[English] 日本語
Yorodumi
- EMDB-50247: CryoEM structure of human Mediator subunit Med23 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-50247
TitleCryoEM structure of human Mediator subunit Med23
Map data
Sample
  • Organelle or cellular component: Human Mediator subunit Med23
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 23
KeywordsMediator / MED23 / transcription / human
Function / homology
Function and homology information


positive regulation of T cell extravasation / core mediator complex / mediator complex / Generic Transcription Pathway / RSV-host interactions / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / PPARA activates gene expression ...positive regulation of T cell extravasation / core mediator complex / mediator complex / Generic Transcription Pathway / RSV-host interactions / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / PPARA activates gene expression / Transcriptional regulation of white adipocyte differentiation / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / transcription regulator complex / transcription coactivator activity / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Mediator complex, subunit Med23 / Mediator complex subunit 23
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 23
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMonte D / Verger A / Lens Z / Villeret V
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-16-CE12-0021 France
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of human Mediator recruitment by the phosphorylated transcription factor Elk-1.
Authors: Didier Monté / Zoé Lens / Frédérique Dewitte / Marcus Fislage / Marc Aumercier / Alexis Verger / Vincent Villeret /
Abstract: One function of Mediator complex subunit MED23 is to mediate transcriptional activation by the phosphorylated transcription factor Elk-1, in response to the Ras-MAPK signaling pathway. Using ...One function of Mediator complex subunit MED23 is to mediate transcriptional activation by the phosphorylated transcription factor Elk-1, in response to the Ras-MAPK signaling pathway. Using cryogenic electron microscopy, we solve a 3.0 Å structure of human MED23 complexed with the phosphorylated activation domain of Elk-1. Elk-1 binds to MED23 via a hydrophobic sequence PSIHFWSTLSP containing one phosphorylated residue (S383), which forms a tight turn around the central Phenylalanine. Binding of Elk-1 induces allosteric changes in MED23 that propagate to the opposite face of the subunit, resulting in the dynamic behavior of a 19-residue segment, which alters the molecular surface of MED23. We design a specific MED23 mutation (G382F) that disrupts Elk--1 binding and consequently impairs Elk-1-dependent serum-induced activation of target genes in the Ras-Raf-MEK-ERK signaling pathway. The structure provides molecular details and insights into a Mediator subunit-transcription factor interface.
History
DepositionMay 3, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_50247.png

Downloads & links

-
Map

FileDownload / File: emd_50247.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 256 pix.
= 260. Å		1.02 Å/pix.
x 256 pix.
= 260. Å		1.02 Å/pix.
x 256 pix.
= 260. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.01563 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.060841992 - 1.7652597
Average (Standard dev.)0.00092536054 (±0.026445126)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 260.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_50247_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_50247_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human Mediator subunit Med23

EntireName: Human Mediator subunit Med23
Components
  • Organelle or cellular component: Human Mediator subunit Med23
    • Protein or peptide: Mediator of RNA polymerase II transcription subunit 23

-
Supramolecule #1: Human Mediator subunit Med23

SupramoleculeName: Human Mediator subunit Med23 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Mediator of RNA polymerase II transcription subunit 23

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 23
type: protein_or_peptide / ID: 1 / Details: Med23 sequence with C-terminal His Tag / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 158.294891 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: METQLQSIFE EVVKTEVIEE AFPGMFMDTP EDEKTKLISC LGAFRQFWGG LSQESHEQCI QWIVKFIHGQ HSPKRISFLY DCLAMAVET GLLPPRLVCE SLINSDTLEW ERTQLWALTF KLVRKIIGGV DYKGVRDLLK VILEKILTIP NTVSSAVVQQ L LAAREVIA ...String:
METQLQSIFE EVVKTEVIEE AFPGMFMDTP EDEKTKLISC LGAFRQFWGG LSQESHEQCI QWIVKFIHGQ HSPKRISFLY DCLAMAVET GLLPPRLVCE SLINSDTLEW ERTQLWALTF KLVRKIIGGV DYKGVRDLLK VILEKILTIP NTVSSAVVQQ L LAAREVIA YILERNACLL PAYFAVTEIR KLYPEGKLPH WLLGNLVSDF VDTFRPTARI NSICGRCSLL PVVNNSGAIC NS WKLDPAT LRFPLKGLLP YDKDLFEPQT ALLRYVLEQP YSRDMVCNML GLNKQHKQRC PVLEDQLVDL VVYAMERSET EEK FDDGGT SQLLWQHLSS QLIFFVLFQF ASFPHMVLSL HQKLAGRGLI KGRDHLMWVL LQFISGSIQK NALADFLPVM KLFD LLYPE KEYIPVPDIN KPQSTHAFAM TCIWIHLNRK AQNDNSKLQI PIPHSLRLHH EFLQQSLRNK SLQMNDYKIA LLCNA YSTN SECFTLPMGA LVETIYGNGI MRIPLPGTNC MASGSITPLP MNLLDSLTVH AKMSLIHSIA TRVIKLAHAK SSVALA PAL VETYSRLLVY MEIESLGIKG FISQLLPTVF KSHAWGILHT LLEMFSYRMH HIQPHYRVQL LSHLHTLAAV AQTNQNQ LH LCVESTALRL ITALGSSEVQ PQFTRFLSDP KTVLSAESEE LNRALILTLA RATHVTDFFT GSDSIQGTWC KDILQTIM S FTPHNWASHT LSCFPGPLQA FFKQNNVPQE SRFNLKKNVE EEYRKWKSMS NENDIITHFS MQGSPPLFLC LLWKMLLET DHINQIGYRV LERIGARALV AHVRTFADFL VYEFSTSAGG QQLNKCIEIL NDMVWKYNIV TLDRLILCLA MRSHEGNEAQ VCYFIIQLL LLKPNDFRNR VSDFVKENSP EHWLQNDWHT KHMNYHKKYP EKLYFEGLAE QVDPPVQIQS PYLPIYFGNV C LRFLPVFD IVIHRFLELL PVSKSLETLL DHLGGLYKFH DRPVTYLYNT LHYYEMHLRD RAFLKRKLVH AIIGSLKDNR PQ GWCLSDT YLKCAMNARE ENPWVPDDTY YCRLIGRLVD TMAGKSPGPF PNCDWRFNEF PNPAAHALHV TCVELMALAV SGK EVGNAL LNVVLKSQPL VPRENITAWM NAIGLIITAL PEPYWIVLHD RIVSVISSPS LTSETEWVGY PFRLFDFTAC HQSY SEMSC SYTLALAHAV WHHSSIGQLS LIPKFLTEVL LPIVKTEFQL LYVYHLVGPF LQRFQQERTR CMIEIGVAFY DMLLN VDQC STHLNYMDPI CDFLYHMKYM FTGDSVKEQV EKIICNLKPA LKLRLRFITH ISKMEPAAVP PQAMNSGSPA PQSNQV PVS LPVTQDVLFQ GPGHHHHHH

UniProtKB: Mediator of RNA polymerase II transcription subunit 23

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 7.5 / Details: 20mM Tris/HCl, 100mM NaCl, 1mM TCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: blotting time 5.6sec, blot force 2.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2559224
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6h02

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 95624
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

-
Atomic model buiding 1

Initial modelPDB ID:

6h03


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9f76:
CryoEM structure of human Mediator subunit Med23

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more