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- PDB-5n9j: Core Mediator of transcriptional regulation -

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Basic information

Entry
Database: PDB / ID: 5n9j
TitleCore Mediator of transcriptional regulation
Components
  • (Mediator of RNA polymerase II transcription subunit ...) x 14
  • Mediator Complex Subunit 9
KeywordsTRANSCRIPTION / RNA polymerase II
Function / homology
Function and homology information


core mediator complex / mediator complex / positive regulation of transcription initiation by RNA polymerase II / transcription coregulator activity / transcription initiation at RNA polymerase II promoter / euchromatin / nuclear envelope / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II ...core mediator complex / mediator complex / positive regulation of transcription initiation by RNA polymerase II / transcription coregulator activity / transcription initiation at RNA polymerase II promoter / euchromatin / nuclear envelope / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Mediator of RNA polymerase II, submodule Med31 (Soh1) / Helix Hairpins - #3490 / Mediator complex, subunit Med19, fungi / Rox3 mediator complex subunit / Mediator complex, subunit Med6, fungi / Hypothetical Protein Pfu-838710-001 / Hypothetical Protein Pfu-838710-001 / Mediator complex, subunit Med10 / Transcription factor subunit Med10 of Mediator complex / Mediator complex, subunit Med4 ...Mediator of RNA polymerase II, submodule Med31 (Soh1) / Helix Hairpins - #3490 / Mediator complex, subunit Med19, fungi / Rox3 mediator complex subunit / Mediator complex, subunit Med6, fungi / Hypothetical Protein Pfu-838710-001 / Hypothetical Protein Pfu-838710-001 / Mediator complex, subunit Med10 / Transcription factor subunit Med10 of Mediator complex / Mediator complex, subunit Med4 / Vitamin-D-receptor interacting Mediator subunit 4 / Mediator complex, subunit Med31 / Mediator complex, subunit Med21 / Mediator of RNA polymerase II, subunit Med31 superfamily / SOH1 / Subunit 21 of Mediator complex / Mediator complex, subunit Med7 / Mediator complex, subunit Med7/Med21-like / Mediator complex, subunit Med7 superfmaily / : / MED7 protein / Mediator complex, subunit Med20 / Mediator complex, subunit Med14 / TATA-binding related factor (TRF) of subunit 20 of Mediator complex / Mediator complex subunit MED14 / Mediator complex, subunit Med6 / Mediator complex, subunit Med17 / Mediator complex, subunit Med6 superfamily / MED6 mediator sub complex component / Subunit 17 of Mediator complex / Mediator of RNA polymerase II transcription subunit 22 / Mediator complex, subunit Med8, fungi/metazoa / Mediator complex, subunit Med11 / Surfeit locus protein 5 subunit 22 of Mediator complex / Mediator of RNA polymerase II transcription complex subunit 8 / Mediator complex protein / Mediator complex, subunit Med18 / Med18 protein / Helix Hairpins / Arc Repressor Mutant, subunit A / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein C24C9.04 / Mediator of RNA polymerase II transcription subunit 22 / Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 7 / Mediator of RNA polymerase II transcription subunit 21 / Mediator of RNA polymerase II transcription subunit 8 / Mediator of RNA polymerase II transcription subunit 17 / Mediator of RNA polymerase II transcription subunit 10 / Mediator of RNA polymerase II transcription subunit 20 / Mediator of RNA polymerase II transcription subunit 11 ...Uncharacterized protein C24C9.04 / Mediator of RNA polymerase II transcription subunit 22 / Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 7 / Mediator of RNA polymerase II transcription subunit 21 / Mediator of RNA polymerase II transcription subunit 8 / Mediator of RNA polymerase II transcription subunit 17 / Mediator of RNA polymerase II transcription subunit 10 / Mediator of RNA polymerase II transcription subunit 20 / Mediator of RNA polymerase II transcription subunit 11 / Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 6 / Mediator of RNA polymerase II transcription subunit 31 / Mediator of RNA polymerase II transcription subunit 19 / Mediator of RNA polymerase II transcription subunit 4
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 3.4 Å
AuthorsNozawa, K. / Schneider, T.R. / Cramer, P.
Funding support Germany, France, Japan, 6items
OrganizationGrant numberCountry
German Research FoundationSFB860, SPP1935 Germany
European Research Council Advanced Investigator Grant TRANSREGULON693023 Germany
Volkswagen Foundation Germany
Human Frontier Science ProgramLT000621/2012-L France
Japan Society for the Promotion of Science Japan
Uehara Memorial Foundation Japan
CitationJournal: Nature / Year: 2017
Title: Core Mediator structure at 3.4 Angstrom extends model of transcription initiation complex.
Authors: Nozawa, K. / Schneider, T.R. / Cramer, P.
History
DepositionFeb 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2May 8, 2024Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mediator of RNA polymerase II transcription subunit 14
B: Mediator of RNA polymerase II transcription subunit 10
C: Mediator of RNA polymerase II transcription subunit 19
D: Mediator of RNA polymerase II transcription subunit 21
E: Mediator of RNA polymerase II transcription subunit 7
F: Mediator Complex Subunit 9
G: Mediator of RNA polymerase II transcription subunit 4
R: Mediator of RNA polymerase II transcription subunit 31
S: Mediator of RNA polymerase II transcription subunit 6
U: Mediator of RNA polymerase II transcription subunit 8
V: Mediator of RNA polymerase II transcription subunit 11
W: Mediator of RNA polymerase II transcription subunit 17
X: Mediator of RNA polymerase II transcription subunit 18
Y: Mediator of RNA polymerase II transcription subunit 20
Z: Mediator of RNA polymerase II transcription subunit 22


Theoretical massNumber of molelcules
Total (without water)403,41515
Polymers403,41515
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area89690 Å2
ΔGint-655 kcal/mol
Surface area142090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.864, 211.768, 267.028
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Mediator of RNA polymerase II transcription subunit ... , 14 types, 14 molecules ABCDEGRSUVWXYZ

#1: Protein Mediator of RNA polymerase II transcription subunit 14 / Mediator complex subunit 14 / Mediator of RNA polymerase II complex subunit pmc1


Mass: 68020.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: med14, pmc1, SPBC1A4.10c, SPBP23A10.01c / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9P7Y4
#2: Protein Mediator of RNA polymerase II transcription subunit 10 / Mediator complex subunit 10


Mass: 16352.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: med10, nut2, SPBC31F10.09c / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P87310
#3: Protein Mediator of RNA polymerase II transcription subunit 19 / Mediator complex subunit 19 / RNA polymerase II mediator complex protein rox3


Mass: 15952.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: med19, rox3, SPCC1450.05c / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y7N2
#4: Protein Mediator of RNA polymerase II transcription subunit 21 / Mediator complex subunit 21 / Suppressor of RNA polymerase B 7


Mass: 15821.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: med21, srb7, SPBC1604.10 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O94376
#5: Protein Mediator of RNA polymerase II transcription subunit 7 / Mediator complex subunit 7


Mass: 43573.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: med7, SPBC14F5.08 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60104
#7: Protein Mediator of RNA polymerase II transcription subunit 4 / Mediator complex subunit 4 / RNA polymerase II mediator complex protein pmc4


Mass: 27370.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: med4, pmc4, SPBC1105.06 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y821
#8: Protein Mediator of RNA polymerase II transcription subunit 31 / Cell separation protein sep10 / Mediator complex subunit 31 / Soh1 homolog


Mass: 16913.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: med31, sep10, SPCP31B10.03c / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9USH1
#9: Protein Mediator of RNA polymerase II transcription subunit 6 / Mediator complex subunit 6 / RNA polymerase II mediator complex protein pmc5


Mass: 24928.947 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: med6, pmc5, SPAC1002.15c / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9US45
#10: Protein Mediator of RNA polymerase II transcription subunit 8 / Cell separation protein sep15 / Mediator complex subunit 8


Mass: 23360.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: med8, sep15, SPBC21.04 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O94646
#11: Protein Mediator of RNA polymerase II transcription subunit 11 / Mediator complex subunit 11


Mass: 12644.226 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: med11, SPAC644.10 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9P6Q0
#12: Protein Mediator of RNA polymerase II transcription subunit 17 / Mediator complex subunit 17 / Suppressor of RNA polymerase B 4 homolog


Mass: 62551.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: med17, srb4, SPBC31F10.04c / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P87306
#13: Protein Mediator of RNA polymerase II transcription subunit 18 / Cell separation protein sep11 / Mediator complex subunit 18 / RNA polymerase II mediator complex protein pmc6


Mass: 24345.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: med18, pmc6, sep11, SPAC5D6.05 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O14198
#14: Protein Mediator of RNA polymerase II transcription subunit 20 / Mediator complex subunit 20


Mass: 22374.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: med20, SPAC17G8.05 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q10317
#15: Protein Mediator of RNA polymerase II transcription subunit 22 / Mediator complex subunit 22 / Suppressor of RNA polymerase B 6 homolog


Mass: 15396.165 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: med22, srb6, SPAC29A4.07 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O14010

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Protein , 1 types, 1 molecules F

#6: Protein Mediator Complex Subunit 9


Mass: 13810.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: SPAC24C9.04 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O13964

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.11 Å3/Da / Density % sol: 75.91 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5
Details: 0.1 M MES pH 6.5, 3.2% PEG 20000, 700 mM ammonium nitrate

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)10.97940, 1.90750, 0.97794, 0.97863
SYNCHROTRONSLS X06SA21.25414, 0.97630, 0.97920
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M-F1PIXELSep 17, 2015
DECTRIS EIGER X 16M2PIXELFeb 16, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
21.90751
30.977941
40.978631
51.254141
60.97631
70.97921
ReflectionResolution: 3.4→98.486 Å / Num. obs: 113813 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.643 % / Biso Wilson estimate: 154.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.063 / Χ2: 1.174 / Net I/σ(I): 17.05
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.4-3.66.6221.6441.06178000.4131.78497.5
3.6-3.856.9450.792.32172290.8020.85499.9
3.85-4.166.8520.3415.21160470.960.36999.9
4.16-4.566.8120.13512.41147740.9940.14799.9
4.56-5.096.5550.07721.72134420.9970.084100
5.09-5.886.6920.06326.52119130.9980.06899.9
5.88-7.26.4930.04635.7100990.9980.0599.8
7.2-10.156.1020.03150.1879310.9990.03499.8
10.15-98.4865.7040.02754.1545780.9980.0399.3

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
SOLVEphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3.4→98.486 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.22 / Phase error: 30.16
RfactorNum. reflection% reflection
Rfree0.256 10950 4.99 %
Rwork0.2331 --
obs0.2343 219292 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 368.86 Å2 / Biso mean: 159.0468 Å2 / Biso min: 80.76 Å2
Refinement stepCycle: final / Resolution: 3.4→98.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23726 0 0 0 23726
Num. residues----2929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00824225
X-RAY DIFFRACTIONf_angle_d1.08132790
X-RAY DIFFRACTIONf_chiral_restr0.0543700
X-RAY DIFFRACTIONf_plane_restr0.0084183
X-RAY DIFFRACTIONf_dihedral_angle_d20.61314804
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.43860.38543690.385669087277100
3.4386-3.47910.39593630.377669997362100
3.4791-3.52150.37943680.376569137281100
3.5215-3.56610.36353610.351469587319100
3.5661-3.6130.36573670.356269157282100
3.613-3.66250.3393730.349369907363100
3.6625-3.71490.36033690.338669457314100
3.7149-3.77030.33653640.337568917255100
3.7703-3.82920.32463670.32469687335100
3.8292-3.8920.34243660.304169107276100
3.892-3.95910.28753610.289170027363100
3.9591-4.03110.32013700.288469207290100
4.0311-4.10870.29793600.279369757335100
4.1087-4.19250.33363660.279869307296100
4.1925-4.28370.3123660.26569427308100
4.2837-4.38330.32083710.256869197290100
4.3833-4.49290.28253630.244869817344100
4.4929-4.61440.23973640.225669257289100
4.6144-4.75020.26643680.221869567324100
4.7502-4.90350.25113650.221169357300100
4.9035-5.07880.26033630.222269817344100
5.0788-5.28210.25673660.233669377303100
5.2821-5.52250.26093670.246769327299100
5.5225-5.81360.28163650.241669847349100
5.8136-6.17780.27083610.249569447305100
6.1778-6.65470.3183620.25169657327100
6.6547-7.32420.25533640.226769637327100
7.3242-8.38350.20833630.191969047267100
8.3835-10.56040.15543540.145269557309100
10.5604-98.52710.21653640.21236895725999

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