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- PDB-6xp5: Head-Middle module of Mediator -

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Basic information

Entry
Database: PDB / ID: 6xp5
TitleHead-Middle module of Mediator
Components
  • (Mediator of RNA polymerase II transcription subunit ...) x 12
  • HEAT
  • Med22
  • Unknown peptide
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


core mediator complex / mediator complex / transcription coregulator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II
Similarity search - Function
Mediator of RNA polymerase II transcription subunit 9 / RNA polymerase II transcription mediator complex subunit 9 / Mediator complex, subunit Med4 / Vitamin-D-receptor interacting Mediator subunit 4 / Mediator complex, subunit Med31 / Mediator complex, subunit Med21 / Mediator of RNA polymerase II, subunit Med31 superfamily / SOH1 / Subunit 21 of Mediator complex / Mediator complex, subunit Med7 ...Mediator of RNA polymerase II transcription subunit 9 / RNA polymerase II transcription mediator complex subunit 9 / Mediator complex, subunit Med4 / Vitamin-D-receptor interacting Mediator subunit 4 / Mediator complex, subunit Med31 / Mediator complex, subunit Med21 / Mediator of RNA polymerase II, subunit Med31 superfamily / SOH1 / Subunit 21 of Mediator complex / Mediator complex, subunit Med7 / Mediator complex, subunit Med7/Med21-like / Mediator complex, subunit Med7 superfmaily / : / MED7 protein / Mediator complex, subunit Med14 / Mediator complex subunit MED14 / Mediator complex, subunit Med6 / Mediator complex, subunit Med17 / Mediator complex, subunit Med6 superfamily / MED6 mediator sub complex component / Subunit 17 of Mediator complex / Mediator of RNA polymerase II transcription subunit 22 / Mediator complex, subunit Med8, fungi/metazoa / Mediator complex, subunit Med11 / Surfeit locus protein 5 subunit 22 of Mediator complex / Mediator of RNA polymerase II transcription complex subunit 8 / Mediator complex protein / Mediator complex, subunit Med18 / Med18 protein / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 17 / Mediator of RNA polymerase II transcription subunit 31 / Mediator of RNA polymerase II transcription subunit 9 / Uncharacterized protein / Mediator of RNA polymerase II transcription subunit 4 / Mediator of RNA polymerase II transcription subunit 21 / Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 8 / Mediator of RNA polymerase II transcription subunit 1 ...Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 17 / Mediator of RNA polymerase II transcription subunit 31 / Mediator of RNA polymerase II transcription subunit 9 / Uncharacterized protein / Mediator of RNA polymerase II transcription subunit 4 / Mediator of RNA polymerase II transcription subunit 21 / Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 8 / Mediator of RNA polymerase II transcription subunit 1 / Mediator of RNA polymerase II transcription subunit 7 / Mediator of RNA polymerase II transcription subunit 6 / Mediator of RNA polymerase II transcription subunit 11
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsZhang, H.Q. / Chen, D.C. / Kornberg, R.D.
CitationJournal: 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
DepositionJul 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.0Mar 3, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 3, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 3, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 3, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 3, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 3, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 3, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 3, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 3, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 3, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 21, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 21, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-22284
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Assembly

Deposited unit
U: Mediator of RNA polymerase II transcription subunit 21
D: Mediator of RNA polymerase II transcription subunit 4
F: Mediator of RNA polymerase II transcription subunit 6
G: Mediator of RNA polymerase II transcription subunit 7
I: Mediator of RNA polymerase II transcription subunit 9
N: Mediator of RNA polymerase II transcription subunit 14
Q: Mediator of RNA polymerase II transcription subunit 17
Z: Mediator of RNA polymerase II transcription subunit 31
H: Mediator of RNA polymerase II transcription subunit 8
K: Mediator of RNA polymerase II transcription subunit 11
R: Mediator of RNA polymerase II transcription subunit 18
V: Med22
a: Mediator of RNA polymerase II transcription subunit 1
b: Unknown peptide
c: HEAT


Theoretical massNumber of molelcules
Total (without water)568,87915
Polymers568,87915
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Mediator of RNA polymerase II transcription subunit ... , 12 types, 12 molecules UDFGINQZHKRa

#1: Protein Mediator of RNA polymerase II transcription subunit 21


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
#2: Protein Mediator of RNA polymerase II transcription subunit 4 / Mediator complex subunit 4


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 Mediator of RNA polymerase II transcription subunit 6 / Mediator complex subunit 6


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 Mediator of RNA polymerase II transcription subunit 7


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 Mediator of RNA polymerase II transcription subunit 9 / Mediator complex subunit 9


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 Mediator of RNA polymerase II transcription subunit 14 / Mediator complex subunit 14


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 Mediator of RNA polymerase II transcription subunit 17 / Mediator complex subunit 17


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 Mediator of RNA polymerase II transcription subunit 31


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 Mediator of RNA polymerase II transcription subunit 8 / Mediator complex subunit 8


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 Mediator of RNA polymerase II transcription subunit 11 / Mediator complex subunit 11


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 Mediator of RNA polymerase II transcription subunit 18 / Mediator complex subunit 18


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 Mediator of RNA polymerase II transcription subunit 1 / Mediator complex subunit 1


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

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Protein , 2 types, 2 molecules Vc

#12: Protein Med22


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
#15: Protein HEAT


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)

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Protein/peptide , 1 types, 1 molecules b

#14: Protein/peptide Unknown 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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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Head-Middle module of Mediator / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chaetomium thermophilum (fungus)
Buffer solutionpH: 8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108348 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00321402
ELECTRON MICROSCOPYf_angle_d0.75829064
ELECTRON MICROSCOPYf_dihedral_angle_d15.3863049
ELECTRON MICROSCOPYf_chiral_restr0.0443415
ELECTRON MICROSCOPYf_plane_restr0.0053801

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