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- PDB-7jmn: Tail module of Mediator complex -

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Basic information

Entry
Database: PDB / ID: 7jmn
TitleTail module of Mediator complex
Components
  • MED15
  • Mediator of RNA polymerase II transcription subunit 14
  • Mediator of RNA polymerase II transcription subunit 16
  • Mediator of RNA polymerase II transcription subunit 5
  • Unknown peptide
KeywordsTRANSCRIPTION / Activation / PolII
Function / homology
Function and homology information


core mediator complex / mediator complex / transcription coregulator activity / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription
Similarity search - Function
Mediator complex, subunit Med5, fungi / Mediator complex subunit Med5 / Mediator complex, subunit Med16 / : / Mediator complex subunit 16, N-terminal / : / Mediator complex, subunit Med14 / Mediator complex subunit MED14 / WD40-repeat-containing domain superfamily
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 16 / Mediator of RNA polymerase II transcription subunit 5 / Mediator complex subunit 15 KIX domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsZhang, H.Q. / Chen, D.C.
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
DepositionAug 2, 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 1.2Mar 6, 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 28, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 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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Assembly

Deposited unit
E: Mediator of RNA polymerase II transcription subunit 5
N: Mediator of RNA polymerase II transcription subunit 14
P: Mediator of RNA polymerase II transcription subunit 16
O: MED15
X: Unknown peptide


Theoretical massNumber of molelcules
Total (without water)555,0995
Polymers555,0995
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Mediator of RNA polymerase II transcription subunit 5 / Mediator complex subunit 5


Mass: 118784.406 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: MED5, CTHT_0065900
Production host: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SGD2
#2: Protein Mediator of RNA polymerase II transcription subunit 14 / Mediator complex subunit 14


Mass: 133223.094 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 var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SCL5
#3: Protein Mediator of RNA polymerase II transcription subunit 16 / Mediator complex subunit 16


Mass: 123395.898 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: MED16, CTHT_0059860
Production host: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SEV7
#4: Protein MED15


Mass: 175252.594 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_0070460
Production host: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0SHL5
#5: Protein Unknown peptide


Mass: 4443.468 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Production host: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
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: T module complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Buffer solutionpH: 8
SpecimenEmbedding 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: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 281144 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00413902
ELECTRON MICROSCOPYf_angle_d0.75118932
ELECTRON MICROSCOPYf_dihedral_angle_d18.3111907
ELECTRON MICROSCOPYf_chiral_restr0.0462220
ELECTRON MICROSCOPYf_plane_restr0.0052478

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