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3j1o

Cryo-EM map of a yeast minimal preinitiation complex interacting with the Mediator Head module

Method: ELECTRON MICROSCOPY Dmax: 155.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Mediator of RNA polymerase II transcription subunit 11

Saccharomyces cerevisiae

UniProt A0A0D3YMY9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count Chain H； UniProt 1–131 Mutation：T16G, M17S Mediator of RNA polymerase II transcription subunit 17 × 1 （P32569） Mediator of RNA polymerase II transcription subunit 8 × 1 （P38304） Mediator of RNA polymerase II transcription subunit 22 × 1 （P32570） Mediator of RNA polymerase II transcription subunit 18 × 1 （P32585） Mediator of RNA polymerase II transcription subunit 20 × 1 （P34162） Mediator of RNA polymerase II transcription subunit 6 × 1 （P38782） ELECTRON MICROSCOPY cryo-EM buffer：25 mM KCl, 25 mM Tris-HCl, 10 mM DTT；pH 8；25 mM KCl, 25 mM Tris-HCl, 10 mM DTT cryo-EM vitrification conditions：Blot for ~2 sec before plunging；77 K；Cryogen ETHANE；Blot for approximately 2 seconds before plunging into liquid ethane. Resolution 16.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A0D3YMY9_YEASX
Isoform —
PDB entities 1
Chains and sequence ranges Author chain H； PDBConstruct 1–131； UniProt 1–131

Mediator of RNA polymerase II transcription subunit 17

Saccharomyces cerevisiae

UniProt P32569

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count Chain I； UniProt 197–616 Chain I； UniProt 669–687 Fragment：SEE REMARK 999 Mediator of RNA polymerase II transcription subunit 11 × 1 （A0A0D3YMY9） Mediator of RNA polymerase II transcription subunit 8 × 1 （P38304） Mediator of RNA polymerase II transcription subunit 22 × 1 （P32570） Mediator of RNA polymerase II transcription subunit 18 × 1 （P32585） Mediator of RNA polymerase II transcription subunit 20 × 1 （P34162） Mediator of RNA polymerase II transcription subunit 6 × 1 （P38782） ELECTRON MICROSCOPY cryo-EM buffer：25 mM KCl, 25 mM Tris-HCl, 10 mM DTT；pH 8；25 mM KCl, 25 mM Tris-HCl, 10 mM DTT cryo-EM vitrification conditions：Blot for ~2 sec before plunging；77 K；Cryogen ETHANE；Blot for approximately 2 seconds before plunging into liquid ethane. Resolution 16.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3J1O Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3RJ1 Architecture of the Mediator Head module Deposited 2011-04-14 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain B 109–616（508 aa）
Chain B 669–687（19 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SE SELENIUM ATOM × 30 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.1 M Tris-HCl (pH 7.6) containing 10-12.5% (w/v) PEG-6K, and 0.4 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 4.30 Å R-free 0.373
3RJ1 Architecture of the Mediator Head module Deposited 2011-04-14 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain I 109–616（508 aa）
Chain I 669–687（19 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SE SELENIUM ATOM × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.1 M Tris-HCl (pH 7.6) containing 10-12.5% (w/v) PEG-6K, and 0.4 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 4.30 Å R-free 0.373
3RJ1 Architecture of the Mediator Head module Deposited 2011-04-14 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain P 109–616（508 aa）
Chain P 669–687（19 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SE SELENIUM ATOM × 32 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.1 M Tris-HCl (pH 7.6) containing 10-12.5% (w/v) PEG-6K, and 0.4 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 4.30 Å R-free 0.373
4GWP Structure of the Mediator Head Module from S. cerevisiae Deposited 2012-09-03 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain B 1–687（687 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.2 K；275mM ammonium citrate tribasic pH 7.0, 10% w/v PEG 3350, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K
Resolution 4.20 Å R-free 0.357
4GWQ Structure of the Mediator Head Module from S. cerevisiae in complex with the carboxy-terminal domain (CTD) of RNA Polymerase II Rpb1 subunit Deposited 2012-09-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–687（687 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；291.2 K；275mM ammonium citrate tribasic pH 7.0, 10% w/v PEG 3350, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K
Resolution 4.50 Å R-free 0.345
4H62 Structure of the Saccharomyces cerevisiae Mediator subcomplex Med17C/Med11C/Med22C Deposited 2012-09-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Q 377–687（311 aa） Fragment：C-terminal region (Unp residues 377-687)
Non-standard monomer：Yes (specific site not provided by mmCIF) MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, 4 M ammonium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.00 Å R-free 0.229
4V1O Architecture of the RNA polymerase II-Mediator core transcription initiation complex Deposited 2014-09-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain W 1–687（687 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE GLOW- DISCHARGED FOR 20 S BEFORE DEPOSITION OF 4 MICROLITERS SAMPLE AND INCUBATED FOR 30 S. GRIDS WERE WASHED TWICE WITH 4 MICROLITERS DISTILLED WATER, BLOTTED, AND VITRIFIED BY PLUNGING INTO LIQUID ETHANE WITH A MANUAL PLUNGER.
Resolution 9.70 Å
5OQM STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR Deposited 2017-08-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain d 1–687（687 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 8 s and plunge-frozen in liquid ethane.
Resolution 5.80 Å
5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain P 1–687（687 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 15.30 Å
7UI9 Core Mediator-PICearly (Copy A) Deposited 2022-03-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain q 1–687（687 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7UIF Mediator-PIC Early (Core B) Deposited 2022-03-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain q 1–687（687 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7UIG Mediator-PIC Early (Mediator A) Deposited 2022-03-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain q 1–687（687 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7UIO Mediator-PIC Early (Composite Model) Deposited 2022-03-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 78 PDB declaration: 80-meric
Chain Aq 1–687（687 aa）
Chain Bq 1–687（687 aa）
Not recorded ZN ZINC ION × 4 THR THREONINE × 1 ALA ALANINE × 1 ASP ASPARTIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å

11 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MED17_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain I； PDBConstruct 1–420； UniProt 197–616 Author chain I； PDBConstruct 466–484； UniProt 669–687

Mediator of RNA polymerase II transcription subunit 8

Saccharomyces cerevisiae

UniProt P38304

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count Chain J； UniProt 1–223 Not recorded Mediator of RNA polymerase II transcription subunit 11 × 1 （A0A0D3YMY9） Mediator of RNA polymerase II transcription subunit 17 × 1 （P32569） Mediator of RNA polymerase II transcription subunit 22 × 1 （P32570） Mediator of RNA polymerase II transcription subunit 18 × 1 （P32585） Mediator of RNA polymerase II transcription subunit 20 × 1 （P34162） Mediator of RNA polymerase II transcription subunit 6 × 1 （P38782） ELECTRON MICROSCOPY cryo-EM buffer：25 mM KCl, 25 mM Tris-HCl, 10 mM DTT；pH 8；25 mM KCl, 25 mM Tris-HCl, 10 mM DTT cryo-EM vitrification conditions：Blot for ~2 sec before plunging；77 K；Cryogen ETHANE；Blot for approximately 2 seconds before plunging into liquid ethane. Resolution 16.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3J1O Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 189–209（21 aa） Fragment：C-terminal domain, residues 189-209
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 189–209（21 aa） Fragment：C-terminal domain, residues 189-209
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 189–209（21 aa） Fragment：C-terminal domain, residues 189-209
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain L 189–209（21 aa） Fragment：C-terminal domain, residues 189-209
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain I 189–209（21 aa） Fragment：C-terminal domain, residues 189-209
Chain J 189–209（21 aa） Fragment：C-terminal domain, residues 189-209
Chain K 189–209（21 aa） Fragment：C-terminal domain, residues 189-209
Chain L 189–209（21 aa） Fragment：C-terminal domain, residues 189-209
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain I 189–209（21 aa） Fragment：C-terminal domain, residues 189-209
Chain J 189–209（21 aa） Fragment：C-terminal domain, residues 189-209
Chain K 189–209（21 aa） Fragment：C-terminal domain, residues 189-209
Chain L 189–209（21 aa） Fragment：C-terminal domain, residues 189-209
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain I 189–209（21 aa） Fragment：C-terminal domain, residues 189-209
Chain K 189–209（21 aa） Fragment：C-terminal domain, residues 189-209
Chain L 189–209（21 aa） Fragment：C-terminal domain, residues 189-209
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain I 189–209（21 aa） Fragment：C-terminal domain, residues 189-209
Chain L 189–209（21 aa） Fragment：C-terminal domain, residues 189-209
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
3RJ1 Architecture of the Mediator Head module Deposited 2011-04-14 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 1–223（223 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SE SELENIUM ATOM × 30 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.1 M Tris-HCl (pH 7.6) containing 10-12.5% (w/v) PEG-6K, and 0.4 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 4.30 Å R-free 0.373
3RJ1 Architecture of the Mediator Head module Deposited 2011-04-14 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain J 1–223（223 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SE SELENIUM ATOM × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.1 M Tris-HCl (pH 7.6) containing 10-12.5% (w/v) PEG-6K, and 0.4 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 4.30 Å R-free 0.373
3RJ1 Architecture of the Mediator Head module Deposited 2011-04-14 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain Q 1–223（223 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SE SELENIUM ATOM × 32 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.1 M Tris-HCl (pH 7.6) containing 10-12.5% (w/v) PEG-6K, and 0.4 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 4.30 Å R-free 0.373
4GWP Structure of the Mediator Head Module from S. cerevisiae Deposited 2012-09-03 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 1–223（223 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.2 K；275mM ammonium citrate tribasic pH 7.0, 10% w/v PEG 3350, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K
Resolution 4.20 Å R-free 0.357
4GWQ Structure of the Mediator Head Module from S. cerevisiae in complex with the carboxy-terminal domain (CTD) of RNA Polymerase II Rpb1 subunit Deposited 2012-09-03 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 1–223（223 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；291.2 K；275mM ammonium citrate tribasic pH 7.0, 10% w/v PEG 3350, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K
Resolution 4.50 Å R-free 0.345
4V1O Architecture of the RNA polymerase II-Mediator core transcription initiation complex Deposited 2014-09-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain U 2–223（222 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE GLOW- DISCHARGED FOR 20 S BEFORE DEPOSITION OF 4 MICROLITERS SAMPLE AND INCUBATED FOR 30 S. GRIDS WERE WASHED TWICE WITH 4 MICROLITERS DISTILLED WATER, BLOTTED, AND VITRIFIED BY PLUNGING INTO LIQUID ETHANE WITH A MANUAL PLUNGER.
Resolution 9.70 Å
5OQM STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR Deposited 2017-08-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain b 1–223（223 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 8 s and plunge-frozen in liquid ethane.
Resolution 5.80 Å
5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain N 1–223（223 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 15.30 Å
7UI9 Core Mediator-PICearly (Copy A) Deposited 2022-03-28 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain h 1–223（223 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7UIF Mediator-PIC Early (Core B) Deposited 2022-03-29 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain h 1–223（223 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7UIG Mediator-PIC Early (Mediator A) Deposited 2022-03-29 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain h 1–223（223 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7UIO Mediator-PIC Early (Composite Model) Deposited 2022-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 78 PDB declaration: 80-meric
Chain Ah 1–223（223 aa）
Chain Bh 1–223（223 aa）
Not recorded ZN ZINC ION × 4 THR THREONINE × 1 ALA ALANINE × 1 ASP ASPARTIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å

11 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MED8_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain J； PDBConstruct 1–223； UniProt 1–223

Mediator of RNA polymerase II transcription subunit 22

Saccharomyces cerevisiae

UniProt P32570

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count Chain K； UniProt 1–121 Not recorded Mediator of RNA polymerase II transcription subunit 11 × 1 （A0A0D3YMY9） Mediator of RNA polymerase II transcription subunit 17 × 1 （P32569） Mediator of RNA polymerase II transcription subunit 8 × 1 （P38304） Mediator of RNA polymerase II transcription subunit 18 × 1 （P32585） Mediator of RNA polymerase II transcription subunit 20 × 1 （P34162） Mediator of RNA polymerase II transcription subunit 6 × 1 （P38782） ELECTRON MICROSCOPY cryo-EM buffer：25 mM KCl, 25 mM Tris-HCl, 10 mM DTT；pH 8；25 mM KCl, 25 mM Tris-HCl, 10 mM DTT cryo-EM vitrification conditions：Blot for ~2 sec before plunging；77 K；Cryogen ETHANE；Blot for approximately 2 seconds before plunging into liquid ethane. Resolution 16.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3J1O Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3R84 Structure of the Mediator head subcomplex Med11/22 Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–89（88 aa） Fragment：Residues 2-89
Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100 mM MES pH 6, 5.5% PEG 6000 and 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.05 Å R-free 0.208
3R84 Structure of the Mediator head subcomplex Med11/22 Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 10 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain T 2–89（88 aa） Fragment：Residues 2-89
Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100 mM MES pH 6, 5.5% PEG 6000 and 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.05 Å R-free 0.208
3R84 Structure of the Mediator head subcomplex Med11/22 Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain V 2–89（88 aa） Fragment：Residues 2-89
Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100 mM MES pH 6, 5.5% PEG 6000 and 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.05 Å R-free 0.208
3R84 Structure of the Mediator head subcomplex Med11/22 Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain X 2–89（88 aa） Fragment：Residues 2-89
Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100 mM MES pH 6, 5.5% PEG 6000 and 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.05 Å R-free 0.208
3R84 Structure of the Mediator head subcomplex Med11/22 Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 13 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2–89（88 aa） Fragment：Residues 2-89
Chain D 2–89（88 aa） Fragment：Residues 2-89
Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100 mM MES pH 6, 5.5% PEG 6000 and 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.05 Å R-free 0.208
3R84 Structure of the Mediator head subcomplex Med11/22 Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 14 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 2–89（88 aa） Fragment：Residues 2-89
Chain H 2–89（88 aa） Fragment：Residues 2-89
Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100 mM MES pH 6, 5.5% PEG 6000 and 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.05 Å R-free 0.208
3R84 Structure of the Mediator head subcomplex Med11/22 Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 15 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain J 2–89（88 aa） Fragment：Residues 2-89
Chain L 2–89（88 aa） Fragment：Residues 2-89
Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100 mM MES pH 6, 5.5% PEG 6000 and 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.05 Å R-free 0.208
3R84 Structure of the Mediator head subcomplex Med11/22 Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 16 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain N 2–89（88 aa） Fragment：Residues 2-89
Chain P 2–89（88 aa） Fragment：Residues 2-89
Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100 mM MES pH 6, 5.5% PEG 6000 and 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.05 Å R-free 0.208
3R84 Structure of the Mediator head subcomplex Med11/22 Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 17 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 2–89（88 aa） Fragment：Residues 2-89
Chain T 2–89（88 aa） Fragment：Residues 2-89
Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100 mM MES pH 6, 5.5% PEG 6000 and 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.05 Å R-free 0.208
3R84 Structure of the Mediator head subcomplex Med11/22 Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 18 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain V 2–89（88 aa） Fragment：Residues 2-89
Chain X 2–89（88 aa） Fragment：Residues 2-89
Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100 mM MES pH 6, 5.5% PEG 6000 and 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.05 Å R-free 0.208
3R84 Structure of the Mediator head subcomplex Med11/22 Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 19 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain B 2–89（88 aa） Fragment：Residues 2-89
Chain D 2–89（88 aa） Fragment：Residues 2-89
Chain F 2–89（88 aa） Fragment：Residues 2-89
Chain H 2–89（88 aa） Fragment：Residues 2-89
Chain J 2–89（88 aa） Fragment：Residues 2-89
Chain L 2–89（88 aa） Fragment：Residues 2-89
Chain N 2–89（88 aa） Fragment：Residues 2-89
Chain P 2–89（88 aa） Fragment：Residues 2-89
Chain R 2–89（88 aa） Fragment：Residues 2-89
Chain T 2–89（88 aa） Fragment：Residues 2-89
Chain V 2–89（88 aa） Fragment：Residues 2-89
Chain X 2–89（88 aa） Fragment：Residues 2-89
Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100 mM MES pH 6, 5.5% PEG 6000 and 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.05 Å R-free 0.208
3R84 Structure of the Mediator head subcomplex Med11/22 Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–89（88 aa） Fragment：Residues 2-89
Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100 mM MES pH 6, 5.5% PEG 6000 and 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.05 Å R-free 0.208
3R84 Structure of the Mediator head subcomplex Med11/22 Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 2–89（88 aa） Fragment：Residues 2-89
Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100 mM MES pH 6, 5.5% PEG 6000 and 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.05 Å R-free 0.208
3R84 Structure of the Mediator head subcomplex Med11/22 Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 2–89（88 aa） Fragment：Residues 2-89
Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100 mM MES pH 6, 5.5% PEG 6000 and 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.05 Å R-free 0.208
3R84 Structure of the Mediator head subcomplex Med11/22 Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain J 2–89（88 aa） Fragment：Residues 2-89
Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100 mM MES pH 6, 5.5% PEG 6000 and 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.05 Å R-free 0.208
3R84 Structure of the Mediator head subcomplex Med11/22 Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 2–89（88 aa） Fragment：Residues 2-89
Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100 mM MES pH 6, 5.5% PEG 6000 and 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.05 Å R-free 0.208
3R84 Structure of the Mediator head subcomplex Med11/22 Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain N 2–89（88 aa） Fragment：Residues 2-89
Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100 mM MES pH 6, 5.5% PEG 6000 and 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.05 Å R-free 0.208
3R84 Structure of the Mediator head subcomplex Med11/22 Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 2–89（88 aa） Fragment：Residues 2-89
Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100 mM MES pH 6, 5.5% PEG 6000 and 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.05 Å R-free 0.208
3R84 Structure of the Mediator head subcomplex Med11/22 Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 2–89（88 aa） Fragment：Residues 2-89
Mutation：M27I Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；100 mM MES pH 6, 5.5% PEG 6000 and 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.05 Å R-free 0.208
3RJ1 Architecture of the Mediator Head module Deposited 2011-04-14 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 1–121（121 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SE SELENIUM ATOM × 30 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.1 M Tris-HCl (pH 7.6) containing 10-12.5% (w/v) PEG-6K, and 0.4 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 4.30 Å R-free 0.373
3RJ1 Architecture of the Mediator Head module Deposited 2011-04-14 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain K 1–121（121 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SE SELENIUM ATOM × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.1 M Tris-HCl (pH 7.6) containing 10-12.5% (w/v) PEG-6K, and 0.4 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 4.30 Å R-free 0.373
3RJ1 Architecture of the Mediator Head module Deposited 2011-04-14 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain R 1–121（121 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SE SELENIUM ATOM × 32 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.1 M Tris-HCl (pH 7.6) containing 10-12.5% (w/v) PEG-6K, and 0.4 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 4.30 Å R-free 0.373
4GWP Structure of the Mediator Head Module from S. cerevisiae Deposited 2012-09-03 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 1–121（121 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.2 K；275mM ammonium citrate tribasic pH 7.0, 10% w/v PEG 3350, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K
Resolution 4.20 Å R-free 0.357
4GWQ Structure of the Mediator Head Module from S. cerevisiae in complex with the carboxy-terminal domain (CTD) of RNA Polymerase II Rpb1 subunit Deposited 2012-09-03 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 1–121（121 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；291.2 K；275mM ammonium citrate tribasic pH 7.0, 10% w/v PEG 3350, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K
Resolution 4.50 Å R-free 0.345
4H62 Structure of the Saccharomyces cerevisiae Mediator subcomplex Med17C/Med11C/Med22C Deposited 2012-09-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain V 96–121（26 aa） Fragment：C-terminal region (Unp residues 96-121)
Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, 4 M ammonium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.00 Å R-free 0.229
4V1O Architecture of the RNA polymerase II-Mediator core transcription initiation complex Deposited 2014-09-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain Z 2–121（120 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE GLOW- DISCHARGED FOR 20 S BEFORE DEPOSITION OF 4 MICROLITERS SAMPLE AND INCUBATED FOR 30 S. GRIDS WERE WASHED TWICE WITH 4 MICROLITERS DISTILLED WATER, BLOTTED, AND VITRIFIED BY PLUNGING INTO LIQUID ETHANE WITH A MANUAL PLUNGER.
Resolution 9.70 Å
5OQM STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR Deposited 2017-08-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain g 1–121（121 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 8 s and plunge-frozen in liquid ethane.
Resolution 5.80 Å
5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain S 1–121（121 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 15.30 Å
7UI9 Core Mediator-PICearly (Copy A) Deposited 2022-03-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain v 1–120（120 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7UIF Mediator-PIC Early (Core B) Deposited 2022-03-29 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain v 1–121（121 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7UIG Mediator-PIC Early (Mediator A) Deposited 2022-03-29 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain v 1–121（121 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7UIO Mediator-PIC Early (Composite Model) Deposited 2022-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 78 PDB declaration: 80-meric
Chain Av 1–120（120 aa）
Chain Bv 1–120（120 aa）
Not recorded ZN ZINC ION × 4 THR THREONINE × 1 ALA ALANINE × 1 ASP ASPARTIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8CEO Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome Deposited 2023-02-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric
Chain g 1–121（121 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å

13 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MED22_YEAST
Isoform —
PDB entities 4
Chains and sequence ranges Author chain K； PDBConstruct 1–121； UniProt 1–121

Mediator of RNA polymerase II transcription subunit 18

Saccharomyces cerevisiae

UniProt P32585

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count Chain L； UniProt 1–108 Chain L； UniProt 141–307 Not recorded Mediator of RNA polymerase II transcription subunit 11 × 1 （A0A0D3YMY9） Mediator of RNA polymerase II transcription subunit 17 × 1 （P32569） Mediator of RNA polymerase II transcription subunit 8 × 1 （P38304） Mediator of RNA polymerase II transcription subunit 22 × 1 （P32570） Mediator of RNA polymerase II transcription subunit 20 × 1 （P34162） Mediator of RNA polymerase II transcription subunit 6 × 1 （P38782） ELECTRON MICROSCOPY cryo-EM buffer：25 mM KCl, 25 mM Tris-HCl, 10 mM DTT；pH 8；25 mM KCl, 25 mM Tris-HCl, 10 mM DTT cryo-EM vitrification conditions：Blot for ~2 sec before plunging；77 K；Cryogen ETHANE；Blot for approximately 2 seconds before plunging into liquid ethane. Resolution 16.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3J1O Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2HZM Structure of the Mediator head subcomplex Med18/20 Deposited 2006-08-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–307（306 aa） Fragment：residues 2-307
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；100 mM Tris, 1.8 M Na/K phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.264
2HZM Structure of the Mediator head subcomplex Med18/20 Deposited 2006-08-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–307（306 aa） Fragment：residues 2-307
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；100 mM Tris, 1.8 M Na/K phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.264
2HZM Structure of the Mediator head subcomplex Med18/20 Deposited 2006-08-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 2–307（306 aa） Fragment：residues 2-307
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；100 mM Tris, 1.8 M Na/K phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.264
2HZM Structure of the Mediator head subcomplex Med18/20 Deposited 2006-08-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 2–307（306 aa） Fragment：residues 2-307
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；100 mM Tris, 1.8 M Na/K phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.264
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–307（306 aa） Fragment：residues 2-307
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 2–307（306 aa） Fragment：residues 2-307
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 2–307（306 aa） Fragment：residues 2-307
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 2–307（306 aa） Fragment：residues 2-307
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 2–307（306 aa） Fragment：residues 2-307
Chain D 2–307（306 aa） Fragment：residues 2-307
Chain F 2–307（306 aa） Fragment：residues 2-307
Chain H 2–307（306 aa） Fragment：residues 2-307
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 2–307（306 aa） Fragment：residues 2-307
Chain D 2–307（306 aa） Fragment：residues 2-307
Chain F 2–307（306 aa） Fragment：residues 2-307
Chain H 2–307（306 aa） Fragment：residues 2-307
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain B 2–307（306 aa） Fragment：residues 2-307
Chain F 2–307（306 aa） Fragment：residues 2-307
Chain H 2–307（306 aa） Fragment：residues 2-307
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 2–307（306 aa） Fragment：residues 2-307
Chain H 2–307（306 aa） Fragment：residues 2-307
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
3RJ1 Architecture of the Mediator Head module Deposited 2011-04-14 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain E 1–108（108 aa）
Chain E 141–307（167 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SE SELENIUM ATOM × 30 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.1 M Tris-HCl (pH 7.6) containing 10-12.5% (w/v) PEG-6K, and 0.4 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 4.30 Å R-free 0.373
3RJ1 Architecture of the Mediator Head module Deposited 2011-04-14 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain L 1–108（108 aa）
Chain L 141–307（167 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SE SELENIUM ATOM × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.1 M Tris-HCl (pH 7.6) containing 10-12.5% (w/v) PEG-6K, and 0.4 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 4.30 Å R-free 0.373
3RJ1 Architecture of the Mediator Head module Deposited 2011-04-14 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain S 1–108（108 aa）
Chain S 141–307（167 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SE SELENIUM ATOM × 32 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.1 M Tris-HCl (pH 7.6) containing 10-12.5% (w/v) PEG-6K, and 0.4 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 4.30 Å R-free 0.373
4GWP Structure of the Mediator Head Module from S. cerevisiae Deposited 2012-09-03 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain E 1–307（307 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.2 K；275mM ammonium citrate tribasic pH 7.0, 10% w/v PEG 3350, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K
Resolution 4.20 Å R-free 0.357
4GWQ Structure of the Mediator Head Module from S. cerevisiae in complex with the carboxy-terminal domain (CTD) of RNA Polymerase II Rpb1 subunit Deposited 2012-09-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 1–307（307 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；291.2 K；275mM ammonium citrate tribasic pH 7.0, 10% w/v PEG 3350, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K
Resolution 4.50 Å R-free 0.345
4V1O Architecture of the RNA polymerase II-Mediator core transcription initiation complex Deposited 2014-09-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain X 1–307（307 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE GLOW- DISCHARGED FOR 20 S BEFORE DEPOSITION OF 4 MICROLITERS SAMPLE AND INCUBATED FOR 30 S. GRIDS WERE WASHED TWICE WITH 4 MICROLITERS DISTILLED WATER, BLOTTED, AND VITRIFIED BY PLUNGING INTO LIQUID ETHANE WITH A MANUAL PLUNGER.
Resolution 9.70 Å
5OQM STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR Deposited 2017-08-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain e 1–307（307 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 8 s and plunge-frozen in liquid ethane.
Resolution 5.80 Å
5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain Q 1–307（307 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 15.30 Å
7UI9 Core Mediator-PICearly (Copy A) Deposited 2022-03-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain r 1–307（307 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7UIF Mediator-PIC Early (Core B) Deposited 2022-03-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain r 1–307（307 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7UIG Mediator-PIC Early (Mediator A) Deposited 2022-03-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain r 1–307（307 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7UIO Mediator-PIC Early (Composite Model) Deposited 2022-03-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 78 PDB declaration: 80-meric
Chain Ar 1–307（307 aa）
Chain Br 1–307（307 aa）
Not recorded ZN ZINC ION × 4 THR THREONINE × 1 ALA ALANINE × 1 ASP ASPARTIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å

12 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MED18_YEAST
Isoform —
PDB entities 5
Chains and sequence ranges Author chain L； PDBConstruct 1–108； UniProt 1–108 Author chain L； PDBConstruct 109–275； UniProt 141–307

Mediator of RNA polymerase II transcription subunit 20

Saccharomyces cerevisiae

UniProt P34162

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count Chain M； UniProt 1–210 Not recorded Mediator of RNA polymerase II transcription subunit 11 × 1 （A0A0D3YMY9） Mediator of RNA polymerase II transcription subunit 17 × 1 （P32569） Mediator of RNA polymerase II transcription subunit 8 × 1 （P38304） Mediator of RNA polymerase II transcription subunit 22 × 1 （P32570） Mediator of RNA polymerase II transcription subunit 18 × 1 （P32585） Mediator of RNA polymerase II transcription subunit 6 × 1 （P38782） ELECTRON MICROSCOPY cryo-EM buffer：25 mM KCl, 25 mM Tris-HCl, 10 mM DTT；pH 8；25 mM KCl, 25 mM Tris-HCl, 10 mM DTT cryo-EM vitrification conditions：Blot for ~2 sec before plunging；77 K；Cryogen ETHANE；Blot for approximately 2 seconds before plunging into liquid ethane. Resolution 16.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3J1O Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2HZM Structure of the Mediator head subcomplex Med18/20 Deposited 2006-08-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–210（210 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；100 mM Tris, 1.8 M Na/K phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.264
2HZM Structure of the Mediator head subcomplex Med18/20 Deposited 2006-08-09 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–210（210 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；100 mM Tris, 1.8 M Na/K phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.264
2HZM Structure of the Mediator head subcomplex Med18/20 Deposited 2006-08-09 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–210（210 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；100 mM Tris, 1.8 M Na/K phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.264
2HZM Structure of the Mediator head subcomplex Med18/20 Deposited 2006-08-09 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–210（210 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；100 mM Tris, 1.8 M Na/K phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.264
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–210（209 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 2–210（209 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 2–210（209 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 2–210（209 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 2–210（209 aa）
Chain C 2–210（209 aa）
Chain E 2–210（209 aa）
Chain G 2–210（209 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 2–210（209 aa）
Chain C 2–210（209 aa）
Chain E 2–210（209 aa）
Chain G 2–210（209 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 2–210（209 aa）
Chain E 2–210（209 aa）
Chain G 2–210（209 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
2HZS Structure of the Mediator head submodule Med8C/18/20 Deposited 2006-08-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 2–210（209 aa）
Chain G 2–210（209 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.272
3RJ1 Architecture of the Mediator Head module Deposited 2011-04-14 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain F 1–210（210 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SE SELENIUM ATOM × 30 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.1 M Tris-HCl (pH 7.6) containing 10-12.5% (w/v) PEG-6K, and 0.4 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 4.30 Å R-free 0.373
3RJ1 Architecture of the Mediator Head module Deposited 2011-04-14 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain M 1–210（210 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SE SELENIUM ATOM × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.1 M Tris-HCl (pH 7.6) containing 10-12.5% (w/v) PEG-6K, and 0.4 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 4.30 Å R-free 0.373
3RJ1 Architecture of the Mediator Head module Deposited 2011-04-14 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain T 1–210（210 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SE SELENIUM ATOM × 32 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.1 M Tris-HCl (pH 7.6) containing 10-12.5% (w/v) PEG-6K, and 0.4 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 4.30 Å R-free 0.373
4GWP Structure of the Mediator Head Module from S. cerevisiae Deposited 2012-09-03 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain F 1–210（210 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.2 K；275mM ammonium citrate tribasic pH 7.0, 10% w/v PEG 3350, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K
Resolution 4.20 Å R-free 0.357
4GWQ Structure of the Mediator Head Module from S. cerevisiae in complex with the carboxy-terminal domain (CTD) of RNA Polymerase II Rpb1 subunit Deposited 2012-09-03 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–210（210 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；291.2 K；275mM ammonium citrate tribasic pH 7.0, 10% w/v PEG 3350, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K
Resolution 4.50 Å R-free 0.345
4V1O Architecture of the RNA polymerase II-Mediator core transcription initiation complex Deposited 2014-09-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain Y 2–210（209 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE GLOW- DISCHARGED FOR 20 S BEFORE DEPOSITION OF 4 MICROLITERS SAMPLE AND INCUBATED FOR 30 S. GRIDS WERE WASHED TWICE WITH 4 MICROLITERS DISTILLED WATER, BLOTTED, AND VITRIFIED BY PLUNGING INTO LIQUID ETHANE WITH A MANUAL PLUNGER.
Resolution 9.70 Å
5OQM STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR Deposited 2017-08-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain f 1–210（210 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 8 s and plunge-frozen in liquid ethane.
Resolution 5.80 Å
5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain R 1–210（210 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 15.30 Å
7UI9 Core Mediator-PICearly (Copy A) Deposited 2022-03-28 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain t 1–210（210 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7UIF Mediator-PIC Early (Core B) Deposited 2022-03-29 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain t 1–210（210 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7UIG Mediator-PIC Early (Mediator A) Deposited 2022-03-29 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain t 1–210（210 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7UIO Mediator-PIC Early (Composite Model) Deposited 2022-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 78 PDB declaration: 80-meric
Chain At 1–210（210 aa）
Chain Bt 1–210（210 aa）
Not recorded ZN ZINC ION × 4 THR THREONINE × 1 ALA ALANINE × 1 ASP ASPARTIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8CEO Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome Deposited 2023-02-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric
Chain f 1–210（210 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å

13 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MED20_YEAST
Isoform —
PDB entities 6
Chains and sequence ranges Author chain M； PDBConstruct 1–210； UniProt 1–210

Mediator of RNA polymerase II transcription subunit 6

Saccharomyces cerevisiae

UniProt P38782

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count Chain N； UniProt 166–190 Not recorded Mediator of RNA polymerase II transcription subunit 11 × 1 （A0A0D3YMY9） Mediator of RNA polymerase II transcription subunit 17 × 1 （P32569） Mediator of RNA polymerase II transcription subunit 8 × 1 （P38304） Mediator of RNA polymerase II transcription subunit 22 × 1 （P32570） Mediator of RNA polymerase II transcription subunit 18 × 1 （P32585） Mediator of RNA polymerase II transcription subunit 20 × 1 （P34162） ELECTRON MICROSCOPY cryo-EM buffer：25 mM KCl, 25 mM Tris-HCl, 10 mM DTT；pH 8；25 mM KCl, 25 mM Tris-HCl, 10 mM DTT cryo-EM vitrification conditions：Blot for ~2 sec before plunging；77 K；Cryogen ETHANE；Blot for approximately 2 seconds before plunging into liquid ethane. Resolution 16.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3J1O Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3RJ1 Architecture of the Mediator Head module Deposited 2011-04-14 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain G 1–295（295 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SE SELENIUM ATOM × 30 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.1 M Tris-HCl (pH 7.6) containing 10-12.5% (w/v) PEG-6K, and 0.4 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 4.30 Å R-free 0.373
3RJ1 Architecture of the Mediator Head module Deposited 2011-04-14 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain N 1–295（295 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SE SELENIUM ATOM × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.1 M Tris-HCl (pH 7.6) containing 10-12.5% (w/v) PEG-6K, and 0.4 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 4.30 Å R-free 0.373
3RJ1 Architecture of the Mediator Head module Deposited 2011-04-14 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain U 1–295（295 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SE SELENIUM ATOM × 32 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.1 M Tris-HCl (pH 7.6) containing 10-12.5% (w/v) PEG-6K, and 0.4 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 4.30 Å R-free 0.373
4GWP Structure of the Mediator Head Module from S. cerevisiae Deposited 2012-09-03 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain G 1–295（295 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.2 K；275mM ammonium citrate tribasic pH 7.0, 10% w/v PEG 3350, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K
Resolution 4.20 Å R-free 0.357
4GWQ Structure of the Mediator Head Module from S. cerevisiae in complex with the carboxy-terminal domain (CTD) of RNA Polymerase II Rpb1 subunit Deposited 2012-09-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 1–295（295 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；291.2 K；275mM ammonium citrate tribasic pH 7.0, 10% w/v PEG 3350, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K
Resolution 4.50 Å R-free 0.345
4V1O Architecture of the RNA polymerase II-Mediator core transcription initiation complex Deposited 2014-09-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain S 1–295（295 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE GLOW- DISCHARGED FOR 20 S BEFORE DEPOSITION OF 4 MICROLITERS SAMPLE AND INCUBATED FOR 30 S. GRIDS WERE WASHED TWICE WITH 4 MICROLITERS DISTILLED WATER, BLOTTED, AND VITRIFIED BY PLUNGING INTO LIQUID ETHANE WITH A MANUAL PLUNGER.
Resolution 9.70 Å
5OQM STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR Deposited 2017-08-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain a 1–295（295 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 8 s and plunge-frozen in liquid ethane.
Resolution 5.80 Å
5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain M 1–295（295 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 15.30 Å
7UI9 Core Mediator-PICearly (Copy A) Deposited 2022-03-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain f 1–295（295 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7UIF Mediator-PIC Early (Core B) Deposited 2022-03-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain f 1–295（295 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7UIG Mediator-PIC Early (Mediator A) Deposited 2022-03-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain f 1–295（295 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7UIO Mediator-PIC Early (Composite Model) Deposited 2022-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 78 PDB declaration: 80-meric
Chain Af 1–295（295 aa）
Chain Bf 1–295（295 aa）
Not recorded ZN ZINC ION × 4 THR THREONINE × 1 ALA ALANINE × 1 ASP ASPARTIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å

10 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MED6_YEAST
Isoform —
PDB entities 7
Chains and sequence ranges Author chain N； PDBConstruct 1–25； UniProt 166–190

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3j1o

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3j1o
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3j1o
Deposition date deposition_date2012-03-29
Structure title titleCryo-EM map of a yeast minimal preinitiation complex interacting with the Mediator Head module
Keywords keywordsRNA polymerase II, mediator head module, preinitiation complex, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier47.60 Å
Radius of gyration Rg (electron density) rg_electron48.10 Å
Forward intensity I(0) i0137316000.00
Molecular weight molecular_weight77763.0 kDa
Excluded volume excluded_volume89544 ų
Envelope volume envelope_volume201020 ų
Hydration-shell volume shell_volume39078 ų
Envelope diameter envelope_diameter158.1 Å
Shell Rg shell_rg45.25 Å
Envelope Rg envelope_rg46.10 Å
Shape Rg shape_rg48.09 Å
Total Rg total_rg47.96 Å
Total atoms total_atoms5560
Residues n_residues1120
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax155.8 Å
Rg (real space) rg_real47.82 Å
Rg uncertainty (real space) rg_real_error1.64 Å
I(0) (real space) i0_real1.3730e+08
I(0) uncertainty (real space) i0_real_error2.5770e+06
Rg (reciprocal space) rg_reciprocal47.60 Å
I(0) (reciprocal space) i0_reciprocal137300000.0000
Solution quality estimate total_estimate0.8320
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.1 Å
Skewness Skewness skewness0.232
Kurtosis Kurtosis kurtosis-0.776
Angular range angular_range— – 0.1650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12170000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.829; Smooth: 0.440
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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8. Citations (1)

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9. Files and Curves (10)