activator or repressor proteins and the general RNA polymerase II (pol II) transcription machinery. Previous structural studies revealed a relatively small part of Mediator and none of the gene activator-binding regions. We have determined the cryo-EM structure of the Mediator at near-atomic resolution. The structure reveals almost all amino acid residues in ordered regions, including the major targets of activator proteins, the Tail module, and the Med1 subunit of the Middle module. Comparison of Mediator structures with and without pol II reveals conformational changes that propagate across the entire Mediator, from Head to Tail, coupling activator- and pol II-interacting regions. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6xp5.cif.gz | 533.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xp5.ent.gz | 407.2 KB | Display | PDB format |
PDBx/mmJSON format | 6xp5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/6xp5 ftp://data.pdbj.org/pub/pdb/validation_reports/xp/6xp5 | HTTPS FTP |
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-Related structure data
Related structure data | 22284MC 7jmnC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Mediator of RNA polymerase II transcription subunit ... , 12 types, 12 molecules UDFGINQZHKRa
#1: Protein | Mass: 15718.674 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0029550 / Production host: Chaetomium thermophilum (fungus) / References: UniProt: G0S8E0 |
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#2: Protein | Mass: 37924.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: MED4, CTHT_0037540 / Production host: Chaetomium thermophilum (fungus) / References: UniProt: G0S7Z4 |
#3: Protein | Mass: 36470.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: MED6, CTHT_0067530 / Production host: Chaetomium thermophilum (fungus) / References: UniProt: G0SGT8 |
#4: Protein | Mass: 27738.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0064270 / Production host: Chaetomium thermophilum (fungus) / References: UniProt: G0SEM4 |
#5: Protein | Mass: 18325.607 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: MED9, CTHT_0016410 / Production host: Chaetomium thermophilum (fungus) / References: UniProt: G0S292 |
#6: Protein | Mass: 133450.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0057660 / Production host: Chaetomium thermophilum (fungus) / References: UniProt: G0SCL5 |
#7: Protein | Mass: 69616.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: MED17, CTHT_0014540 / Production host: Chaetomium thermophilum (fungus) / References: UniProt: G0S1R5 |
#8: Protein | Mass: 14486.557 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0015060 / Production host: Chaetomium thermophilum (fungus) / References: UniProt: G0S1W4 |
#9: Protein | Mass: 32098.467 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: MED8, CTHT_0058900 / Production host: Chaetomium thermophilum (fungus) / References: UniProt: G0SCZ3 |
#10: Protein | Mass: 25504.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: MED11, CTHT_0068270 / Production host: Chaetomium thermophilum (fungus) / References: UniProt: G0SH09 |
#11: Protein | Mass: 38725.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: MED18, CTHT_0007510 / Production host: Chaetomium thermophilum (fungus) / References: UniProt: G0RYQ4 |
#13: Protein | Mass: 81633.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0063280 / Production host: Chaetomium thermophilum (fungus) / References: UniProt: G0SEC7 |
-Protein , 2 types, 2 molecules Vc
#12: Protein | Mass: 18341.615 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0021510 / Production host: Chaetomium thermophilum (fungus) / References: UniProt: G0S3J8 |
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#15: Protein | Mass: 17038.955 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Production host: Chaetomium thermophilum (fungus) |
-Protein/peptide , 1 types, 1 molecules b
#14: Protein/peptide | Mass: 1805.216 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0063280 / Production host: Chaetomium thermophilum (fungus) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Head-Middle module of Mediator / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Chaetomium thermophilum (fungus) |
Buffer solution | pH: 8 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108348 / Symmetry type: POINT | ||||||||||||||||||||||||
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